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Patent Analysis of

Glucose-regulating polypeptides and methods of making and using same

Updated Time 12 June 2019

Patent Registration Data

Publication Number

US10000543

Application Number

US15/365792

Application Date

30 November 2016

Publication Date

19 June 2018

Current Assignee

AMUNIX OPERATING INC.

Original Assignee (Applicant)

AMUNIX OPERATING INC.

International Classification

C07K14/605,A61K38/00

Cooperative Classification

C07K14/605,A23V2200/328,A61K38/00,C07K2319/31,Y10S514/866

Inventor

SCHELLENBERGER, VOLKER,SILVERMAN, JOSHUA,STEMMER, WILLEM P.,WANG, CHIA-WEI,GEETHING, NATHAN,CLELAND, JEFFREY L.

Patent Images

This patent contains figures and images illustrating the invention and its embodiment.

US10000543 Glucose-regulating polypeptides 1 US10000543 Glucose-regulating polypeptides 2 US10000543 Glucose-regulating polypeptides 3
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Abstract

The present invention relates to compositions comprising glucose regulating peptides linked to extended recombinant polypeptide (XTEN), isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of making and using such compositions in treatment of glucose regulating peptide-related diseases, disorders, and conditions.

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Claims

1. A kit comprising a pharmaceutical composition for use in treating a glucose regulating peptide-related condition in a subject, wherein the kit comprises(a) a first container;(b) the pharmaceutical composition comprising:(i) a fusion protein comprising a glucose regulating peptide that is at least 90% identical to a glucose regulating peptide sequence selected from Tables 1-3, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN), wherein the XTEN sequence exhibits at least 90% sequence identity to a sequence selected from Table 5; and ii) an amount of a pharmaceutically acceptable carrier.

2. The kit of claim 1, wherein the glucose regulating peptide-related condition is selected from the group consisting of juvenile diabetes, type I diabetes, type II diabetes, obesity, acute hypoglycemia, acute hyperglycemia, nocturnal hypoglycemia, chronic hyperglycemia, glucagonomas, secretory disorders of the airway, arthritis, osteoporosis, central nervous system disease, restenosis, neurodegenerative disease, renal failure, congestive heart failure nephrotic syndrome, cirrhosis, hypertension, irritable bowel syndrome, myocardial infarction, post-surgical catabolic changes, diabetic cardiomyopathy, insufficient urinary sodium excretion, excessive urinary potassium concentration, polycystic ovary syndrome, respiratory distress, nephropathy, left ventricular systolic dysfunction, gastrointestinal disorders, postoperative dumping syndrome, irritable bowel syndrome, dyslipidemia, and critical illness polyneuropathy (CIPN).

3. The kit of claim 1, wherein the fusion protein comprises a glucose regulating peptide that is at least 90% identical to SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or SEQ ID NO:10 linked to an XTEN, wherein the XTEN sequence is at least 90% identical to a sequence selected from SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 206, or SEQ ID NO: 207.

4. The kit of claim 3, wherein the glucose regulating peptide of the fusion protein is at least 90% identical to the amino acid sequence SEQ ID NO:4.

5. The kit of claim 3, wherein the glucose regulating peptide of the fusion protein is at least 90% identical to the amino acid sequence SEQ ID NO:5.

6. The kit of claim 3, wherein the glucose regulating peptide of the fusion protein is at least 90% identical to the amino acid sequence SEQ ID NO:6.

7. The kit of claim 3, wherein the glucose regulating peptide of the fusion protein is at least 90% identical to the amino acid sequence SEQ ID NO:10.

8. The kit of claim 3, wherein the XTEN sequence is at least 90% identical to SEQ ID NO:189, SEQ ID NO:191, SEQ ID NO: 195, or SEQ ID NO:199.

9. The kit of claim 1, wherein the fusion protein is at least 90% identical to SEQ ID NO: 882, SEQ ID NO: 884, SEQ ID NO: 890, SEQ ID NO: 896, SEQ ID NO: 979, SEQ ID NO: 980, SEQ ID NO: 983, or SEQ ID NO: 986.

10. The kit of claim 1, wherein the fusion protein comprises the sequence of SEQ ID NO: 896.

11. The kit of any one of claim 1 or claim 9, comprising a second container that can carry a suitable diluent for the pharmaceutical composition, and a sheet of instructions for the reconstitution and/or administration of the pharmaceutical composition to a subject.

12. A syringe comprising a pharmaceutical composition for use in treating a glucose regulating peptide-related condition in a subject, wherein the pharmaceutical composition is supplied as a liquid in a pre-filled syringe, the pharmaceutical composition comprising:(a) a fusion protein comprising a glucose regulating peptide that is at least 90% identical to a glucose regulating peptide sequence selected from Tables 1-3, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN), wherein the XTEN sequence exhibits at least 90% sequence identity to a sequence selected from Table 5; and(b) an amount of a pharmaceutically acceptable carrier in the liquid.

13. The syringe of claim 12, wherein the liquid formulation is an aqueous formulation.

14. The syringe of claim 12, wherein the liquid formulation is capable of passing through a needle of gauge size 25 to 32 for administration to the subject.

15. The syringe of claim 12, wherein the syringe is for administration of the pharmaceutical composition to a subject via a route selected from the group consisting of intravenous, intramuscular, intraarticular, and subcutaneous.

16. The syringe of any one of claims 12-15, wherein the fusion protein is at least 90% identical to SEQ ID NO: 882, SEQ ID NO: 884, SEQ ID NO: 890, SEQ ID NO: 896, SEQ ID NO: 979, SEQ ID NO: 980, SEQ ID NO: 983, or SEQ ID NO: 986.

17. The syringe of claim 16, wherein the fusion protein comprises the amino acid sequence of SEQ ID NO: 896.

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Claim Tree

  • 1
    1. A kit comprising a pharmaceutical composition for use in treating a glucose regulating peptide-related condition in a subject, wherein the kit comprises
    • (a) a first container;
    • (b) the pharmaceutical composition comprising:(i) a fusion protein comprising a glucose regulating peptide that is at least 90% identical to a glucose regulating peptide sequence selected from Tables 1-3, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN), wherein the XTEN sequence exhibits at least 90% sequence identity to a sequence selected from Table 5; and ii) an amount of a pharmaceutically acceptable carrier.
    • 2. The kit of claim 1, wherein
      • the glucose regulating peptide-related condition is selected from the group consisting of
    • 3. The kit of claim 1, wherein
      • the fusion protein comprises
    • 9. The kit of claim 1, wherein
      • the fusion protein is at least 90% identical to SEQ ID NO: 882, SEQ ID NO: 884, SEQ ID NO: 890, SEQ ID NO: 896, SEQ ID NO: 979, SEQ ID NO: 980, SEQ ID NO: 983, or SEQ ID NO: 986.
    • 10. The kit of claim 1, wherein
      • the fusion protein comprises
    • 11. The kit of any one of claim 1 or claim 9, comprising
      • a second container that can carry a suitable diluent for the pharmaceutical composition, and a sheet of instructions for the reconstitution and/or administration of the pharmaceutical composition to a subject.
  • 12
    12. A syringe comprising a pharmaceutical composition for use in treating a glucose regulating peptide-related condition in a subject, wherein the pharmaceutical composition is supplied as a liquid in a pre-filled syringe, the pharmaceutical composition comprising:
    • (a) a fusion protein comprising a glucose regulating peptide that is at least 90% identical to a glucose regulating peptide sequence selected from Tables 1-3, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN), wherein the XTEN sequence exhibits at least 90% sequence identity to a sequence selected from Table 5; and
    • (b) an amount of a pharmaceutically acceptable carrier in the liquid.
    • 13. The syringe of claim 12, wherein
      • the liquid formulation is an aqueous formulation.
    • 14. The syringe of claim 12, wherein
      • the liquid formulation is capable of passing through a needle of gauge size 25 to 32 for administration to the subject.
    • 15. The syringe of claim 12, wherein
      • the syringe is for administration of the pharmaceutical composition to a subject via a route selected from the group consisting of
    • 16. The syringe of any one of claims 12-15, wherein
      • the fusion protein is at least 90% identical to SEQ ID NO: 882, SEQ ID NO: 884, SEQ ID NO: 890, SEQ ID NO: 896, SEQ ID NO: 979, SEQ ID NO: 980, SEQ ID NO: 983, or SEQ ID NO: 986.
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Description

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 28, 2010, is named 32887122.txt and is 3,692,063 bytes in size.

BACKGROUND OF THE INVENTION

Glucose-regulating peptides are critical regulatory components of human metabolism. Various peptides have been described with biological effects that result in either an increase or decrease in serum glucose levels. These peptides tend to be highly homologous to each other, even when they possess opposite biological functions. Many glucose regulating peptides, including those used as therapeutics, are typically labile molecules exhibiting short shelf-lives, particularly when formulated in aqueous solutions. In addition, many glucose regulating peptides have limited solubility, or become aggregated during recombinant productions, requiring complex solubilization and refolding procedures. Various chemical polymers can be attached to such peptides and proteins to modify their properties. Of particular interest are hydrophilic polymers that have flexible conformations and are well hydrated in aqueous solutions. A frequently used polymer is polyethylene glycol (PEG). These polymers tend to have large hydrodynamic radii relative to their molecular weight (Kubetzko, S., et al. (2005) Mol Pharmacol, 68: 1439-54), and can result in enhanced pharmacokinetic properties. However, the chemical conjugation of polymers to proteins requires complex multi-step processes; typically, the protein component needs to be produced and purified prior to the chemical conjugation step and the conjugation step can result in the formation of heterogeneous product mixtures that need to be separated, leading to significant product loss. Alternatively, such mixtures can be used as the final pharmaceutical product, but are difficult to standardize. Some examples are currently marketed PEGylated Interferon-alpha products that are used as mixtures (Wang, B. L., et al. (1998) J Submicrosc Cytol Pathol, 30: 503-9; Dhalluin, C., et al. (2005) Bioconjug Chem, 16: 504-17). Such mixtures are difficult to reproducibly manufacture and characterize as they contain isomers with reduced or no therapeutic activity.

Albumin and immunoglobulin fragments such as Fc regions have been used to conjugate other biologically active proteins, with unpredictable outcomes with respect to increases in half-life or immunogenicity. Unfortunately, the Fc domain does not fold efficiently during recombinant expression and tends to form insoluble precipitates known as inclusion bodies. These inclusion bodies must be solubilized and functional protein must be renatured. This is a time-consuming, inefficient, and expensive process that requires additional manufacturing steps and often complex purification procedures.

Thus, there remains a significant need for compositions and methods that would improve the biological, pharmacological, safety, and/or pharmaceutical properties of glucose regulating peptides.

SUMMARY OF THE INVENTION

The present disclosure is directed to compositions and methods that can be useful for or the treatment of any disease, disorder or condition that is improved, ameliorated, or inhibited by the administration of a glucose regulating peptide. In particular, the present invention provides compositions of fusion proteins comprising one or more extended recombinant polypeptides with a non-repetitive sequence and/or unstructured conformation (XTEN) linked to glucose regulating peptide (GP). In part, the present disclosure is directed to pharmaceutical compositions comprising the fusion proteins and the uses thereof for treating glucose regulating peptide-related diseases, disorders or conditions.

In one embodiment, the invention provides an isolated fusion protein, comprising a glucose regulating peptide that is at least about 90%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% identical to an amino acid sequence selected from Table 1, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN) of at least about 100, or at least about 200, or at least about 400, or at least about 800, or at least about 900, or at least about 1000, or at least about 2000, up to about 3000 amino acids residues, wherein the XTEN is characterized in that (a) the XTEN comprises at least about 200 contiguous amino acids that exhibits at least about 90%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% identical to a comparable length of an amino acid sequence selected from a sequence shown in Table 5; (b) the XTEN sequence lacks a predicted T-cell epitope when analyzed by TEPITOPE algorithm, wherein the TEPITOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of −5, or −6, or −7, or −8, or −9 or greater; (c) the XTEN has a subsequence score of less than 10, or less than 9, or less than 8, or less than 7, or less than 6, or less than 5, or even less; and (d) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% of the total amino acid residues of the XTEN. In one embodiment, the glucose regulating peptide of the isolated fusion protein is human glucose regulating peptide. In another embodiment, the isolated fusion protein comprises at least a second XTEN, wherein the fusion protein adopts a multiple-XTEN configuration shown in Table 5, or a variant thereof.

In another embodiment, the XTEN sequence of the GPXTEN fusion proteins is characterized in that is has greater than 90% random coil formation, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% random coil formation as determined by GOR algorithm; and the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by the Chou-Fasman algorithm.

In another embodiment, the invention provides GPXTEN fusion proteins, wherein the XTEN is characterized in that the sum of asparagine and glutamine residues is less than 10% of the total amino acid sequence of the XTEN, the sum of methionine and tryptophan residues is less than 2% of the total amino acid sequence of the XTEN, the XTEN sequence has less than 5% amino acid residues with a positive charge, the XTEN sequence has greater than 90% random coil formation, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% random coil formation as determined by GOR algorithm; and the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by the Chou-Fasman algorithm.

In another embodiment, the invention provides GPXTEN fusion proteins, wherein the XTEN is characterized in that at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% of the XTEN sequence consists of non-overlapping sequence motifs wherein each of the sequence motifs has about 9 to about 14 amino acid residues and wherein the sequence of any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs the sequence motifs consist of four to six types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P).

In some embodiments, no one type of amino acid constitutes more than 30% of the XTEN sequence of the GPXTEN. In other embodiments, the XTEN has a sequence in which no three contiguous amino acids are identical unless the amino acid is serine, in which case no more than three contiguous amino acids are serine residues. In still other embodiments, at least about 80%, or about 90%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99%, or 100% of the XTEN sequence consists of non-overlapping sequence motifs, wherein each of the sequence motifs has 12 amino acid residues. In one embodiment, the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are from one or more sequences of Table 2.

In some embodiments, GPXTEN fusion proteins exhibits enhanced pharmacokinetic properties compared to GP not linked to XTEN, wherein the enhanced properties include but are not limited to longer terminal half-life, larger area under the curve, increased time in which the blood concentration remains within the therapeutic window, increased time between consecutive doses, and decreased dose in moles over time. In some embodiments, the terminal half-life of the GPXTEN fusion protein administered to a subject is increased at least about two fold, or at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about eight-fold, or at least about ten-fold, or at least about 20-fold, or at least about 40-fold, or at least about 60-fold, or at least about 100-fold compared to GP not linked to XTEN and administered to a subject at a comparable dose. In other embodiments, the enhanced pharmacokinetic property is reflected by the fact that the blood concentrations that remain within the therapeutic window for the GPXTEN fusion protein for a given period are at least about two fold, or at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about eight-fold, or at least about ten-fold longer, or at least about 20-fold, or at least about 40-fold, or at least about 60-fold, or at least about 100-fold, or ever higher as compared to GP not linked to XTEN and administered to a subject at a comparable dose. The increase in half-life and time spent within the therapeutic window permits less frequent dosing and decreased amounts of the fusion protein (in moles equivalent) that are administered to a subject, compared to the corresponding GP not linked to XTEN. In one embodiment, the therapeutically effective dose regimen results in a gain in time of at least two-fold, or at least three-fold, or at least four-fold, or at least five-fold, or at least six-fold, or at least eight-fold, or at least 10-fold, or at least about 20-fold, or at least about 40-fold, or at least about 60-fold, or at least about 100-fold between at least two consecutive Cmax peaks and/or Cmin troughs for blood levels of the fusion protein compared to the corresponding GP not linked to the fusion protein and administered using a comparable dose regimen to a subject.

In some embodiments, the XTEN enhances thermostability of a biologically active protein when linked to the biologically active protein wherein the thermostability is ascertained by measuring the retention of biological activity after exposure to a temperature of about 37° C. for at least about 7 days of the biologically active protein in comparison to the XTEN linked to the biologically active protein. In one embodiment of the foregoing, the retention of biological activity in increased by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, or about 150%, at least about 200%, at least about 300%, or about 500% longer compared to the GP not linked to the XTEN comprises of the XTEN.

In some embodiments, the isolated fusion protein with at least a first XTEN comprises a GP wherein the GP is human glucose regulating peptide. In some embodiments, the isolated fusion protein further comprises a second XTEN, which can be identical or can be different from the first XTEN, and wherein the fusion protein adopts a multiple-XTEN configuration shown in Table 7. In one embodiment of the foregoing, the first and the second XTEN can each be a sequence selected from Table 5, or can exhibit at least at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% or 100% sequence identity to a sequence selected from Table 5. In another embodiment, the isolated fusion protein comprising a second XTEN sequence adopts a multiple-XTEN configuration shown in Table 7.

In one embodiment, the isolated fusion protein is less immunogenic compared to the GP not linked to the XTEN, wherein immunogenicity is ascertained by, e.g., measuring production of IgG antibodies selectively binding to the biologically active protein after administration of comparable doses to a subject.

In some embodiments, the glucose regulating peptide and the XTEN of the fusion protein is linked via a spacer, wherein the spacer sequence comprises between about 1 to about 50 amino acid residues that optionally comprises a cleavage sequence. In one embodiment, the cleavage sequence is susceptible to cleavage by a protease. Non-limiting examples of such protease include FXIa, FXIIa, kallikrein, FVIIa, FIXa, FXa, thrombin, elastase-2, granzyme B, MMP-12, MMP-13, MMP-17 or MMP-20, TEV, enterokinase, rhinovirus 3C protease, and sortase A.

In some embodiments, the isolated fusion protein is configured to have reduced binding affinity for a target receptor of the corresponding GP, as compared to the corresponding GP not linked to the fusion protein. In one embodiment, the GPXTEN fusion protein exhibits binding affinity for a target receptor of the GP in the range of about 0.01%-30%, or about 0.1% to about 20%, or about 1% to about 15%, or about 2% to about 10% of the binding affinity of the corresponding GP that lacks the XTEN. In another embodiment, the GPXTEN fusion protein exhibits binding affinity for a target receptor of the GP that is reduced at least about 3-fold, or at least about 5-fold, or at least about 6-fold, or at least about 7-fold, or at least about 8-fold, or at least about 9-fold, or at least about 10-fold, or at least about 12-fold, or at least about 15-fold, or at least about 17-fold, or at least about 20-fold, or at least about 30-fold, or at least about 50-fold, or at least about 100-fold less binding affinity compared to GP not linked to XTEN. In a related embodiment, a fusion protein with reduced affinity can have reduced receptor-mediated clearance and a corresponding increase in half-life of at least about 3-fold, or at least about 5-fold, or at least about 6-fold, or at least about 7-fold, or at least about 8-fold, or at least about 9-fold, or at least about 10-fold, or at least about 12-fold, or at least about 15-fold, or at least about 17-fold, or at least about 20-fold, or at least about 30-fold, or at least about 50-fold, or at least about 100-fold longer compared to the corresponding GP that is not linked to the fusion protein.

In one embodiment, the invention provides an isolated GPXTEN fusion protein comprising an amino acids sequence that has at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99%, or 100% sequence identity to a sequence selected from Table 35, Table 36, and Table 37.

In some embodiments, the invention provides GPXTEN fusion proteins wherein the GPXTEN exhibits increased solubility of at least three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about seven-fold, or at least about eight-fold, or at least about nine-fold, or at least about ten-fold, or at least about 15-fold, or at least a 20-fold, or at least 40-fold, or at least 60-fold at physiologic conditions compared to the GP not linked to the fusion protein.

In some embodiments, GPXTEN fusion proteins exhibit an increased apparent molecular weight as determined by size exclusion chromatography, compared to the actual molecular weight, wherein the apparent molecular weight is at least about 100 kD, or at least about 150 kD, or at least about 200 kD, or at least about 300 kD, or at least about 400 kD, or at least about 500 kD, or at least about 600 kD, or at least about 700 kD, while the actual molecular weight of each GP component of the fusion protein is less than about 25 kD. Accordingly, the GPXTEN fusion proteins can have an Apparent Molecular Weight that is about 4-fold greater, or about 5-fold greater, or about 6-fold greater, or about 7-fold greater, or about 8-fold greater than the actual molecular weight of the fusion protein. In some cases, the isolated GPXTEN fusion protein of the foregoing embodiments exhibits an apparent molecular weight factor under physiologic conditions that is greater than about 4, or about 5, or about 6, or about 7, or about 8.

The invention contemplates GPXTEN fusion proteins compositions comprising, but not limited to GP selected from Table 1 (or fragments or sequence variants thereof), XTEN selected from Table 5 (or sequence variants thereof) that are in a configuration selected from Table 5. Generally, the resulting GPXTEN will retain at least a portion of the biological activity of the corresponding GP not linked to the XTEN. In other cases, the GP component either becomes biologically active or has an increase in activity upon its release from the XTEN by cleavage of an optional cleavage sequence incorporated within spacer sequences into the GPXTEN.

In one embodiment of the GPXTEN composition, the invention provides a fusion protein of formula I:

(XTEN)x-GP-(XTEN)y  I

wherein independently for each occurrence, GP is a is a glucose regulating peptide; x is either 0 or 1 and y is either 0 or 1 wherein x+y≥1; and XTEN is an extended recombinant polypeptide.

In some embodiments, the XTEN is fused to the glucose regulating peptide on an N- or C-terminus of the glucose regulating peptide. In some embodiments, the isolated fusion protein comprises a human glucose regulating peptide and a first and a second XTEN selected from AE912, AM923, AE144, and AE288.

In another embodiment of the GPXTEN composition, the invention provides a fusion protein of formula II:

(XTEN)x-(GP)-(S)y-(XTEN)y  II

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1 and y is either 0 or 1 wherein x+y≥1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula III:

(GP)-(S)x-(XTEN)-(S)y-(GP)-(S)z-(XTEN)z  III

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; z is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula IV:

(XTEN)x-(S)y-(GP)-(S)z-(XTEN)-(GP)  IV

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; z is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion glucose regulating peptide, wherein the fusion protein is of formula V:

(GP)x-(S)x-(GP)-(S)y-(XTEN)  V

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula VI:

(XTEN)-(S)x-(GP)-(S)y-(GP)  VI

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula VII:

(XTEN)-(S)x-(GP)-(S)y-(GP)-(XTEN)  VII

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula VIII:

((S)m-(GP)x-(S)n-(XTEN)y-(S)0)t  VIII

wherein t is an integer that is greater than 0 (1, 2, 3, etc.); independently each of m, n, o, x, and y is an integer (0, 1, 2, 3, etc.), GP is a is a glucose regulating S is an spacer, optionally comprising a cleavage site; and XTEN is an extended recombinant polypeptide, with the proviso that: (1) x+y>1, (2) when t=1, x>0 and y>0, (3) when there is more than one GP, S, or XTEN, each GP, XTEN, or S are the same or are independently different; and (4) when t>1, each m, n, o, x, or y within each subunit are the same or are independently different.

In some embodiments, administration of a therapeutically effective dose of a fusion protein of an embodiment of formulas I-VIII to a subject in need thereof can result in a gain in time of at least two-fold, or at least three-fold, or at least four-fold, or at least five-fold or more spent within a therapeutic window for the fusion protein compared to the corresponding GP not linked to the XTEN of and administered at a comparable dose to a subject. In other cases, administration of a therapeutically effective dose of a fusion protein of an embodiment of formulas I-VIII to a subject in need thereof can result in a gain in time between consecutive doses necessary to maintain a therapeutically effective dose regimen of at least 48 h, or at least 72 h, or at least about 96 h, or at least about 120 h, or at least about 7 days, or at least about 14 days, or at least about 21 days between consecutive doses compared to a GP not linked to XTEN and administered at a comparable dose.

The fusion proteins can be designed to have different configurations, N- to C-terminus, of a GP, XTEN, and optional spacer sequences, including but not limited to XTEN-GP, GP-XTEN, XTEN-S-GP, GP-S-XTEN, XTEN-GP-XTEN, GP-GP-XTEN, XTEN-GP-GP, GP-S-GP-XTEN, XTEN-GP-S-GP, and multimers thereof, or be of a configuration shown in Table 7. The choice of configuration can, as disclosed herein, confer particular pharmacokinetic, physicochemical, or pharmacologic properties.

In some embodiments, the isolated fusion protein is characterized in that: (i) it has a longer half-life compared to the corresponding glucose regulating peptide that lacks the XTEN; (ii) when a smaller molar amount of the fusion protein is administered to a subject in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject under an otherwise equivalent dose regimen, the fusion protein achieves a comparable area under the curve (AUC) as the corresponding glucose regulating peptide that lacks the XTEN; (iii) when a smaller molar amount of the fusion protein is administered to a subject in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject under an otherwise equivalent dose regimen, the fusion protein achieves a comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN; (iv) when the fusion protein is administered to a subject less frequently in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject using an otherwise equivalent molar amount, the fusion protein achieves a comparable area under the curve (AUC) as the corresponding glucose regulating peptide that lacks the XTEN; (v) when the fusion protein is administered to a subject less frequently in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject using an otherwise equivalent molar amount, the fusion protein achieves a comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN; (vi) when an accumulatively smaller molar amount of the fusion protein is administered to a subject in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject under an otherwise equivalent dose period, the fusion protein achieves comparable area under the curve (AUC) as the corresponding glucose regulating peptide that lacks the XTEN; or (vii) when an accumulatively smaller molar amount of the fusion protein is administered to a subject in comparison to the corresponding glucose regulating peptide that lacks the XTEN administered to a subject under an otherwise equivalent dose period, the fusion protein achieves comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN.

In one embodiment, the GPXTEN fusion proteins of formulas I-VIII described above exhibit a biological activity of at least about 0.1%, or at least about 1%, or at least about 2%, or at least about 3%, or at least about 4%, or at least about 5%, or at least about 10%, or at least about 20%, or at least about 30%, or at least 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95% of the biological activity compared to the GP not linked to the fusion protein. In another embodiment, the GPXTEN fusion proteins of formulas I-VIII bind the same receptors as the corresponding parental GP that is not covalently linked to the fusion protein.

The invention provides a method of producing a fusion protein comprising a glucose regulating peptide fused to one or more extended recombinant polypeptides (XTEN), comprising: (a) providing host cell comprising a recombinant polynucleotide molecule encoding the fusion protein (b) culturing the host cell under conditions permitting the expression of the fusion protein; and (c) recovering the fusion protein. In one embodiment of the method, the glucose regulating peptide of the fusion protein has at least 90% sequence identity to human glucose regulating peptide or a sequence selected from Table 1. In another embodiment of the method, the one or more XTEN of the expressed fusion protein has at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% to about 100% sequence identity to a sequence selected from Table 5. In another embodiment of the method, the polynucleotide encoding the XTEN is codon optimized for enhanced expression of said fusion protein in the host cell. In another embodiment of the method, the host cell is a prokaryotic cell. In another embodiment of the method, the host cell is E. coli. In another embodiment of the method the isolated fusion protein is recovered from the host cell cytoplasm in substantially soluble form.

The invention provides isolated nucleic acids comprising a polynucleotide sequence selected from (a) a polynucleotide encoding the fusion protein of any of the foregoing embodiments, or (b) the complement of the polynucleotide of (a). In one embodiment, the invention provides an isolated nucleic acid comprising a polynucleotide sequence that has at least 80% sequence identity, or about 85%, or at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% to about 100% sequence identity to (a) a polynucleotide sequence of comparable length selected from Table 35, Table 36, and Table 37; or (b) the complement of the polynucleotide of (a). The invention provides expression vectors comprising the nucleic acid of any of the embodiments hereinabove described in this paragraph. In one embodiment, the expression vector of the foregoing further comprises a recombinant regulatory sequence operably linked to the polynucleotide sequence. In another embodiment, the polynucleotide sequence of the expression vectors of the foregoing is fused in frame to a polynucleotide encoding a secretion signal sequence, which can be a prokaryotic signal sequence. In one embodiment, the secretion signal sequence is selected from OmpA, DsbA, and PhoA signal sequences.

The invention provides a host cell, which can comprise an expression vector disclosed in the foregoing paragraph. In one embodiment, the host cell is a prokaryotic cell. In another embodiment, the host cell is E. coli. In another embodiment, the host cell is a eukaryotic cell.

In one embodiment, the invention provides pharmaceutical compositions comprising the fusion protein of any of the foregoing embodiments and a pharmaceutically acceptable carrier. In another embodiment, the invention provides kits, comprising packaging material and at least a first container comprising the pharmaceutical composition of the foregoing embodiment and a label identifying the pharmaceutical composition and storage and handling conditions, and a sheet of instructions for the reconstitution and/or administration of the pharmaceutical compositions to a subject.

The invention provides a method of treating a glucose regulating peptide-related condition in a subject, comprising administering to the subject a therapeutically effective amount of the fusion protein of any of the foregoing embodiments. In one embodiment of the method, the glucose regulating peptide-related condition is selected from, but not limited to, juvenile diabetes, type I diabetes, type II diabetes, obesity, acute hypoglycemia, acute hyperglycemia, nocturnal hypoglycemia, chronic hyperglycemia, glucagonomas, secretory disorders of the airway, arthritis, osteoporosis, central nervous system disease, restenosis, neurodegenerative disease, renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, hypertension, and disorders wherein the reduction of food intake is desired, stroke, irritable bowel syndrome, myocardial infarction (e.g., reducing the morbidity and/or mortality associated therewith), stroke, acute coronary syndrome (e.g., characterized by an absence of Q-wave) myocardial infarction, post-surgical catabolic changes, hibernating myocardium or diabetic cardiomyopathy, insufficient urinary sodium excretion, excessive urinary potassium concentration, conditions or disorders associated with toxic hypervolemia, (e.g., renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, and hypertension), polycystic ovary syndrome, respiratory distress, nephropathy, left ventricular systolic dysfunction, (e.g., with abnormal left ventricular ejection fraction), gastrointestinal disorders such as diarrhea, postoperative dumping syndrome and irritable bowel syndrome, (i.e., via inhibition of antro-duodenal motility), critical illness polyneuropathy (CIPN), dyslipidemia, organ tissue injury caused by reperfusion of blood flow following ischemia, and coronary heart disease risk factor (CHDRF) syndrome, and any other indication for which the unmodified glucose-regulating peptide (e.g. exendin-4, GLP-1 or glucagon) is utilized, or any other indication for which GP can be utilized (but for which endogenous glucose regulating peptide levels in a subject are not necessarily deficient).

In some embodiments, the composition can be administered subcutaneously, intramuscularly, or intravenously. In one embodiment, the composition is administered at a therapeutically effective amount. In one embodiment, the therapeutically effective amount results in a gain in time spent within a therapeutic window for the fusion protein compared to the corresponding GP of the fusion protein not linked to the fusion protein and administered at a comparable dose to a subject. The gain in time spent within the therapeutic window can at least three-fold longer than the corresponding GP not linked to the fusion protein, or alternatively, at least four-fold, or five-fold, or six-fold, or seven-fold, or eight-fold, or nine-fold, or at least 10-fold, or at least 20-fold, or at least about 30-fold, or at least about 50-fold, or at least about 100-fold longer than the corresponding GP not linked to the fusion protein. In some embodiments of the method of treatment, (i) a smaller molar amount of (e.g. of about two-fold less, or about three-fold less, or about four-fold less, or about five-fold less, or about six-fold less, or about eight-fold less, or about 100 fold-less or greater) the fusion protein is administered in comparison to the corresponding glucose regulating peptide that lacks the XTEN under an otherwise same dose regimen, and the fusion protein achieves a comparable area under the curve and/or a comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN; (ii) the fusion protein is administered less frequently (e.g., every two days, about every seven days, about every 14 days, about every 21 days, or about, monthly) in comparison to the corresponding glucose regulating peptide that lacks the XTEN under an otherwise same dose amount, and the fusion protein achieves a comparable area under the curve and/or a comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN; or (iii) an accumulative smaller molar amount (e.g. about 5%, or about 10%, or about 20%, or about 40%, or about 50%, or about 60%, or about 70%, or about 80%, or about 90% less) of the fusion protein is administered in comparison to the corresponding glucose regulating peptide that lacks the XTEN under the otherwise same dose regimen the fusion protein achieves a comparable area under the curve and/or a comparable therapeutic effect as the corresponding glucose regulating peptide that lacks the XTEN. The accumulative smaller molar amount is measure for a period of at least about one week, or about 14 days, or about 21 days, or about one month. In some embodiments of the method, the therapeutic effect is a measured parameter selected from HbA1c concentrations, insulin concentrations, stimulated C peptide, fasting plasma glucose (FPG), serum cytokine levels, CRP levels, insulin secretion and Insulin-sensitivity index derived from an oral glucose tolerance test (OGTT), body weight, and food consumption.

In another embodiment, invention provides a method of treating a disease, disorder or condition, comprising administering the pharmaceutical composition described above to a subject using multiple consecutive doses of the pharmaceutical composition administered using a therapeutically effective dose regimen. In one embodiment of the foregoing, the therapeutically effective dose regimen can result in a gain in time of at least three-fold, or alternatively, at least four-fold, or five-fold, or six-fold, or seven-fold, or eight-fold, or nine-fold, or at least 10-fold, or at least 20-fold, or at least about 30-fold, or at least about 50-fold, or at least about 100-fold longer time between at least two consecutive Cmax peaks and/or Cmin troughs for blood levels of the fusion protein compared to the corresponding GP of the fusion protein not linked to the fusion protein and administered at a comparable dose regimen to a subject. In another embodiment of the foregoing, the administration of the fusion protein results in improvement in at least one measured parameter of a glucose regulating peptide-related disease using less frequent dosing or a lower total dosage in moles of the fusion protein of the pharmaceutical composition compared to the corresponding biologically active protein component(s) not linked to the fusion protein and administered to a subject d using a therapeutically effective regimen to a subject.

The invention further provides use of the compositions comprising the fusion protein of any of the foregoing embodiments in the preparation of a medicament for treating a disease, disorder or condition in a subject in need thereof. In one embodiment of the foregoing, the disease, disorder or condition is selected from, but not limited to, juvenile diabetes, type I diabetes, type II diabetes, obesity, acute hypoglycemia, acute hyperglycemia, nocturnal hypoglycemia, chronic hyperglycemia, glucagonomas, secretory disorders of the airway, arthritis, osteoporosis, central nervous system disease, restenosis, neurodegenerative disease, renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, hypertension, and disorders wherein the reduction of food intake is desired, stroke, irritable bowel syndrome, myocardial infarction (e.g., reducing the morbidity and/or mortality associated therewith), stroke, acute coronary syndrome (e.g., characterized by an absence of Q-wave) myocardial infarction, post-surgical catabolic changes, hibernating myocardium or diabetic cardiomyopathy, insufficient urinary sodium excretion, excessive urinary potassium concentration, conditions or disorders associated with toxic hypervolemia, (e.g., renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, and hypertension), polycystic ovary syndrome, respiratory distress, nephropathy, left ventricular systolic dysfunction, (e.g., with abnormal left ventricular ejection fraction), gastrointestinal disorders such as diarrhea, postoperative dumping syndrome and irritable bowel syndrome, (i.e., via inhibition of antro-duodenal motility), critical illness polyneuropathy (CIPN), dyslipidemia, organ tissue injury caused by reperfusion of blood flow following ischemia, and coronary heart disease risk factor (CHDRF) syndrome, and any other indication for which the unmodified glucose-regulating peptide (e.g. exendin-4, GLP-1 or glucagon) is utilized, or any other indication for which GP can be utilized (but for which endogenous glucose regulating peptide levels in a subject are not necessarily deficient). Any of the disclosed embodiments can be practiced alone or in combination depending on the interested application.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

FIG. 1 shows schematic representations of exemplary GPXTEN fusion proteins (FIGS. 1A-H), all depicted in an N- to C-terminus orientation. FIG. 1A shows two different configurations of GPXTEN fusion proteins (100), each comprising a single GP and an XTEN, the first of which has an XTEN molecule (102) attached to the C-terminus of a GP (103), and the second of which has an XTEN molecule attached to the N-terminus of a GP (103). FIG. 1B shows two different configurations of GPXTEN fusion proteins (100), each comprising a single GP, a spacer sequence and an XTEN, the first of which has an XTEN molecule (102) attached to the C-terminus of a spacer sequence (104) and the spacer sequence attached to the C-terminus of a GP (103) and the second of which has an XTEN molecule attached to the N-terminus of a spacer sequence (104) and the spacer sequence attached to the N-terminus of a GP (103). FIG. 1C shows two different configurations of GPXTEN fusion proteins (101), each comprising two molecules of a single GP and one molecule of an XTEN, the first of which has an XTEN linked to the C-terminus of a first GP and that GP is linked to the C-terminus of a second GP, and the second of which is in the opposite orientation in which the XTEN is linked to the N-terminus of a first GP and that GP is linked to the N-terminus of a second GP. FIG. 1D shows two different configurations of GPXTEN fusion proteins (101), each comprising two molecules of a single GP, a spacer sequence and one molecule of an XTEN, the first of which has an XTEN linked to the C-terminus of a spacer sequence and the spacer sequence linked to the C-terminus of a first GP which is linked to the C-terminus of a second GP, and the second of which is in the opposite orientation in which the XTEN is linked to the N-terminus of a spacer sequence and the spacer sequence is linked to the N-terminus of a first GP that that GP is linked to the N-terminus of a second GP. FIG. 1E shows two different configurations of GPXTEN fusion proteins (101), each comprising two molecules of a single GP, a spacer sequence and one molecule of an XTEN, the first of which has an XTEN linked to the C-terminus of a first GP and the first GP linked to the C-terminus of a spacer sequence which is linked to the C-terminus of a second GP molecule, and the second of which is in the opposite configuration of XTEN linked to the N-terminus of a first GP which is linked to the N-terminus of a spacer sequence which in turn is linked to the N-terminus of a second molecule of GP. FIG. 1F shows a configuration of GPXTEN fusion protein (105), each comprising one molecule of GP and two molecules of an XTEN linked to the N-terminus and the C-terminus of the GP. FIG. 1G shows a configuration (105) of a single GP linked to two XTEN, with the second XTEN separated from the GP by a spacer sequence. FIG. 1H is a configuration (106) of a two GP linked to two XTEN, with the second XTEN linked to the C-terminus of the first GP and the N-terminus of the second GP, which is at the C-terminus of the GPXTEN.

FIG. 2 is a schematic illustration of exemplary polynucleotide constructs (FIGS. 2A-H) of GPXTEN genes that encode the corresponding GPXTEN polypeptides of FIG. 1; all depicted in a 5′ to 3′ orientation. In these illustrative examples the genes encode GPXTEN fusion proteins with one GP and XTEN (200); or one GP, one spacer sequence and one XTEN (200); two GP and one XTEN (201); or two GP, a spacer sequence and one XTEN (201); one GP and two XTEN (205); or two GP and two XTEN (206). In these depictions, the polynucleotides encode the following components: XTEN (202), GP (203), and spacer amino acids that can include a cleavage sequence (204), with all sequences linked in frame.

FIG. 3 is a schematic illustration of two exemplary monomeric GPXTEN and the ability of the monomeric fusion proteins to bind to a target receptor on a cell surface, with subsequent cell signaling. FIG. 3A shows a GPXTEN fusion protein (100) consisting of a GP (103) and an XTEN (102) and a second GPXTEN fusion protein (105) consisting of a GP linked to two XTEN (105). FIG. 3B shows the interaction of the GPXTEN with the GP on the C-terminus (100) and the GPXTEN with an XTEN on the C-terminus (105) with target receptors (108) to GP on a cell surface (107). In this case, binding to the receptor with high affinity is exhibited when GP has a free C-terminus, while the GPXTEN with a C-terminal XTEN does not bind tightly to the receptor, and disassociates, as seen in FIG. 3C. FIG. 3D shows that the bound GPXTEN (100) with high binding affinity remains bound to the receptor (106) and has been internalized into an endosome (110) within the cell, illustrating receptor-mediated clearance of the bound GP and triggering cell signaling (109), portrayed as stippled cytoplasm.

FIG. 4 is a schematic flowchart of representative steps in the assembly, production and the evaluation of a XTEN.

FIG. 5 is a schematic flowchart of representative steps in the assembly of a GP-XTEN polynucleotide construct encoding a fusion protein. Individual oligonucleotides 501 are annealed into sequence motifs 502 such as a 12 amino acid motif (“12-mer”), which is subsequently ligated with an oligo containing BbsI, and KpnI restriction sites 503. Additional sequence motifs from a library are annealed to the 12-mer until the desired length of the XTEN gene 504 is achieved. The XTEN gene is cloned into a stuffer vector. The vector encodes a Flag sequence 506 followed by a stopper sequence that is flanked by BsaI, BbsI, and KpnI sites 507 and an exendin-4 (Ex4) gene 508, resulting in the gene 500 encoding an GPXTEN fusion protein.

FIG. 6 is a schematic flowchart of representative steps in the assembly of a gene encoding fusion protein comprising a biologically active protein (GP) and XTEN, its expression and recovery as a fusion protein, and its evaluation as a candidate GPXTEN product.

FIG. 7 is a schematic representation of the design of Ex4XTEN expression vectors with different processing strategies. FIG. 7A shows an exemplary expression vector encoding XTEN fused to the 3′ end of the sequence encoding biologically active protein Ex4. Note that no additional leader sequences are required in this vector. FIG. 7B depicts an expression vector encoding XTEN fused to the 5′ end of the sequence encoding Ex4 with a CBD leader sequence and a TEV protease site. FIG. 7C depicts an expression vector as in FIG. 7B where the CBD and TEV processing site have been replaced with an optimized N-terminal leader sequence (NTS). FIG. 7D depicts an expression vector encoding an NTS sequence, an XTEN, a sequence encoding Ex4, and than a second sequence encoding an XTEN.

FIG. 8 is a schematic representation of the step-wise construction of GPXTEN genes that contain N-terminal XTEN encoding sequences linked to a sequence encoding exendin-4 (Ex4) and the subsequent linkage of sequences encoding either 144 or 288 XTEN linked to the C-terminus of XTEN, as described in Example 18.

FIG. 9 shows results of expression assays for the indicated constructs comprising GFP and XTEN sequences. The expression cultures were assayed using a fluorescence plate reader (excitation 395 nm, emission 510 nm) to determine the amount of GFP reporter present. The results, graphed as box and whisker plots, indicate that while median expression levels were approximately half of the expression levels compared to the “benchmark” CBD N-terminal helper domain, the best clones from the libraries were much closer to the benchmarks, indicating that further optimization around those sequences was warranted. The results also show that the libraries starting with amino acids MA had better expression levels than those beginning with ME (see Example 14).

FIG. 10 shows three randomized libraries used for the third and fourth codons in the N-terminal sequences of clones from LCW546, LCW547 and LCW552, as described in Example 15. The libraries were designed with the third and fourth residues modified such that all combinations of allowable XTEN codons were present at these positions, as shown. In order to include all the allowable XTEN codons for each library, nine pairs of oligonucleotides encoding 12 amino acids with codon diversities of third and fourth residues were designed, annealed and ligated into the NdeI/BsaI restriction enzyme digested stuffer vector pCW0551 (Stuffer-XTEN_AM875-GFP), and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of the three libraries LCW0569 (DNA and protein sequences disclosed as SEQ ID NOS 1338 and 1339, respectively), LCW0570 (DNA and protein sequences disclosed as SEQ ID NOS 1340 and 1341, respectively), and LCW0571 (DNA and protein sequences disclosed as SEQ ID NOS 1342 and 1343, respectively).

FIG. 11 shows a histogram of a retest of the top 75 clones after the optimization step, as described in Example 15, for GFP fluorescence signal, relative to the benchmark CBD_AM875 construct. The results indicated that several clones were now superior to the benchmark clones.

FIG. 12 is a schematic of a combinatorial approach undertaken for the union of codon optimization preferences for two regions of the N-terminus 48 amino acids, as described in Example 16. The approach created novel 48 mers at the N-terminus of the XTEN protein for evaluation of the optimization of expression that resulted in leader sequences that may be a solution for expression of XTEN proteins where the XTEN is N-terminal to the GP.

FIG. 13 shows an SDS-PAGE gel confirming expression of preferred clones obtained from the XTEN N-terminal codon optimization experiments, in comparison to benchmark XTEN clones comprising CBD leader sequences at the N-terminus of the construct sequences.

FIG. 14 shows an SDS-PAGE gel of samples from a stability study of the fusion protein of XTEN_AE864 fused to the N-terminus of GFP (see Example 24). The GFP-XTEN was incubated in cynomolgus plasma and rat kidney lysate for up to 7 days at 37° C. In addition, GFP-XTEN administered to cynomolgus monkeys was also assessed. Samples were withdrawn at 0, 1 and 7 days and analyzed by SDS PAGE followed by detection using Western analysis and detection with antibodies against GFP.

FIG. 15 shows an SDS-PAGE gel confirming expression of glucagon fused to XTEN of various lengths; i.e., Y288, Y144, Y72 and Y36, in comparison to molecular weight standards.

FIG. 16 shows results of a of a size exclusion chromatography analysis of glucagon-XTEN construct samples measured against protein standards of known molecular weight, with the graph output as absorbance versus retention volume, as described in Example 22. The glucagon-XTEN constructs are 1) glucagon-Y288; 2) glucagonY-144; 3) glucagon-Y72; and 4) glucagon-Y36. The results indicate an increase in apparent molecular weight with increasing length of XTEN moiety.

FIG. 17 shows the pharmacokinetic results of the GPXTEN Ex4-AE864 administered to cynomolgus monkeys by the subcutaneous and intravenous routes (see Example 27 for experimental details).

FIG. 18 illustrates allometric scaling results for predicted human response to Ex4-XTEN_AE864 based on measured results from four animal species; i.e., mice, rats, cynomolgus monkeys and dogs, as described in Example 28. FIG. 18A shows measured terminal half-life versus body mass, with a predicted T½ in humans of 139 h. FIG. 18B shows measured drug clearance versus body mass, with a predicted clearance rate value of 30 ml/h in humans. FIG. 18C shows measured volume of distribution versus body mass, with a predicted value of 5970 ml in humans.

FIG. 19 shows results of studies of the biophysical characterization and stability of Gcg-XTEN (see Example 21 for experimental details). FIG. 19A is a SDS-PAGE analysis of the purified protein product (lane 2). Molecular weight markers are shown in lane 1 with relevant size markers labeled at the left. Note that the true molecular weight of the molecule is 16305 Daltons (confirmed by mass spectrometry; not shown). Slow migration in SDS-PAGE relative to globular protein standards is typical of XTEN fusion proteins due to differences in primary amino acid composition. FIG. 19B shows results of a glucagon receptor (GcgR) Ca2+-flux assay comparing the efficacy of Gcg-XTEN to unmodified glucagon. Calculated EC50 values for each curve fit are shown. FIG. 19C shows results of a reverse phase C18 HPLC analysis. FIG. 19D shows results of a size exclusion chromatography HPLC analysis of the purified Gcg-XTEN construct at the time of production. FIG. 19E shows results of a reverse phase C18 HPLC analysis. FIG. 19F shows results of size exclusion chromatography HPLC analyses of Gcg-XTEN after 6 months storage at either −80° C., 2-8° C., or 25° C., with all three curves essentially superimposed.

FIG. 20 shows results of a pharmacodynamic study in dogs dosed with glucagon or Gcg-XTEN (see Example 29 for experimental details). Glucagon (FIG. 20A) or Gcg-XTEN (FIG. 20B) was injected at 14 or 12 nmol/kg, respectively, into fasted beagle dogs (n=4 per group) and blood glucose levels were monitored in comparison to placebo injection, as shown in FIG. 20C. The difference in blood glucose area under the curve for the first hour after injection of placebo, Gcg-XTEN, or Glucagon (Gcg) relative to pre-injection baseline is shown (n=4-8 animals per group). The dose level for each group is indicated.

FIG. 21 shows results of a pharmacodynamic study in dogs dosed with glucagon or Gcg-XTEN and challenged with insulin in order to test whether Gcg-XTEN confers temporally-controlled resistance to insulin-induced hypoglycemia in dogs (see Example 30 for experimental details). Beagle dogs were fed three hours prior to the start of the experiment and fasted thereafter. At time=0, animals received either a dose of 0.6 nmol/kg Gcg-XTEN or placebo (open arrows). Animals (n=4 per group) received a challenge of 0.05 U/kg insulin to induce hypoglycemia at either 6 hr (FIG. 21A), indicated by solid arrow, or 12 hr (FIG. 21B) after initial dose, indicated by solid arrow. FIG. 21C represents a hypothetical timeline for human administration over a meal-sleep-wake cycle that is intended to correspond to the dosage administration and experimental design of the experiment.

FIG. 22 shows results of a pharmacodynamic experiment dosed with glucagon or Gcg-XTEN_Y288 (Construct 1) to test the ability of the compounds to inhibit an increase in blood glucose after the end of fasting in cynomolgus monkeys (see Example 31 for experimental details). FIGS. 22A-C show overlaid plots of blood glucose profiles after placebo or Gcg-XTEN288 administration for three individual cynomolgus monkeys. Solid arrows mark the time when food was returned to the animals (t=6 hours).

FIG. 23 shows body weight results from a pharmacodynamic and metabolic study using a combination of two GPXTEN fusion proteins; i.e., glucagon linked to Y288 (Gcg-XTEN) and exendin-4 linked to AE864 (Ex4-XTEN) to evaluate the combination for efficacy in a diet-induced obesity model in mice (see Example 26 for experimental details). The graph shows change in body weight in Diet-Induced Obese mice over the course of 28 days continuous drug administration. Values shown are the average+/−SEM of 10 animals per group (20 animals in the placebo group).

FIG. 24 shows change in fasting glucose levels from a pharmacodynamic and metabolic study using single and combinations of two GPXTEN fusion proteins; i.e., glucagon linked to Y288 (Gcg-XTEN) and exendin-4 linked to AE864 (Ex4-XTEN) in a diet-induced obesity model in mice (see Example 26 for experimental details). Groups are as follows: Gr. 1 Tris Vehicle; Gr. 2 Ex4-AE576, 10 mg/kg; Gr. 3 Ex4-AE576, 20 mg/kg; Gr. 4 Vehicle, 50% DMSO; Gr. 5 Exenatide, 30 μg/kg/day; Gr. 6 Exenatide, 30 uL/kg/day+Gcg-Y288 20 μg/kg; Gr. 7 Gcg-Y288, 20 μg/kg; Gr. 8 Gcg-Y288, 40 μg/kg; Gr. 9 Ex4-AE576 10 mg/kg+Gcg-Y288 20 μg/kg; Gr. 10 Gcg-Y288 40 μg/kg+Ex4-AE576 20 mg/kg. The graph shows the change in fasting blood glucose levels in Diet-Induced Obese mice over the course of 28 days continuous drug administration. Values shown are the average+/−SEM of 10 animals per group (20 animals in the placebo group).

FIG. 25 shows the triglyceride and cholesterol levels in Diet-Induced Obese mice after 28 days continuous drug administration of Gcg-XTEN and exendin-4, either singly or in combination (see Example 26 for experimental details). Values shown are the average+/−SEM of 10 animals per group.

FIG. 26 shows the results of a pharmacokinetic study in cynomolgus monkeys testing the effects of XTEN length with different compositions of GFP linked to XTEN administered either subcutaneously or intravenously, as described in Example 23. The compositions were GFP-L288, GFP-L576, GFP-AF576, GFP-Y576 and AD836-GFP. Results are presented as the plasma concentration versus time (h) after dosing.

FIG. 27 shows the near UV circular dichroism spectrum of Ex4-XTEN_AE864, performed as described in Example 34.

FIG. 28 shows the results of blood levels over time for glucagon-XTEN fusion proteins administered to cynomolgus monkeys, as described in Example 32. The GPXTEN administered were glucagon-Y288, glucagonY-144, and glucagon-Y72. The results from the glucagon-Y144 dosing shows <3-fold variation in blood levels over 0-6 hrs, with blood levels dropping below the 10× threshold from the Cmax at 10-12 hours.

FIG. 29 shows the results of an in vitro cellular assay for GLP-1 activity, comparing exendin-4 from two commercial sources (closed triangles) to exendin-4 linked to Y288 (closed squares), with untreated cells (closed diamonds) used as a negative control (see Example 35 for experimental details). The EC50 is indicated by the dashed line.

DETAILED DESCRIPTION OF THE INVENTION

Before the embodiments of the invention are described, it is to be understood that such embodiments are provided by way of example only, and that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention.

Definitions

As used herein, the following terms have the meanings ascribed to them unless specified otherwise.

As used in the specification and claims, the singular forms “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes a plurality of cells, including mixtures thereof.

The terms “polypeptide”, “peptide”, and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non amino acids. The terms also encompass an amino acid polymer that has been modified, for example, by disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component.

As used herein the term “amino acid” refers to either natural and/or unnatural or synthetic amino acids, including but not limited to glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics. Standard single or three letter codes are used to designate amino acids.

The term “natural L-amino acid” means the L optical isomer forms of glycine (G), proline (P), alanine (A), valine (V), leucine (L), isoleucine (I), methionine (M), cysteine (C), phenylalanine (F), tyrosine (Y), tryptophan (W), histidine (H), lysine (K), arginine (R), glutamine (Q), asparagine (N), glutamic acid (E), aspartic acid (D), serine (S), and threonine (T).

The term “non-naturally occurring,” as applied to sequences and as used herein, means polypeptide or polynucleotide sequences that do not have a counterpart to, are not complementary to, or do not have a high degree of homology with a wild-type or naturally-occurring sequence found in a mammal. For example, a non-naturally occurring polypeptide may share no more than 99%, 98%, 95%, 90%, 80%, 70%, 60%, 50% or even less amino acid sequence identity as compared to a natural sequence when suitably aligned.

The terms “hydrophilic” and “hydrophobic” refer to the degree of affinity that a substance has with water. A hydrophilic substance has a strong affinity for water, tending to dissolve in, mix with, or be wetted by water, while a hydrophobic substance substantially lacks affinity for water, tending to repel and not absorb water and tending not to dissolve in or mix with or be wetted by water Amino acids can be characterized based on their hydrophobicity. A number of scales have been developed. An example is a scale developed by Levitt, M, et al., J Mol Biol (1976) 104:59, which is listed in Hopp, T P, et al., Proc Natl Acad Sci USA (1981) 78:3824. Examples of “hydrophilic amino acids” are arginine, lysine, threonine, alanine, asparagine, and glutamine. Of particular interest are the hydrophilic amino acids aspartate, glutamate, and serine, and glycine. Examples of “hydrophobic amino acids” are tryptophan, tyrosine, phenylalanine, methionine, leucine, isoleucine, and valine.

A “fragment” is a truncated form of a native biologically active protein that retains at least a portion of the therapeutic and/or biological activity. A “variant” is a protein with sequence homology to the native biologically active protein that retains at least a portion of the therapeutic and/or biological activity of the biologically active protein. For example, a variant protein may share at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity with the reference biologically active protein. As used herein, the term “biologically active protein moiety” includes proteins modified deliberately, as for example, by site directed mutagenesis, insertions, or accidentally through mutations.

A “host cell” includes an individual cell or cell culture which can be or has been a recipient for the subject vectors. Host cells include progeny of a single host cell. The progeny may not necessarily be completely identical (in morphology or in genomic of total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation. A host cell includes cells transfected in vivo with a vector of this invention.

“Isolated,” when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. As is apparent to those of skill in the art, a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, does not require “isolation” to distinguish it from its naturally occurring counterpart. In addition, a “concentrated”, “separated” or “diluted” polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, is distinguishable from its naturally occurring counterpart in that the concentration or number of molecules per volume is generally greater than that of its naturally occurring counterpart. In general, a polypeptide made by recombinant means and expressed in a host cell is considered to be “isolated.”

An “isolated” polynucleotide or polypeptide-encoding nucleic acid or other polypeptide-encoding nucleic acid is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the polypeptide-encoding nucleic acid. An isolated polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated polypeptide-encoding nucleic acid molecules therefore are distinguished from the specific polypeptide-encoding nucleic acid molecule as it exists in natural cells. However, an isolated polypeptide-encoding nucleic acid molecule includes polypeptide-encoding nucleic acid molecules contained in cells that ordinarily express the polypeptide where, for example, the nucleic acid molecule is in a chromosomal or extra-chromosomal location different from that of natural cells.

A “chimeric” protein contains at least one fusion polypeptide comprising regions in a different position in the sequence than that which occurs in nature. The regions may normally exist in separate proteins and are brought together in the fusion polypeptide; or they may normally exist in the same protein but are placed in a new arrangement in the fusion polypeptide. A chimeric protein may be created, for example, by chemical synthesis, or by creating and translating a polynucleotide in which the peptide regions are encoded in the desired relationship.

“Conjugated”, “linked,”“fused,” and “fusion” are used interchangeably herein. These terms refer to the joining together of two or more chemical elements or components, by whatever means including chemical conjugation or recombinant means. For example, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and in reading phase or in-frame. An “in-frame fusion” refers to the joining of two or more open reading frames (ORFs) to form a continuous longer ORF, in a manner that maintains the correct reading frame of the original ORFs. Thus, the resulting recombinant fusion protein is a single protein containing two or more segments that correspond to polypeptides encoded by the original ORFs (which segments are not normally so joined in nature).

In the context of polypeptides, a “linear sequence” or a “sequence” is an order of amino acids in a polypeptide in an amino to carboxyl terminus direction in which residues that neighbor each other in the sequence are contiguous in the primary structure of the polypeptide. A “partial sequence” is a linear sequence of part of a polypeptide that is known to comprise additional residues in one or both directions.

“Heterologous” means derived from a genotypically distinct entity from the rest of the entity to which it is being compared. For example, a glycine rich sequence removed from its native coding sequence and operatively linked to a coding sequence other than the native sequence is a heterologous glycine rich sequence. The term “heterologous” as applied to a polynucleotide, a polypeptide, means that the polynucleotide or polypeptide is derived from a genotypically distinct entity from that of the rest of the entity to which it is being compared.

The terms “polynucleotides”, “nucleic acids”, “nucleotides” and “oligonucleotides” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.

The term “complement of a polynucleotide” denotes a polynucleotide molecule having a complementary base sequence and reverse orientation as compared to a reference sequence, such that it could hybridize with a reference sequence with complete fidelity.

“Recombinant” as applied to a polynucleotide means that the polynucleotide is the product of various combinations of in vitro cloning, restriction and/or ligation steps, and other procedures that result in a construct that can potentially be expressed in a host cell.

The terms “gene” or “gene fragment” are used interchangeably herein. They refer to a polynucleotide containing at least one open reading frame that is capable of encoding a particular protein after being transcribed and translated. A gene or gene fragment may be genomic or cDNA, as long as the polynucleotide contains at least one open reading frame, which may cover the entire coding region or a segment thereof. A “fusion gene” is a gene composed of at least two heterologous polynucleotides that are linked together.

“Homology” or “homologous” refers to sequence similarity or interchangeability between two or more polynucleotide sequences or two or more polypeptide sequences. When using a program such as BestFit to determine sequence identity, similarity or homology between two different amino acid sequences, the default settings may be used, or an appropriate scoring matrix, such as blosum45 or blosum80, may be selected to optimize identity, similarity or homology scores. Preferably, polynucleotides that are homologous are those which hybridize under stringent conditions as defined herein and have at least 70%, or at least 80%, or at least 90%, or 95%, or 97%, or 98%, or 99% sequence identity to those sequences.

“Ligation” refers to the process of forming phosphodiester bonds between two nucleic acid fragments or genes, linking them together. To ligate the DNA fragments or genes together, the ends of the DNA must be compatible with each other. In some cases, the ends will be directly compatible after endonuclease digestion. However, it may be necessary to first convert the staggered ends commonly produced after endonuclease digestion to blunt ends to make them compatible for ligation.

The terms “stringent conditions” or “stringent hybridization conditions” includes reference to conditions under which a polynucleotide will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g., at least 2-fold over background). Generally, stringency of hybridization is expressed, in part, with reference to the temperature and salt concentration under which the wash step is carried out. Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short polynucleotides (e.g., 10 to 50 nucleotides) and at least about 60° C. for long polynucleotides (e.g., greater than 50 nucleotides)—for example, “stringent conditions” can include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and three washes for 15 min each in 0.1×SSC/1% SDS at 60 to 65° C. Alternatively, temperatures of about 65° C., 60° C., 55° C., or 42° C. may be used. SSC concentration may be varied from about 0.1 to 2×SSC, with SDS being present at about 0.1%. Such wash temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization are well known and can be found in Sambrook, J. et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; specifically see volume 2 and chapter 9. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, sheared and denatured salmon sperm DNA at about 100-200 μg/ml. Organic solvent, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as for RNA:DNA hybridizations. Useful variations on these wash conditions will be readily apparent to those of ordinary skill in the art.

The terms “percent identity” and “% identity,” as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences. Percent identity may be measured over the length of an entire defined polynucleotide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polynucleotide sequence, for instance, a fragment of at least 45, at least 60, at least 90, at least 120, at least 150, at least 210 or at least 450 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

“Percent (%) amino acid sequence identity,” with respect to the polypeptide sequences identified herein, is defined as the percentage of amino acid residues in a query sequence that are identical with the amino acid residues of a second, reference polypeptide sequence or a portion thereof, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

The term “non-repetitiveness” as used herein in the context of a polypeptide refers to a lack or limited degree of internal homology in a peptide or polypeptide sequence. The term “substantially non-repetitive” can mean, for example, that there are few or no instances of four contiguous amino acids in the sequence that are identical amino acid types or that the polypeptide has a subsequence score (defined infra) of 10 or less or that there isn't a pattern in the order, from N- to C-terminus, of the sequence motifs that constitute the polypeptide sequence. The term “repetitiveness” as used herein in the context of a polypeptide refers to the degree of internal homology in a peptide or polypeptide sequence. In contrast, a “repetitive” sequence may contain multiple identical copies of short amino acid sequences. For instance, a polypeptide sequence of interest may be divided into n-mer sequences and the number of identical sequences can be counted. Highly repetitive sequences contain a large fraction of identical sequences while non-repetitive sequences contain few identical sequences. In the context of a polypeptide, a sequence can contain multiple copies of shorter sequences of defined or variable length, or motifs, in which the motifs themselves have non-repetitive sequences, rendering the full-length polypeptide substantially non-repetitive. The length of polypeptide within which the non-repetitiveness is measured can vary from 3 amino acids to about 200 amino acids, about from 6 to about 50 amino acids, or from about 9 to about 14 amino acids. “Repetitiveness” used in the context of polynucleotide sequences refers to the degree of internal homology in the sequence such as, for example, the frequency of identical nucleotide sequences of a given length. Repetitiveness can, for example, be measured by analyzing the frequency of identical sequences.

A “vector” is a nucleic acid molecule, preferably self-replicating in an appropriate host, which transfers an inserted nucleic acid molecule into and/or between host cells. The term includes vectors that function primarily for insertion of DNA or RNA into a cell, replication of vectors that function primarily for the replication of DNA or RNA, and expression vectors that function for transcription and/or translation of the DNA or RNA. Also included are vectors that provide more than one of the above functions. An “expression vector” is a polynucleotide which, when introduced into an appropriate host cell, can be transcribed and translated into a polypeptide(s). An “expression system” usually connotes a suitable host cell comprised of an expression vector that can function to yield a desired expression product.

“Serum degradation resistance,” as applied to a polypeptide, refers to the ability of the polypeptides to withstand degradation in blood or components thereof, which typically involves proteases in the serum or plasma. The serum degradation resistance can be measured by combining the protein with human (or mouse, rat, monkey, as appropriate) serum or plasma, typically for a range of days (e.g. 0.25, 0.5, 1, 2, 4, 8, 16 days), typically at about 37° C. The samples for these time points can be run on a Western blot assay and the protein is detected with an antibody. The antibody can be to a tag in the protein. If the protein shows a single band on the western, where the protein's size is identical to that of the injected protein, then no degradation has occurred. In this exemplary method, the time point where 50% of the protein is degraded, as judged by Western blots or equivalent techniques, is the serum degradation half-life or “serum half-life” of the protein.

The term “t1/2” as used herein means the terminal half-life calculated as ln(2)/Kel. Kel is the terminal elimination rate constant calculated by linear regression of the terminal linear portion of the log concentration vs. time curve. Half-life typically refers to the time required for half the quantity of an administered substance deposited in a living organism to be metabolized or eliminated by normal biological processes. The terms “t1/2”, “terminal half-life”, “elimination half-life” and “circulating half-life” are used interchangeably herein.

“Apparent Molecular Weight Factor” or “Apparent Molecular Weight” are related terms referring to a measure of the relative increase or decrease in apparent molecular weight exhibited by a particular amino acid sequence. The Apparent Molecular Weight is determined using size exclusion chromatography (SEC) and similar methods compared to globular protein standards and is measured in “apparent kD” units. The Apparent Molecular Weight Factor is the ratio between the Apparent Molecular Weight and the actual molecular weight; the latter predicted by adding, based on amino acid composition, the calculated molecular weight of each type of amino acid in the composition.

The “hydrodynamic radius” or “Stokes radius” is the effective radius (Rh in nm) of a molecule in a solution measured by assuming that it is a body moving through the solution and resisted by the solution's viscosity. In the embodiments of the invention, the hydrodynamic radius measurements of the XTEN fusion proteins correlate with the ‘Apparent Molecular Weight Factor’, which is a more intuitive measure. The “hydrodynamic radius” of a protein affects its rate of diffusion in aqueous solution as well as its ability to migrate in gels of macromolecules. The hydrodynamic radius of a protein is determined by its molecular weight as well as by its structure, including shape and compactness. Methods for determining the hydrodynamic radius are well known in the art, such as by the use of size exclusion chromatography (SEC), as described in U.S. Pat. Nos. 6,406,632 and 7,294,513. Most proteins have globular structure, which is the most compact three-dimensional structure a protein can have with the smallest hydrodynamic radius. Some proteins adopt a random and open, unstructured, or ‘linear’ conformation and as a result have a much larger hydrodynamic radius compared to typical globular proteins of similar molecular weight.

“Physiological conditions” refer to a set of conditions in a living host as well as in vitro conditions, including temperature, salt concentration, pH, that mimic those conditions of a living subject. A host of physiologically relevant conditions for use in in vitro assays have been established. Generally, a physiological buffer contains a physiological concentration of salt and is adjusted to a neutral pH ranging from about 6.5 to about 7.8, and preferably from about 7.0 to about 7.5. A variety of physiological buffers is listed in Sambrook et al. (1989). Physiologically relevant temperature ranges from about 25° C. to about 38° C., and preferably from about 35° C. to about 37° C.

A “reactive group” is a chemical structure that can be coupled to a second reactive group. Examples for reactive groups are amino groups, carboxyl groups, sulfhydryl groups, hydroxyl groups, aldehyde groups, azide groups. Some reactive groups can be activated to facilitate coupling with a second reactive group. Examples for activation are the reaction of a carboxyl group with carbodiimide, the conversion of a carboxyl group into an activated ester, or the conversion of a carboxyl group into an azide function.

“Controlled release agent”, “slow release agent”, “depot formulation” or “sustained release agent” are used interchangeably to refer to an agent capable of extending the duration of release of a polypeptide of the invention relative to the duration of release when the polypeptide is administered in the absence of agent. Different embodiments of the present invention may have different release rates, resulting in different therapeutic amounts.

The terms “antigen”, “target antigen” or “immunogen” are used interchangeably herein to refer to the structure or binding determinant that an antibody fragment or an antibody fragment-based therapeutic binds to or has specificity against.

The term “payload” as used herein refers to a protein or peptide sequence that has biological or therapeutic activity; the counterpart to the pharmacophore of small molecules. Examples of payloads include, but are not limited to, cytokines, enzymes, hormones and blood and growth factors. Payloads can further comprise genetically fused or chemically conjugated moieties such as chemotherapeutic agents, antiviral compounds, toxins, or contrast agents. These conjugated moieties can be joined to the rest of the polypeptide via a linker that may be cleavable or non-cleavable.

The term “antagonist”, as used herein, includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native polypeptide disclosed herein. Methods for identifying antagonists of a polypeptide may comprise contacting a native polypeptide with a candidate antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the native polypeptide. In the context of the present invention, antagonists may include proteins, nucleic acids, carbohydrates, antibodies or any other molecules that decrease the effect of a biologically active protein.

The term “agonist” is used in the broadest sense and includes any molecule that mimics a biological activity of a native polypeptide disclosed herein. Suitable agonist molecules specifically include agonist antibodies or antibody fragments, fragments or amino acid sequence variants of native polypeptides, peptides, small organic molecules, etc. Methods for identifying agonists of a native polypeptide may comprise contacting a native polypeptide with a candidate agonist molecule and measuring a detectable change in one or more biological activities normally associated with the native polypeptide.

“Activity” for the purposes herein refers to an action or effect of a component of a fusion protein consistent with that of the corresponding native biologically active protein, wherein “biological activity” refers to an in vitro or in vivo biological function or effect, including but not limited to receptor binding, antagonist activity, agonist activity, or a cellular or physiologic response.

As used herein, “treatment” or “treating,” or “palliating” or “ameliorating” is used interchangeably herein. These terms refer to an approach for obtaining beneficial or desired results including but not limited to a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. For prophylactic benefit, the compositions may be administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.

A “therapeutic effect”, as used herein, refers to a physiologic effect, including but not limited to the cure, mitigation, amelioration, or prevention of disease in humans or other animals, or to otherwise enhance physical or mental wellbeing of humans or animals, caused by a fusion polypeptide of the invention other than the ability to induce the production of an antibody against an antigenic epitope possessed by the biologically active protein. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

The terms “therapeutically effective amount” and “therapeutically effective dose”, as used herein, refers to an amount of a biologically active protein, either alone or as a part of a fusion protein composition, that is capable of having any detectable, beneficial effect on any symptom, aspect, measured parameter or characteristics of a disease state or condition when administered in one or repeated doses to a subject. Such effect need not be absolute to be beneficial.

The term “therapeutically effective dose regimen”, as used herein, refers to a schedule for consecutively administered doses of a biologically active protein, either alone or as a part of a fusion protein composition, wherein the doses are given in therapeutically effective amounts to result in sustained beneficial effect on any symptom, aspect, measured parameter or characteristics of a disease state or condition.

I) General Techniques

The practice of the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which are within the skill of the art. See Sambrook, J. et al., “Molecular Cloning: A Laboratory Manual,” 3rd edition, Cold Spring Harbor Laboratory Press, 2001; “Current protocols in molecular biology”, F. M. Ausubel, et al. eds., 1987; the series “Methods in Enzymology,” Academic Press, San Diego, Calif.; “PCR 2: a practical approach”, M. J. MacPherson, B. D. Hames and G. R. Taylor eds., Oxford University Press, 1995; “Antibodies, a laboratory manual” Harlow, E. and Lane, D. eds., Cold Spring Harbor Laboratory, 1988; “Goodman & Gilman's The Pharmacological Basis of Therapeutics,” 11th Edition, McGraw-Hill, 2005; and Freshney, R. I., “Culture of Animal Cells: A Manual of Basic Technique,” 4th edition, John Wiley & Sons, Somerset, N J, 2000, the contents of which are incorporated in their entirety herein by reference.

II) Glucose Regulating Peptides

The present invention relates in part to fusion protein compositions comprising glucose regulating peptides (GP). Such compositions can have utility in the treatment or prevention of certain diseases, disorder or conditions related to glucose homeostasis, obesity, insulin resistance, dyslipidemia, hypertension, and the like.

Endocrine and obesity-related diseases or disorders have reached epidemic proportions in most developed nations, and represent a substantial and increasing health care burden in most developed nations, which include a large variety of conditions affecting the organs, tissues, and circulatory system of the body. Of particular concern are endocrine and obesity-related diseases and disorders, which. Chief amongst these is diabetes; one of the leading causes of death in the United States. Diabetes is divided into two major sub-classes-Type I, also known as juvenile diabetes, or Insulin-Dependent Diabetes Mellitus (IDDM), and Type II, also known as adult onset diabetes, or Non-Insulin-Dependent Diabetes Mellitus (NIDDM). Type I Diabetes is a form of autoimmune disease that completely or partially destroys the insulin producing cells of the pancreas in such subjects, and requires use of exogenous insulin during their lifetime. Even in well-managed subjects, episodic complications can occur, some of which are life-threatening.

In Type II diabetics, rising blood glucose levels after meals do not properly stimulate insulin production by the pancreas. Additionally, peripheral tissues are generally resistant to the effects of insulin, and such subjects often have higher than normal plasma insulin levels (hyperinsulinemia) as the body attempts to overcome its insulin resistance. In advanced disease states insulin secretion is also impaired.

Insulin resistance and hyperinsulinemia have also been linked with two other metabolic disorders that pose considerable health risks: impaired glucose tolerance and metabolic obesity. Impaired glucose tolerance is characterized by normal glucose levels before eating, with a tendency toward elevated levels (hyperglycemia) following a meal. These individuals are considered to be at higher risk for diabetes and coronary artery disease. Obesity is also a risk factor for the group of conditions called insulin resistance syndrome, or “Syndrome X,” as is hypertension, coronary artery disease (arteriosclerosis), and lactic acidosis, as well as related disease states. The pathogenesis of obesity is believed to be multifactorial but an underlying problem is that in the obese, nutrient availability and energy expenditure are not in balance until there is excess adipose tissue. Other related diseases or disorders include, but are not limited to, gestational diabetes, juvenile diabetes, obesity, excessive appetite, insufficient satiety, metabolic disorder, glucagonomas, retinal neurodegenerative processes, and the “honeymoon period” of Type I diabetes.

Dyslipidemia is a frequent occurrence among diabetics; typically characterized by elevated plasma triglycerides, low HDL (high density lipoprotein) cholesterol, normal to elevated levels of LDL (low density lipoprotein) cholesterol and increased levels of small dense, LDL particles in the blood. Dyslipidemia is a main contributor to an increased incidence of coronary events and deaths among diabetic subjects.

Most metabolic processes in glucose homeostasis and insulin response are regulated by multiple peptides and hormones, and many such peptides and hormones, as well as analogues thereof, have found utility in the treatment of metabolic diseases and disorders. Many of these peptides tend to be highly homologous to each other, even when they possess opposite biological functions. Glucose-increasing peptides are exemplified by the peptide hormone glucagon, while glucose-lowering peptides include exendin-4, glucagon-like peptide 1, and amylin. However, the use of therapeutic peptides and/or hormones, even when augmented by the use of small molecule drugs, has met with limited success in the management of such diseases, disorders and conditions. In particular, dose optimization is important for drugs and biologics used in the treatment of metabolic diseases, especially those with a narrow therapeutic window. Hormones in general, and peptides involved in glucose homeostasis often have a narrow therapeutic window. The narrow therapeutic window, coupled with the fact that such hormones and peptides typically have a short half-life, which necessitates frequent dosing in order to achieve clinical benefit, results in difficulties in the management of such patients. While chemical modifications to a therapeutic protein, such as pegylation, can modify its in vivo clearance rate and subsequent serum half-life, it requires additional manufacturing steps and results in a heterogeneous final product. In addition, unacceptable side effects from chronic administration have been reported. Alternatively, genetic modification by fusion of an Fc domain to the therapeutic protein or peptide increases the size of the therapeutic protein, reducing the rate of clearance through the kidney, and promotes recycling from lysosomes by the FcRn receptor. Unfortunately, the Fc domain does not fold efficiently during recombinant expression and tends to form insoluble precipitates known as inclusion bodies. These inclusion bodies must be solubilized and functional protein must be renatured; a time-consuming, inefficient, and expensive process.

Thus, one aspect of the present invention is the incorporation of peptides involved in glucose homeostasis, insulin resistance and obesity (collectively, “glucose regulating peptides”) in GPXTEN fusion proteins to create compositions that can be used in the treatment of glucose, insulin, and obesity disorders, diseases and related conditions (referred to herein as “glucose regulating peptide-related diseases, disorders or conditions”). Glucose regulating peptides can include any protein of biologic, therapeutic, or prophylactic interest or function that is useful for preventing, treating, mediating, or ameliorating a disease, disorder or condition of glucose homeostasis or insulin resistance or obesity. Suitable glucose-regulating peptides that can be linked to the XTEN to create GPXTEN include all biologically active polypeptides that increase glucose-dependent secretion of insulin by pancreatic beta-cells or potentiate the action of insulin or play a role in glucose homeostasis. Glucose-regulating peptides can also include all biologically active polypeptides that stimulate pro-insulin gene transcription in the pancreatic beta-cells. Furthermore, glucose-regulating peptides can also include all biologically active polypeptides that slow down gastric emptying time and reduce food intake. Glucose-regulating peptides can also include all biologically active polypeptides that inhibit glucagon release from the alpha cells of the Islets of Langerhans. Table 1 provides a non-limiting list of sequences of glucose regulating peptides that are encompassed by the GPXTEN fusion proteins of the invention. Glucose regulating peptides of the inventive GPXTEN compositions can be a peptide that exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a protein sequence selected from Table 1.


TABLE 1
Glucose regulating peptides from animal species
Name of
Protein
(Synonym)
Sequence
SEQ ID NO:
Amylin, rat
KCNTATCATQRLANFLVRSSNNLGPVLPPTNVGSNTY
1
Amylin,
KCNTATCATQRLANFLVHSSNNFGAILSSTNVGSNTY
2
human
Exendin-3
HSDGTFTSDLSKQMEEEAVRLFIEWLKNGGPSSGAPPPS
3
Exendin-4
HGEGTFTSDLSKQMEEEAVR
4
LFIEWLKNGGPSSGAPPPS
Glucagon
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
5
Glucagon-like
HDEFERHAEGTFTSDVSSTLEGQAALEFIAWLVKGRG
6
peptide-1
(hGLP-
1)(GLP-1; 1-
37)
GLP-1 (7-36),
HAEGTFTSDVSSYLEGQAALEFIAWLVKGR
7
human
GLP-1 (7-37),
HAEGTFTSDVSSTLEGQAALEFIAWLVKGRG
8
human
GLP-1, frog
HAEGTYTNDVTEYLEEKAAKEFIEWLIKGKPKKIRYS
9
Glucagon-like
HADGSFSDEMNTILDNLAARDFINWLIETKITD
10
peptide 2
(GLP-2),
human
GLP-2, frog
HAEGTFTNDMTNYLEEKAAKEFVGWLIKGRP-OH
11

“Amylin” means the human peptide hormone referred to as amylin, pramlintide, and species variations thereof, as described in U.S. Pat. No. 5,234,906, having at least a portion of the biological activity of native amylin. Amylin is a 37-amino acid polypeptide hormone co-secreted with insulin by pancreatic beta cells in response to nutrient intake (Koda et al., Lancet 339:1179-1180. 1992), and has been reported to modulate several key pathways of carbohydrate metabolism, including incorporation of glucose into glycogen. Amylin-containing fusion proteins of the invention may find particular use in diabetes and obesity for regulating gastric-emptying, suppressing glucagon secretion and food intake, thereby affecting the rate of glucose appearance in the circulation. Thus, the fusion proteins may complement the action of insulin, which regulates the rate of glucose disappearance from the circulation and its uptake by peripheral tissues. Amylin analogues have been cloned, as described in U.S. Pat. Nos. 5,686,411 and 7,271,238. Amylin mimetics can be created that retain biologic activity. For example, pramlintide has the sequence KCNTATCATNRLANFLVHSSNNFGPILPPTNVGSNTY (SEQ ID NO: 12), wherein amino acids from the rat amylin sequence are substituted for amino acids in the human amylin sequence. In one embodiment, the invention contemplates fusion proteins comprising amylin mimetics of the sequence


(SEQ ID NO: 13)
KCNTATCATX1RLANFLVHSSNNFGX2ILX2X2TNVGSNTY

wherein X1 is independently N or Q and X2 is independently S, P or G. In one embodiment, the amylin mimetic incorporated into a GPXTEN has the sequence KCNTATCATNRLANFLVHSSNNFGGILGGTNVGSNTY (SEQ ID NO: 14). In another embodiment, wherein the amylin mimetic is used at the C-terminus of the GPXTEN, the mimetic has the sequence


(SEQ ID NO: 15)
KCNTATCATNRLANFLVHSSNNFGGILGGTNVGSNTY(NH2)

“Exendin-3” means a glucose regulating peptide isolated from Heloderma horridum and sequence variants thereof having at least a portion of the biological activity of native exendin-3. Exendin-3 amide is a specific exendin receptor antagonist from that mediates an increase in pancreatic cAMP, and release of insulin and amylase. Exendin-3-containing fusion proteins of the invention may find particular use in the treatment of diabetes and insulin resistance disorders. The sequence and methods for its assay are described in U.S. Pat. No. 5,424,286.

“Exendin-4” means a glucose regulating peptide found in the saliva of the Gila-monster Heloderma suspectum, as well as species and sequence variants thereof, and includes the native 39 amino acid sequence His-Gly-Glu-Gly-Thr-Phe-Thr-Ser-Asp-Leu-Ser-Lys-Gln-Met-Glu-Glu-Glu-Ala-Val-Arg-Leu-Phe-Ile-Glu-Trp-Leu-Lys-Asn-Gly-Gly-Pro-Ser-Ser-Gly-Ala-Pro-Pro-Pro-Ser (SEQ ID NO: 16) and homologous sequences and peptide mimetics, and variants thereof; natural sequences, such as from primates and non-natural having at least a portion of the biological activity of native exendin-4. Exendin-4 is an incretin polypeptide hormone that decreases blood glucose, promotes insulin secretion, slows gastric emptying and improves satiety, providing a marked improvement in postprandial hyperglycemia. The exendins have some sequence similarity to members of the glucagon-like peptide family, with the highest identity being to GLP-1 (Goke, et al., J. Biol. Chem., 268:19650-55 (1993)). A variety of homologous sequences can be functionally equivalent to native exendin-4 and GLP-1. Conservation of GLP-1 sequences from different species are presented in Regulatory Peptides 2001 98 p. 1-12. Table 2 shows the sequences from a wide variety of species, while Table 3 shows a list of synthetic GLP-1 analogs; all of which are contemplated for use as glucose regulating peptides in the GPXTEN described herein. Exendin-4 binds at GLP-1 receptors on insulin-secreting βTC1 cells, and also stimulates somatostatin release and inhibits gastrin release in isolated stomachs (Goke, et al., J. Biol. Chem. 268:19650-55, 1993). As a mimetic of GLP-1, exendin-4 displays a similar broad range of biological activities, yet has a longer half-life than GLP-1, with a mean terminal half-life of 2.4 h. Exenatide is a synthetic version of exendin-4, marketed as Byetta. However, due to its short half-life, exenatide is currently dosed twice daily, limiting its utility. Exendin-4-containing fusion proteins of the invention may find particular use in the treatment of diabetes and insulin resistance disorders.

“Glucagon” means the human glucagon glucose regulating peptide, or species and sequence variants thereof, including the native 29 amino acid sequence and homologous sequences; natural, such as from primates, and non-natural sequence variants having at least a portion of the biological activity of native glucagon. The term “glucagon” as used herein also includes peptide mimetics of glucagon. Native glucagon is produced by the pancreas, released when blood glucose levels start to fall too low, causing the liver to convert stored glycogen into glucose and release it into the bloodstream. While the action of glucagon is opposite that of insulin, which signals the body's cells to take in glucose from the blood, glucagon also stimulates the release of insulin, so that newly-available glucose in the bloodstream can be taken up and used by insulin-dependent tissues. Glucagon-containing fusion proteins of the invention may find particular use in increasing blood glucose levels in individuals with extant hepatic glycogen stores and maintaining glucose homeostasis in diabetes. Glucagon has been cloned, as disclosed in U.S. Pat. No. 4,826,763.

“GLP-1” means human glucagon like peptide-1 and sequence variants thereof having at least a portion of the biological activity of native GLP-1. The term “GLP-1” includes human GLP-1(1-37), GLP-1(7-37), and GLP-1(7-36)amide. GLP-1 stimulates insulin secretion, but only during periods of hyperglycemia. The safety of GLP-1 compared to insulin is enhanced by this property and by the observation that the amount of insulin secreted is proportional to the magnitude of the hyperglycemia. The biological half-life of GLP-1(7-37)OH is a mere 3 to 5 minutes (U.S. Pat. No. 5,118,666). GLP-1-containing fusion proteins of the invention may find particular use in the treatment of diabetes and insulin-resistance disorders for glucose regulation. GLP-1 has been cloned and derivatives prepared, as described in U.S. Pat. No. 5,118,666. Non-limited examples of GLP-1 sequences from a wide variety of species are shown in Table 2, while Table 3 shows the sequences of a number of synthetic GLP-1 analogs; all of which are contemplated for use as glucose regulating peptides in the GPXTEN compositions described herein.


TABLE 2
Naturally GLP-1 Homologs
Gene Name
[Source]
Sequence
SEQ ID NO:
GLP-1 [frog]
HAEGTYTNDVTEYLEEKAAKEFIEWLIKGKPKKIRYS
17
GLP-1a [Xenopus
HAEGTFTSDVTQQLDEKAAKEFIDWLINGGPSKEIIS
18
laevis]
GLP-1b [Xenopus
HAEGTYTNDVTEYLEEKAAKEFIIEWLIKGKPK
19
laevis]
GLP-1c [Xenopus
HAEGTFTNDMTNYLEEKAAKEFVGWLIKGRPK
20
laevis]
Gastric Inhibitory
HAEGTFISDYSIAMDKIRQQDFVNWLL
21
Polypeptide [Mus
musculus]
Glucose-dependent
HAEGTFISDYSIAMDKIRQQDFVNWLL
22
insulinotropic
polypeptide [Equus
caballus]
Glucagon-like
HADGTFTNDMTSYLDAKAARDFVSWLARSDKS
23
peptide [Petromyzon
marinus]
Glucagon-like
HAEGTYTSDVSSYLQDQAAKEFVSWLKTGR
24
peptide
[Anguilla rostrata]
Glucagon-like
HAEGTYTSDVSSYLQDQAAKEFVSWLKTGR
25
peptide
[Anguilla anguilla]
Glucagon-like
HADGIYTSDVASLTDYLKSKRFVESLSNYNKRQNDRRM
26
peptide
[Hydrolagus colliei]
Glucagon-like
YADAPYISDVYSYLQDQVAKKWLKSGQDRRE
27
peptide
[Amia calva]
GLUC_ICTPU/38-
HADGTYTSDVSSYLQEQAAKDFITWLKS
28
65
GLUCL_ANGRO/1-
HAEGTYTSDVSSYLQDQAAKEFVSWLKT
29
28
GLUC_BOVIN/98-
HAEGTFTSDVSSYLEGQAAKEFIAWLVK
30
125
GLUC1_LOPAM/91-
HADGTFTSDVSSYLKDQAIKDFVDRLKA
31
118
GLUCL_HYDCO/1-
HADGIYTSDVASLTDYLKSKRFVESLSN
32
28
GLUC_CAVPO/53-
HSQGTFTSDYSKYLDSRRAQQFLKWLLN
33
80
GLUC_CHIBR/1-28
HSQGTFTSDYSKHLDSRYAQEFVQWLMN
34
GLUC1_LOPAM/53-
HSEGTFSNDYSKYLEDRKAQEFVRWLMN
35
80
GLUC_HYDCO/1-28
HTDGIFSSDYSKYLDNRRTKDFVQWLLS
36
GLUC_CALM1/1-28
HSEGTFSSDYSKYLDSRRAKDFVQWLMS
37
GIP_BOVIN/1-28
YAEGTFISDYSIAMDKIRQQDFVNWLLA
38
VIP_MELGA/89-
HADGIFTTVYSHLLAKLAVKRYLHSLIR
39
116
PACA_CHICK/131-
HIDGIFTDSYSRYRKQMAVKKYLAAVLG
40
158
VIP_CAVPO/45-72
HSDALFTDTYTRLRKQMAMKKYLNSVLN
41
VIP_DIDMA/1-28
HSDAVFTDSYTRLLKQMAMRKYLDSILN
42
EXE1_HELSU/1-28
HSDATFTAEYSKLLAKLALQKYLESILG
43
SLIB_CAPHI/1-28
YADAIFTNSYRKVLGQLSARKLLQDIMN
44
SLIB_RAT/31-58
HADAIFTSSYRRILGQLYARKLLHEIMN
45
SLIB_MOUSE/31-
HVDAIFTTNYRKLLSQLYARKVIQDIMN
46
58
PACA_HUMAN/83-
VAHGILNEAYRKVLDQLSAGKHLQSLVA
47
110
PACA_SHEEP/83-
VAHGILDKAYRKVLDQLSARRYLQTLMA
48
110
PACA_ONCNE/82-
HADGMFNKAYRKALGQLSARKYLHSLMA
49
109
GLUC_BOVIN/146-
HADGSFSDEMNTVLDSLATRDFINWLLQ
50
173
SECR_CANFA/1-27
HSDGTFTSELSRLRESARLQRLLQGLV
51
SECR_CHICK/1-27
HSDGLFTSEYSKMRGNAQVQKFIQNLM
52
EXE3_HELH0/48-
HSDGTFTSDLSKQMEEEAVRLFIEWLKN
53
75

GLP native sequences may be described by several sequence motifs, which are presented below. Letters in brackets represent acceptable amino acids at each sequence position: [HVY] [AGISTV] [DEHQ] [AG] [ILMPSTV] [FLY] [DINST] [ADEKNST] [ADENSTV] [LMVY] [ANRSTY] [EHIKNQRST] [AHILMQVY] [LMRT] [ADEGKQS] [ADEGKNQSY] [AEIKLMQR] [AKQRSVY] [AILMQSTV] [GKQR] [DEKLQR] [FHLVWY] [ILV] [ADEGPIKNQRST] [ADEGNRSTW] [GILVW] [AIKLMQSV] [ADGIKNQRST] [GKRSY]. In addition, synthetic analogs of GLP-1 and pramlintide can be useful as fusion partners to XTEN to create GPXTEN with biological activity useful in treatment of glucose-related disorders. Non-limited examples of synthetic GLP-1 and pramlintide sequences can be found in Table 3. In addition, further sequences homologous to GLP-1, pramlintide, as well as sequences homologous to exendin-4, amylin, or glucagon may be found by standard homology searching techniques.


TABLE 3
GLP-1 and pramlintide synthetic analogs
SEQ
ID
Analog Sequence
NO:
HAEGTFTSDVSSYLEGQAAREFIAWLVKGRG
54
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG
55
HAEGTFTSDVSSYLEGQAAKEFIAWLVKGKG
56
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKG
57
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKGR
58
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
59
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
60
HAEGTFTSDVSSYLEGQAAREFIAWLVKGKG
61
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGKG
62
HAEGTFTSDVSSYLEGQAAREFIAWLVKGRGRK
63
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRGRRK
64
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKGRK
65
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKGRRK
66
HGEGTFTSDVSSYLEGQAAREFIAWLVKGRG
67
HGEGTFTSDVSSYLEGQAAKEFIAWLVRGRG
68
HGEGTFTSDVSSYLEGQAAKEFIAWLVKGKG
69
HGEGTFTSDVSSYLEGQAAREFIAWLVRGKG
70
HGEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
71
HGEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
72
HGEGTFTSDVSSYLEGQAAREFIAWLVKGKG
73
HGEGTFTSDVSSYLEGQAAKEFIAWLVRGKG
74
HGEGTFTSDVSSYLEGQAAREFIAWLVKGRGRK
75
HGEGTFTSDVSSYLEGQAAKEFIAWLVRGRGRRK
76
HGEGTFTSDVSSYLEGQAAREFIAWLVRGKGRK
77
HGEGTFTSDVSSYLEGQAAREFIAWLVRGKGRRK
78
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
79
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
80
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
81
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
82
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
83
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
84
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
85
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
86
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
87
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
88
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
89
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
90
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
91
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
92
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
93
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
94
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
95
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
96
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
97
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
98
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
99
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
100
DEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
101
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
102
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
103
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
104
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
105
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
106
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
107
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
108
EFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
109
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
110
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
111
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
112
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
113
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
114
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
115
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
116
FERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
117
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
118
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
119
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
120
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
121
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
122
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
123
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
124
ERHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
125
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
126
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRK
127
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRRK
128
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREK
129
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFK
130
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPK
131
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEK
132
RHAEGTFTSDVSSYLEGQAAREFIAWLVRGRGRREFPEEK
133
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVKGRGK
134
HDEFERHAEGTFTSDVSSYLEGQAAKEFIAWLVRGRGK
135
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGKGK
136
HAEGTFTSDVSSYLEGQAAREFIAWLVKGRGK
137
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRGK
138
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKGK
139
HAEGTFTSDVSSYLEGQAAREFIAWLVRGRGK
140
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVKGRGRK
141
HDEFERHAEGTFTSDVSSYLEGQAAKEFIAWLVRGRGRK
142
HDEFERHAEGTFTSDVSSYLEGQAAREFIAWLVRGKGRK
143
HAEGTFTSDVSSYLEGQAAREFIAWLVKGRGRK
144
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRGRK
145
HAEGTFTSDVSSYLEGQAAREFIAWLVRGKGRK
146
HGEGTFTSDVSSYLEGQAAREFIAWLVKGRGK
147
HGEGTFTSDVSSYLEGQAAREFIAWLVRGKGK
148
KCNTATCATNRLANFLVHSSNNFGPILPPTNVGSNTY
149
KCNTATCATNRLANFLVHSSNNFGGILPPTNVGSNTY
150
KCNTATCATNRLANFLVHSSNNFGPILGPTNVGSNTY
151
KCNTATCATNRLANFLVHSSNNFGPILPGTNVGSNTY
152
KCNTATCATNRLANFLVHSSNNFGGILGPTNVGSNTY
153
KCNTATCATNRLANFLVHSSNNFGPILGGTNVGSNTY
154
KCNTATCATNRLANFLVHSSNNFGGILPGTNVGSNTY
155
KCNTATCATNRLANFLVHSSNNFGGILGGTNVGSNTY
156

“GLP-2” means human glucagon like peptide-2 and sequence variants thereof having at least a portion of the biological activity of native GLP-2. More particularly, GLP-2 is a 33 amino acid peptide, co-secreted along with GLP-1 from intestinal endocrine cells in the small and large intestine.

III) Glucose Regulating Peptide Fusion Protein Compositions

The present invention relates in part to fusion protein compositions comprising glucose regulating peptides (GP). In one aspect, the invention provides isolated monomeric fusion proteins of GP comprising the full-length sequence or sequence variants of GP covalently linked to extended recombinant polypeptides (“XTEN” or “XTENs”). As described more fully below, the fusion proteins can optionally include spacer sequences that further comprise cleavage sequences to release the GP from the fusion protein when acted on by a protease, releasing GP from the XTEN sequence(s).

In some cases, the invention provides an isolated fusion protein comprising at least a first biologically active glucose regulating peptide covalently linked to one or more extended recombinant polypeptides (“XTEN”), resulting in a glucose regulating peptide-XTEN fusion protein composition (hereinafter “GPXTEN”). In other cases, the glucose regulating peptide linked to one or more XTEN is inactive or has reduced activity that can optionally include spacer sequences that can further comprise cleavage sequences to release the GP from the fusion protein when acted on by a protease in a more active form.

The term “GPXTEN”, as used herein, is meant to encompass fusion polypeptides that comprise one or more payload regions each comprising a biologically active GP that mediates one or more biological or therapeutic activities associated with a glucose regulating peptide and at least one other region comprising at least a first XTEN polypeptide that serves as a carrier.

The GP of the subject compositions, particularly those disclosed in Table 1, together with their corresponding nucleic acid and amino acid sequences, are well known in the art and descriptions and sequences are available in public databases such as Chemical Abstracts Services Databases (e.g., the CAS Registry), GenBank, The Universal Protein Resource (UniProt) and subscription provided databases such as GenSeq (e.g., Derwent). Polynucleotide sequences may be a wild type polynucleotide sequence encoding a given GP (e.g., either full length or mature), or in some instances the sequence may be a variant of the wild type polynucleotide sequence (e.g., a polynucleotide which encodes the wild type biologically active protein, wherein the DNA sequence of the polynucleotide has been optimized, for example, for expression in a particular species; or a polynucleotide encoding a variant of the wild type protein, such as a site directed mutant or an allelic variant. It is well within the ability of the skilled artisan to use a wild-type or consensus cDNA sequence or a codon-optimized variant of a GP to create GPXTEN constructs contemplated by the invention using methods known in the art and/or in conjunction with the guidance and methods provided herein, and described more fully in the Examples.

The GP for inclusion in the GPXTEN of the invention include any glucose regulating peptide or sequence variant of biologic, therapeutic, prophylactic, or diagnostic interest or function, or that is useful for mediating or preventing or ameliorating a disease, disorder or condition associated with a glucose regulating peptide deficiency or a defect in sensitivity to one or more GP by the subject. Of particular interest are GPXTEN fusion protein compositions for which an increase in a pharmacokinetic parameter, increased solubility, increased stability, or some other enhanced pharmaceutical property compared to native GP is sought, or for which increasing the terminal half-life would improve efficacy, safety, or result in reduce dosing frequency and/or improve patient compliance. Thus, the GPXTEN fusion protein compositions are prepared with various objectives in mind, including improving the therapeutic efficacy of the bioactive GP by, for example, increasing the in vivo exposure or the length that the GPXTEN remains within the therapeutic window when administered to a subject, compared to a GP not linked to XTEN.

In one embodiment, the GP incorporated into the subject compositions can be a recombinant polypeptide with a sequence corresponding to a protein found in nature. In another embodiment, the GP can be sequence variants, fragments, homologs, and mimetics of a natural sequence that retain at least a portion of the biological activity of the native GP. In some cases, the GP for incorporation into the GPXTEN of the invention can be a sequence that exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity to a protein sequence selected from the sequences of Table 1, Table 2 and Table 3. In one embodiment, a GPXTEN fusion protein can comprise a single GP molecule linked to an XTEN (as described more fully below). In another embodiment, the GPXTEN can comprise a first GP and a second molecule of the same GP, resulting in a fusion protein comprising the two GP linked to one or more XTEN (for example, two molecules of GLP-1). In another embodiment, the GPXTEN fusion protein can comprise a single GP molecule linked to a first and a second XTEN, with an N- to C-terminus configuration of XTEN-GP-XTEN, in which the GP can be a sequence that exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity to a sequence selected from the sequences of Table 1, Table 2 and Table 3, and the first and/or the second XTEN can be sequences that exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity to a sequence selected from the sequence of Table 5.

In general, the GP fusion partner component of the GPXTEN will exhibit a binding specificity to a given target or another desired biological characteristic when used in vivo or when utilized in an in vitro assay. For example, the GPXTEN can be an agonist, having the ability to bind to a cell receptor for a glucose regulating peptide. In one embodiment, the binding of GPXTEN to its receptor can lead to at least a portion of the activation of intercellular signal transduction pathway compared to the corresponding native glucose regulating peptide not linked to XTEN. In one embodiment, the GPXTEN bound to a cell receptor for a glucose regulating peptide can exhibit at least about 1%, or about 5%, or about 10%, or about 15%, or about 20%, or about 25%, or about 30%, or about 40%, or about 50%, or about 60%, or about 70%, or about 80%, or about 90%, or at least about 95% of the activation of intercellular signal transduction pathway compared to native glucose regulating peptide not linked to XTEN.

The subject GPXTEN of the present invention can exhibit an enhancement of one or more pharmacokinetic parameters, which optionally could be enhanced for a biologic effect by release of GP from the fusion protein by cleavage of a spacer sequence. The GPXTEN with enhanced pharmacokinetic parameters would permit less frequent dosing or an enhanced pharmacologic effect, such as but not limited to maintaining the biologically active GPXTEN within the therapeutic window between the minimum effective dose or blood concentration (Cmin) and the maximum tolerated dose or blood concentration (Cmax). In such cases, the linking of the GP to a fusion protein comprising a select XTEN sequence(s) can result in an improvement in these properties, making them more useful as therapeutic or preventive agents compared to GP not linked to XTEN.

IV) Xtended Recombinant Polypeptides

In one aspect, the invention provides XTEN polypeptide compositions that are useful as a fusion protein partner to which GP is linked, resulting in a GPXTEN fusion protein. XTEN are generally extended length polypeptides with non-naturally occurring, substantially non-repetitive sequences that are composed mainly of small hydrophilic amino acids, with the sequence having a low degree or no secondary or tertiary structure under physiologic conditions.

XTENs can have utility as a fusion protein partners partner in that they can serve as a “carrier”, conferring certain desirable pharmacokinetic, physicochemical and pharmaceutical properties when linked to a GP protein to a create a fusion protein. Such desirable properties include but are not limited to enhanced pharmacokinetic parameters and solubility characteristics of the compositions, amongst other properties described below. Such fusion protein compositions have utility to treat certain glucose regulating peptide-related diseases, disorders or conditions, as described herein. As used herein, “XTEN” specifically excludes antibodies or antibody fragments such as single-chain antibodies or Fc fragments of a light chain or a heavy chain.

In some embodiments, XTEN are long polypeptides having greater than about 100 to about 3000 amino acid residues, preferably greater than 400 to about 3000 residues when used as a carrier or cumulatively when more than one XTEN unit is used in a single fusion protein. In other cases, when used as a linker between fusion protein components or where an increase in half-life of the fusion protein is not needed but where an increase in solubility or other physicochemical property for the GP fusion partner component is desired, an XTEN sequence shorter than 100 amino acid residues, such as about 96, or about 84, or about 72, or about 60, or about 48, or about 36 amino acid residues may be incorporated into a fusion protein composition with the GP to effect the property.

The selection criteria for the XTEN to be linked to the biologically active proteins used to create the inventive fusion proteins compositions generally relate to attributes of physical/chemical properties and conformational structure of the XTEN that can be, in turn, used to confer enhanced pharmaceutical and pharmacokinetic properties to the fusion protein compositions. The XTEN of the present invention may exhibit one or more of the following advantageous properties: conformational flexibility, enhanced aqueous solubility, high degree of protease resistance, low immunogenicity, low binding to mammalian receptors, and increased hydrodynamic (or Stokes) radii; properties that can make them particularly useful as fusion protein partners. Non-limiting examples of the properties of the fusion proteins comprising GP that may be enhanced by XTEN include increases in the overall solubility and/or metabolic stability, reduced susceptibility to proteolysis, reduced immunogenicity, reduced rate of absorption when administered subcutaneously or intramuscularly, and enhanced pharmacokinetic properties such as longer terminal half-life and increased area under the curve (AUC), slower absorption after subcutaneous or intramuscular injection compared to GP not linked to XTEN and administered by a similar route such that the Cmax is lower, which may, in turn, result in reductions in adverse effects of the GP that, collectively with increased half-life and/or AUC, can result in an increased period of time that a fusion protein of a GPXTEN composition administered to a subject retains therapeutic activity.

A variety of methods and assays are known in the art for determining the physical/chemical properties of proteins such as the compositions comprising the inventive XTEN; properties such as solubility, secondary or tertiary structure, solubility, protein aggregation, melting properties, contamination and water content. Such methods include analytical centrifugation, EPR, HPLC-ion exchange, HPLC-size exclusion, HPLC-reverse phase, light scattering, capillary electrophoresis, circular dichroism, differential scanning calorimetry, fluorescence, HPLC-ion exchange, HPLC-size exclusion, IR, NMR, Raman spectroscopy, refractometry, and UV/Visible spectroscopy. Additional methods are disclosed in Arnau et al., Prot Expr and Purif (2006) 48, 1-13. Application of these methods to the invention would be within the grasp of a person skilled in the art.

Typically, XTEN are designed to behave like denatured peptide sequences under physiological conditions, despite the extended length of the polymer. Denatured describes the state of a peptide in solution that is characterized by a large conformational freedom of the peptide backbone. Most peptides and proteins adopt a denatured conformation in the presence of high concentrations of denaturants or at elevated temperature. Peptides in denatured conformation have, for example, characteristic circular dichroism (CD) spectra and are characterized by a lack of long-range interactions as determined by NMR. “Denatured conformation” and “unstructured conformation” are used synonymously herein. In some cases, the invention provides XTEN sequences that, under physiologic conditions, can resemble denatured sequences largely devoid in secondary structure. In other cases, the XTEN sequences can be substantially devoid of secondary structure under physiologic conditions. “Largely devoid,” as used in this context, means that less than 50% of the XTEN amino acid residues of the XTEN sequence contribute to secondary structure as measured or determined by the means described herein. “Substantially devoid,” as used in this context, means that at least about 60%, or about 70%, or about 80%, or about 90%, or about 95%, or at least about 99% of the XTEN amino acid residues of the XTEN sequence do not contribute to secondary structure, as measured or determined by the means described herein.

A variety of methods have been established in the art to discern the presence or absence of secondary and tertiary structures in a given polypeptide. In particular, secondary structure can be measured spectrophotometrically, e.g., by circular dichroism spectroscopy in the “far-UV” spectral region (190-250 nm). Secondary structure elements, such as alpha-helix and beta-sheet, each give rise to a characteristic shape and magnitude of CD spectra. Secondary structure can also be predicted for a polypeptide sequence via certain computer programs or algorithms, such as the well-known Chou-Fasman algorithm (Chou, P. Y., et al. (1974) Biochemistry, 13: 222-45) and the Garnier-Osguthorpe-Robson (“GOR”) algorithm (Garnier J, Gibrat J F, Robson B. (1996), GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266:540-553), as described in US Patent Application Publication No. 20030228309A1. For a given sequence, the algorithms can predict whether there exists some or no secondary structure at all, expressed as the total and/or percentage of residues of the sequence that form, for example, alpha-helices or beta-sheets or the percentage of residues of the sequence predicted to result in random coil formation (which lacks secondary structure).

In some cases, the XTEN sequences used in the inventive fusion protein compositions can have an alpha-helix percentage ranging from 0% to less than about 5% as determined by a Chou-Fasman algorithm. In other cases, the XTEN sequences of the fusion protein compositions can have a beta-sheet percentage ranging from 0% to less than about 5% as determined by a Chou-Fasman algorithm. In some cases, the XTEN sequences of the fusion protein compositions can have an alpha-helix percentage ranging from 0% to less than about 5% and a beta-sheet percentage ranging from 0% to less than about 5% as determined by a Chou-Fasman algorithm. In preferred embodiments, the XTEN sequences of the fusion protein compositions will have an alpha-helix percentage less than about 2% and a beta-sheet percentage less than about 2%. In other cases, the XTEN sequences of the fusion protein compositions can have a high degree of random coil percentage, as determined by a GOR algorithm. In some embodiments, an XTEN sequence can have at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, and most preferably at least about 99% random coil, as determined by a GOR algorithm.

1. Non-Repetitive Sequences

XTEN sequences of the subject compositions can be substantially non-repetitive. In general, repetitive amino acid sequences have a tendency to aggregate or form higher order structures, as exemplified by natural repetitive sequences such as collagens and leucine zippers, or form contacts resulting in crystalline or pseudocrystaline structures. In contrast, the low tendency of non-repetitive sequences to aggregate enables the design of long-sequence XTENs with a relatively low frequency of charged amino acids that would be likely to aggregate if the sequences were otherwise repetitive. Typically, the GPXTEN fusion proteins comprise XTEN sequences of greater than about 100 to about 3000 amino acid residues, preferably greater than 400 to about 3000 cumulative residues, wherein the sequences are substantially non-repetitive. In one embodiment, the XTEN sequences can have greater than about 100 to about 3000 amino acid residues in which no three contiguous amino acids in the sequence are identical amino acid types unless the amino acid is serine, in which case no more than three contiguous amino acids are serine residues. In the foregoing embodiment, the XTEN sequence would be substantially non-repetitive.

The degree of repetitiveness of a polypeptide or a gene can be measured by computer programs or algorithms or by other means known in the art. Repetitiveness in a polypeptide sequence can, for example, be assessed by determining the number of times shorter sequences of a given length occur within the polypeptide. For example, a polypeptide of 200 amino acid residues has 192 overlapping 9-amino acid sequences (or 9-mer “frames”) and 198 3-mer frames, but the number of unique 9-mer or 3-mer sequences will depend on the amount of repetitiveness within the sequence. A score can be generated (hereinafter “subsequence score”) that is reflective of the degree of repetitiveness of the subsequences in the overall polypeptide sequence. In the context of the present invention, “subsequence score” means the sum of occurrences of each unique 3-mer frame across a 200 consecutive amino acid sequence of the polypeptide divided by the absolute number of unique 3-mer subsequences within the 200 amino acid sequence. Examples of such subsequence scores derived from the first 200 amino acids of repetitive and non-repetitive polypeptides are presented in Example 40. In some embodiments, the present invention provides GPXTEN each comprising one or more XTEN in which the XTEN can have a subsequence score less than 12, more preferably less than 10, more preferably less than 9, more preferably less than 8, more preferably less than 7, more preferably less than 6, and most preferably less than 5 when derived from a segment of 200 contiguous amino acid residues. In the embodiments hereinabove described in this paragraph, an XTEN with a subsequence score less than about 10 (i.e., 9, 8, 7, etc.) would be “substantially non-repetitive.”

The non-repetitive characteristic of XTEN can impart to fusion proteins with GP a greater degree of solubility and less tendency to aggregate compared to polypeptides having repetitive sequences. These properties can facilitate the formulation of XTEN-comprising pharmaceutical preparations containing extremely high drug concentrations, in some cases exceeding 100 mg/ml.

Furthermore, the XTEN polypeptide sequences of the embodiments are designed to have a low degree of internal repetitiveness in order to reduce or substantially eliminate immunogenicity when administered to a mammal Polypeptide sequences composed of short, repeated motifs largely limited to three amino acids, such as glycine, serine and glutamate, may result in relatively high antibody titers when administered to a mammal despite the absence of predicted T-cell epitopes in these sequences. This may be caused by the repetitive nature of polypeptides, as it has been shown that immunogens with repeated epitopes, including protein aggregates, cross-linked immunogens, and repetitive carbohydrates are highly immunogenic and can, for example, result in the cross-linking of B-cell receptors causing B-cell activation. (Johansson, J., et al. (2007) Vaccine, 25:1676-82; Yankai, Z., et al. (2006) Biochem Biophys Res Commun, 345:1365-71; Hsu, C. T., et al. (2000) Cancer Res, 60:3701-5); Bachmann M F, et al. Eur J Immunol. (1995) 25(12):3445-3451).

2. Exemplary Sequence Motifs

The present invention encompasses XTEN that can comprise multiple units of shorter sequences, or motifs, in which the amino acid sequences of the motifs are non-repetitive. In designing XTEN sequences, it was discovered that the non-repetitive criterion may be met despite the use of a “building block” approach using a library of sequence motifs that are multimerized to create the XTEN sequences. Thus, while an XTEN sequence may consist of multiple units of as few as four different types of sequence motifs, because the motifs themselves generally consist of non-repetitive amino acid sequences, the overall XTEN sequence is rendered substantially non-repetitive.

In one embodiment, XTEN can have a non-repetitive sequence of greater than about 100 to about 3000 amino acid residues, or greater than 400 to about 3000 residues, wherein at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or about 100% of the XTEN sequence consists of non-overlapping sequence motifs, wherein each of the motifs has about 9 to 36 amino acid residues. In other embodiments, at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or about 100% of the XTEN sequence consists of non-overlapping sequence motifs wherein each of the motifs has 9 to 14 amino acid residues. In still other embodiments, at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or about 100% of the XTEN sequence component consists of non-overlapping sequence motifs wherein each of the motifs has 12 amino acid residues. In these embodiments, it is preferred that the sequence motifs be composed mainly of small hydrophilic amino acids, such that the overall sequence has an unstructured, flexible characteristic. Examples of amino acids that can be included in XTEN, are, e.g., arginine, lysine, threonine, alanine, asparagine, glutamine, aspartate, glutamate, serine, and glycine. As a result of testing variables such as codon optimization, assembly polynucleotides encoding sequence motifs, expression of protein, charge distribution and solubility of expressed protein, and secondary and tertiary structure, it was discovered that XTEN compositions with enhanced characteristics mainly include glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues wherein the sequences are designed to be substantially non-repetitive. In a preferred embodiment, XTEN sequences have predominately four to six types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) or proline (P) that are arranged in a substantially non-repetitive sequence that is greater than about 100 to about 3000 amino acid residues, or greater than 400 to about 3000 residues in length. In some embodiments, XTEN can have sequences of greater than about 100 to about 3000 amino acid residues, or greater than 400 to about 3000 residues, wherein at least about 80% of the sequence consists of non-overlapping sequence motifs wherein each of the motifs has 9 to 36 amino acid residues wherein each of the motifs consists of 4 to 6 types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the content of any one amino acid type in the full-length XTEN does not exceed 30%. In other embodiments, at least about 90% of the XTEN sequence consists of non-overlapping sequence motifs wherein each of the motifs has 9 to 36 amino acid residues wherein the motifs consist of 4 to 6 types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the content of any one amino acid type in the full-length XTEN does not exceed 30%. In other embodiments, at least about 90% of the XTEN sequence consists of non-overlapping sequence motifs wherein each of the motifs has 12 amino acid residues consisting of 4 to 6 types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the content of any one amino acid type in the full-length XTEN does not exceed 30%. In yet other embodiments, at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99%, to about 100% of the XTEN sequence consists of non-overlapping sequence motifs wherein each of the motifs has 12 amino acid residues consisting of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the content of any one amino acid type in the full-length XTEN does not exceed 30%.

In still other embodiments, XTENs comprise non-repetitive sequences of greater than about 100 to about 3000 amino acid residues, or greater than 400 to about 3000 amino acid residues wherein at least about 80%, or at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% of the sequence consists of non-overlapping sequence motifs of 9 to 14 amino acid residues wherein the motifs consist of 4 to 6 types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the sequence of any two contiguous amino acid residues in any one motif is not repeated more than twice in the sequence motif. In other embodiments, at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% of an XTEN sequence consists of non-overlapping sequence motifs of 12 amino acid residues wherein the motifs consist of 4 to 6 types of amino acids selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the sequence of any two contiguous amino acid residues in any one sequence motif is not repeated more than twice in the sequence motif. In other embodiments, at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% of an XTEN sequence consists of non-overlapping sequence motifs of 12 amino acid residues wherein the motifs consist of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the sequence of any two contiguous amino acid residues in any one sequence motif is not repeated more than twice in the sequence motif. In yet other embodiments, XTENs consist of 12 amino acid sequence motifs wherein the amino acids are selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), and wherein the sequence of any two contiguous amino acid residues in any one sequence motif is not repeated more than twice in the sequence motif, and wherein the content of any one amino acid type in the full-length XTEN does not exceed 30%. In the foregoing embodiments hereinabove described in this paragraph, the XTEN sequences would be substantially non-repetitive.

In some cases, the invention provides compositions comprising non-repetitive XTEN sequence(s) of greater than about 100 to about 3000 amino acid residues, or of cumulatively greater than 400 to about 3000 residues, wherein at least about 80%, or at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% to about 100% of the sequence consists of multiple units of two or more non-overlapping sequence motifs selected from the amino acid sequences of Table 4. In some cases, the XTEN comprises non-overlapping sequence motifs in which about 80%, or at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% to about 100% of the sequence consists of two or more non-overlapping sequences selected from a single motif family of Table 4, resulting in a “family” sequence in which the overall sequence remains substantially non-repetitive. Accordingly, in these embodiments, an XTEN sequence can comprise multiple units of non-overlapping sequence motifs of the AD motif family, or the AE motif family, or the AF motif family, or the AG motif family, or the AM motif family, or the AQ motif family, or the BC family, or the BD family of sequences of Table 4. In other cases, the XTEN comprises motif sequences from two or more of the motif families of Table 4.


TABLE 4
XTEN Sequence Motifs of 12 Amino
Acids and Motif Families
Motif
Family*
MOTIF SEQUENCE
SEQ ID NO:
AD
GESPGGSSGSES
157
AD
GSEGSSGPGESS
158
AD
GSSESGSSEGGP
159
AD
GSGGEPSESGSS
160
AE, AM
GSPAGSPTSTEE
161
AE, AM, AQ
GSEPATSGSETP
162
AE, AM, AQ
GTSESATPESGP
163
AE, AM, AQ
GTSTEPSEGSAP
164
AF, AM
GSTSESPSGTAP
165
AF, AM
GTSTPESGSASP
166
AF, AM
GTSPSGESSTAP
167
AF, AM
GSTSSTAESPGP
168
AG, AM
GTPGSGTASSSP
169
AG, AM
GSSTPSGATGSP
170
AG, AM
GSSPSASTGTGP
171
AG, AM
GASPGTSSTGSP
172
AQ
GEPAGSPTSTSE
173
AQ
GTGEPSSTPASE
174
AQ
GSGPSTESAPTE
175
AQ
GSETPSGPSETA
176
AQ
GPSETSTSEPGA
177
AQ
GSPSEPTEGTSA
178
BC
GSGASEPTSTEP
179
BC
GSEPATSGTEPS
180
BC
GTSEPSTSEPGA
181
BC
GTSTEPSEPGSA
182
BD
GSTAGSETSTEA
183
BD
GSETATSGSETA
184
BD
GTSESATSESGA
185
BD
GTSTEASEGSAS
186
*Denotes individual motif sequences that, when used together in various permutations, results in a “family sequence”

In other cases, GPXTEN composition can comprise one or more non-repetitive XTEN sequences of greater than about 100 to about 3000 amino acid residues, or cumulatively greater than 400 to about 3000 residues, wherein at least about 80%, or at least about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99% to about 100% of the sequence consists of non-overlapping 36 amino acid sequence motifs selected from one or more of the polypeptide sequences of Tables 10-13.

In those embodiments wherein the XTEN component of the GPXTEN fusion protein has less than 100% of its amino acids consisting of four to six amino acid selected from glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), or less than 100% of the sequence consisting of the sequence motifs of Table 4, or less than 100% sequence identity with an XTEN from Table 5, the other amino acid residues can be selected from any other of the 14 natural L-amino acids, but are preferentially selected from hydrophilic amino acids such that the XTEN sequence contains at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% hydrophilic amino acids. The XTEN amino acids that are not glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) are interspersed throughout the XTEN sequence, are located within or between the sequence motifs, or are concentrated in one or more short stretches of the XTEN sequence. In such cases where the XTEN component of the GPXTEN comprises amino acids other than glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P), it is preferred that the amino acids not be hydrophobic residues and should not substantially confer secondary structure of the XTEN component. Hydrophobic residues that are less favored in construction of XTEN include tryptophan, phenylalanine, tyrosine, leucine, isoleucine, valine, and methionine. Additionally, one can design the XTEN sequences to contain few (e.g. less than 5%) or none of the following amino acids: cysteine (to avoid disulfide formation and oxidation), methionine (to avoid oxidation), asparagine and glutamine (to avoid desamidation). Thus, in a preferred embodiment of the foregoing, the XTEN component of the GPXTEN fusion protein comprising other amino acids in addition to glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) would have a sequence with less than 5% of the residues contributing to alpha-helices and beta-sheets as measured by the Chou-Fasman algorithm and would have at least 90%, or at least about 95% or more random coil formation as measured by the GOR algorithm.

3. Length of Sequence

In another aspect of the present invention, the invention encompasses GPXTEN compositions comprising carriers of XTEN polypeptides with extended length sequences. The present invention makes use of the discovery that increasing the length of non-repetitive, unstructured polypeptides enhances the unstructured nature of the XTENs and correspondingly enhances the biological and pharmacokinetic properties of fusion proteins comprising the XTEN carrier. As described more fully in the Examples, proportional increases in the length of the XTEN, even if created by a fixed repeat order of single family sequence motifs (e.g., the four AE motifs of Table 4), can result in a sequence with a higher percentage of random coil formation, as determined by GOR algorithm, compared to shorter XTEN lengths. In general, increasing the length of the unstructured polypeptide fusion partner can, as described in the Examples, results in a fusion protein with a disproportional increase in terminal half-life compared to fusion proteins with unstructured polypeptide partners with shorter sequence lengths.

Non-limiting examples of XTEN contemplated for inclusion in the GPXTEN of the invention are presented in Table 5. In one embodiment, the invention provides GPXTEN compositions wherein the XTEN sequence length of the fusion protein(s) is greater than about 100 to about 3000 amino acid residues, and in some cases is greater than 400 to about 3000 amino acid residues, wherein the XTEN confers enhanced pharmacokinetic properties on the GPXTEN in comparison to GP not linked to XTEN. In some cases, the XTEN sequences of the GPXTEN compositions of the present invention can be about 100, or about 144, or about 288, or about 401, or about 500, or about 600, or about 700, or about 800, or about 900, or about 1000, or about 1500, or about 2000, or about 2500 or up to about 3000 amino acid residues in length. In other cases, the XTEN sequences can be about 100 to 150, about 150 to 250, about 250 to 400, 401 to about 500, about 500 to 900, about 900 to 1500, about 1500 to 2000, or about 2000 to about 3000 amino acid residues in length. In one embodiment, the GPXTEN can comprise an XTEN sequence wherein the sequence exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a XTEN selected from Table 5. In some cases, the XTEN sequence is designed for optimized expression as the N-terminal component of the GPXTEN by inclusion of encoding nucleotides for an optimized N-terminal leader sequence (NTS) in the XTEN portion of the gene encoding the fusion protein. In one embodiment of the foregoing, the N-terminal XTEN sequence of the expressed GPXTEN has at least 90% sequence identity to the sequence of AE48 or AM48, AE624, or AE912 or AM923. In another embodiment of the foregoing, the XTEN has the N-terminal residues described in Examples 14-17.

In other cases, the GPXTEN fusion protein can comprise a first and a second XTEN sequence, wherein the cumulative total of the residues in the XTEN sequences is greater than about 400 to about 3000 amino acid residues. In embodiments of the foregoing, the GPXTEN fusion protein can comprise a first and a second XTEN sequence wherein the sequences each exhibit at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least a first or additionally a second XTEN selected from Table 5.

As described more fully below, the invention provides methods in which the GPXTEN is designed by selecting the length of the XTEN to confer a target half-life on a fusion protein administered to a subject. In general, XTEN lengths longer that about cumulative 400 residues incorporated into the GPXTEN compositions result in longer half-life compared to shorter cumulative lengths; e.g., shorter than about 280 residues. However, in another embodiment, GPXTEN fusion proteins can be designed to comprise XTEN with a longer sequence length that is selected to additionally confer slower rates of systemic absorption after subcutaneous or intramuscular administration to a subject. In such cases, the Cmax is reduced in comparison to a comparable dose of a GP not linked to XTEN, thereby contributing to the ability to keep the GPXTEN within the therapeutic window for the composition. Thus, the XTEN confers the property of a depot to the administered GPXTEN, in addition to the other physical/chemical properties described herein.


TABLE 5
XTEN Polypeptides
XTEN
Name
Amino Acid Sequence
SEQ ID NO:
AE48
MAEPAGSPTSTEEGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGS
187
AM48
MAEPAGSPTSTEEGASPGTSSTGSPGSSTPSGATGSPGSSTPSGATGS
188
AE144
GSEPATSGSETPGTSESATPESGPGSEPATSGSETPGSPAGSPTSTEEGTSTEPSEGSAPGSEP
189
ATSGSETPGSEPATSGSETPGSEPATSGSETPGTSTEPSEGSAPGTSESATPESGPGSEPATSG
SETPGTSTEPSEGSAP
AF144
GTSTPESGSASPGTSPSGESSTAPGTSPSGESSTAPGSTSSTAESPGPGSTSESPSGTAPGSTSS
190
TAESPGPGTSPSGESSTAPGTSTPESGSASPGSTSSTAESPGPGTSPSGESSTAPGTSPSGESST
APGTSPSGESSTAP
AE288
GTSESATPESGPGSEPATSGSETPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTST
191
EPSEGSAPGSPAGSPTSTEEGTSESATPESGPGSEPATSGSETPGTSESATPESGPGSPAGSPT
STEEGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSESATPESGP
GSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGSEP
ATSGSETPGTSESATPESGPGTSTEPSEGSAP
AF504
GASPGTSSTGSPGSSPSASTGTGPGSSPSASTGTGPGTPGSGTASSSPGSSTPSGATGSPGSXPS
192
ASTGTGPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGATGSPGTPGSGTASSSPGASPGTSST
GSPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGSPGTPGSGTASSSPGS
STPSGATGSPGSXPSASTGTGPGSSPSASTGTGPGSSTPSGATGSPGSSTPSGATGSPGASPGT
SSTGSPGASPGTSSTGSPGASPGTSSTGSPGTPGSGTASSSPGASPGTSSTGSPGASPGTSSTGS
PGASPGTSSTGSPGSSPSASTGTGPGTPGSGTASSSPGASPGTSSTGSPGASPGTSSTGSPGAS
PGTSSTGSPGSSTPSGATGSPGSSTPSGATGSPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGA
TGSPGSSTPSGATGSPGSSTPSGATGSPGSSPSASTGTGPGASPGTSSTGSP
AF540
GSTSSTAESPGPGSTSSTAESPGPGSTSESPSGTAPGSTSSTAESPGPGSTSSTAESPGPGTSTP
193
ESGSASPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGTSPSGESST
APGSTSESPSGTAPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGST
SESPSGTAPGTSTPESGSASPGSTSESPSGTAPGTSTPESGSASPGSTSSTAESPGPGSTSSTAE
SPGPGTSTPESGSASPGTSTPESGSASPGSTSESPSGTAPGTSTPESGSASPGTSTPESGSASPG
STSESPSGTAPGSTSESPSGTAPGSTSESPSGTAPGSTSSTAESPGPGTSTPESGSASPGTSTPE
SGSASPGSTSESPSGTAPGSTSESPSGTAPGTSTPESGSASPGSTSESPSGTAPGSTSESPSGTA
PGTSTPESGSASPGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPGSTSSTAESPGPGTST
PESGSASPGSTSESPSGTAP
AD576
GSSESGSSEGGPGSGGEPSESGSSGSSESGSSEGGPGSSESGSSEGGPGSSESGSSEGGPGSSESG
194
SSEGGPGSSESGSSEGGPGESPGGSSGSESGSEGSSGPGESSGSSESGSSEGGPGSSESGSSEGGP
GSSESGSSEGGPGSGGEPSESGSSGESPGGSSGSESGESPGGSSGSESGSGGEPSESGSSGSSESG
SSEGGPGSGGEPSESGSSGSGGEPSESGSSGSEGSSGPGESSGESPGGSSGSESGSGGEPSESGSS
GSGGEPSESGSSGSGGEPSESGSSGSSESGSSEGGPGESPGGSSGSESGESPGGSSGSESGESPG
GSSGSESGESPGGSSGSESGESPGGSSGSESGSSESGSSEGGPGSGGEPSESGSSGSEGSSGPGES
SGSSESGSSEGGPGSGGEPSESGSSGSSESGSSEGGPGSGGEPSESGSSGESPGGSSGSESGESPG
GSSGSESGSSESGSSEGGPGSGGEPSESGSSGSSESGSSEGGPGSGGEPSESGSSGSGGEPSESGS
SGESPGGSSGSESGSEGSSGPGESSGSSESGSSEGGPGSEGSSGPGESS
AE576
GSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTST
195
EPSEGSAPGTSESATPESGPGSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSESATP
ESGPGTSTEPSEGSAPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAP
GTSESATPESGPGTSTEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSTEPSEGSAPGTST
EPSEGSAPGTSESATPESGPGTSESATPESGPGSPAGSPTSTEEGTSESATPESGPGSEPATSG
SETPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAP
GTSTEPSEGSAPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGSEP
ATSGSETPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTSTEPSEGSAPGTSESATP
ESGPGSPAGSPTSTEEGSPAGSPTSTEEGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAP
AF576
GSTSSTAESPGPGSTSSTAESPGPGSTSESPSGTAPGSTSSTAESPGPGSTSSTAESPGPGTSTP
196
ESGSASPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGTSPSGESST
APGSTSESPSGTAPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGST
SESPSGTAPGTSTPESGSASPGSTSESPSGTAPGTSTPESGSASPGSTSSTAESPGPGSTSSTAE
SPGPGTSTPESGSASPGTSTPESGSASPGSTSESPSGTAPGTSTPESGSASPGTSTPESGSASPG
STSESPSGTAPGSTSESPSGTAPGSTSESPSGTAPGSTSSTAESPGPGTSTPESGSASPGTSTPE
SGSASPGSTSESPSGTAPGSTSESPSGTAPGTSTPESGSASPGSTSESPSGTAPGSTSESPSGTA
PGTSTPESGSASPGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPGSTSSTAESPGPGTST
PESGSASPGSTSESPSGTAPGSTSSTAESPGPGTSTPESGSASPGTSTPESGSASP
AE624
MAEPAGSPTSTEEGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGSPGSPAGSPTSTEEGTS
197
ESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESAT
PESGPGSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSA
PGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGTS
TEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSTEPSEGSAPGTSTEPSEGSAPGTSESAT
PESGPGTSESATPESGPGSPAGSPTSTEEGTSESATPESGPGSEPATSGSETPGTSESATPESG
PGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTS
TEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSESAT
PESGPGSEPATSGSETPGTSESATPESGPGTSTEPSEGSAPGTSESATPESGPGSPAGSPTSTE
EGSPAGSPTSTEEGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAP
AD836
GSSESGSSEGGPGSSESGSSEGGPGESPGGSSGSESGSGGEPSESGSSGESPGGSSGSESGESPG
198
GSSGSESGSSESGSSEGGPGSSESGSSEGGPGSSESGSSEGGPGESPGGSSGSESGESPGGSSGSE
SGESPGGSSGSESGSSESGSSEGGPGSSESGSSEGGPGSSESGSSEGGPGSSESGSSEGGPGSSES
GSSEGGPGSSESGSSEGGPGSGGEPSESGSSGESPGGSSGSESGESPGGSSGSESGSGGEPSESG
SSGSEGSSGPGESSGSSESGSSEGGPGSGGEPSESGSSGSEGSSGPGESSGSSESGSSEGGPGSGG
EPSESGSSGESPGGSSGSESGSGGEPSESGSSGSGGEPSESGSSGSSESGSSEGGPGSGGEPSESG
SSGSGGEPSESGSSGSEGSSGPGESSGESPGGSSGSESGSEGSSGPGESSGSEGSSGPGESSGSGG
EPSESGSSGSSESGSSEGGPGSSESGSSEGGPGESPGGSSGSESGSGGEPSESGSSGSEGSSGPGE
SSGESPGGSSGSESGSEGSSGPGSSESGSSEGGPGSGGEPSESGSSGSEGSSGPGESSGSEGSSGP
GESSGSEGSSGPGESSGSGGEPSESGSSGSGGEPSESGSSGESPGGSSGSESGESPGGSSGSESGS
GGEPSESGSSGSEGSSGPGESSGESPGGSSGSESGSSESGSSEGGPGSSESGSSEGGPGSSESGSS
EGGPGSGGEPSESGSSGSSESGSSEGGPGESPGGSSGSESGSGGEPSESGSSGSSESGSSEGGPG
ESPGGSSGSESGSGGEPSESGSSGESPGGSSGSESGSGGEPSESGSS
AE864
GSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTST
199
EPSEGSAPGTSESATPESGPGSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSESATP
ESGPGTSTEPSEGSAPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAP
GTSESATPESGPGTSTEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSTEPSEGSAPGTST
EPSEGSAPGTSESATPESGPGTSESATPESGPGSPAGSPTSTEEGTSESATPESGPGSEPATSG
SETPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAP
GTSTEPSEGSAPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGSEP
ATSGSETPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTSTEPSEGSAPGTSESATP
ESGPGSPAGSPTSTEEGSPAGSPTSTEEGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAP
GTSESATPESGPGSEPATSGSETPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTST
EPSEGSAPGSPAGSPTSTEEGTSESATPESGPGSEPATSGSETPGTSESATPESGPGSPAGSPT
STEEGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSESATPESGP
GSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGSEP
ATSGSETPGTSESATPESGPGTSTEPSEGSAP
AF864
GSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGTSTPESGSASPGTSTP
200
ESGSASPGSTSESPSGTAPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGTSPSGESST
APGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPGTSPSGESSTAPGSTSSTAESPGPGTS
TPESGSASPGTSTPESGSASPGSTSESPSGTAPGSTSESPSGTAPGTSTPESGSASPGSTSSTAE
SPGPGTSTPESGSASPGSTSESPSGTAPGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPG
TSTPESGSASPGSTSSTAESPGPGSTSSTAESPGPGSTSSTAESPGPGSTSSTAESPGPGTSPSG
ESSTAPGSTSESPSGTAPGSTSESPSGTAPGTSTPESGPXXXGASASGAPSTXXXXSESPSGTA
PGSTSESPSGTAPGSTSESPSGTAPGSTSESPSGTAPGSTSESPSGTAPGSTSESPSGTAPGTST
PESGSASPGTSPSGESSTAPGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPGTSTPESGS
ASPGSTSESPSGTAPGSTSESPSGTAPGTSPSGESSTAPGSTSESPSGTAPGTSTPESGSASPGT
STPESGSASPGSTSESPSGTAPGTSTPESGSASPGSTSSTAESPGPGSTSESPSGTAPGSTSESP
SGTAPGTSPSGESSTAPGSTSSTAESPGPGTSPSGESSTAPGTSTPESGSASPGTSPSGESSTAP
GTSPSGESSTAPGTSPSGESSTAPGSTSSTAESPGPGSTSSTAESPGPGTSPSGESSTAPGSSPS
ASTGTGPGSSTPSGATGSPGSSTPSGATGSP
AG864
GASPGTSSTGSPGSSPSASTGTGPGSSPSASTGTGPGTPGSGTASSSPGSSTPSGATGSPGSSPS
201
ASTGTGPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGATGSPGTPGSGTASSSPGASPGTSST
GSPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGSPGTPGSGTASSSPGS
STPSGATGSPGSSPSASTGTGPGSSPSASTGTGPGSSTPSGATGSPGSSTPSGATGSPGASPGT
SSTGSPGASPGTSSTGSPGASPGTSSTGSPGTPGSGTASSSPGASPGTSSTGSPGASPGTSSTGS
PGASPGTSSTGSPGSSPSASTGTGPGTPGSGTASSSPGASPGTSSTGSPGASPGTSSTGSPGAS
PGTSSTGSPGSSTPSGATGSPGSSTPSGATGSPGASPGTSSTGSPGTPGSGTASSSPGSSTPSGA
TGSPGSSTPSGATGSPGSSTPSGATGSPGSSPSASTGTGPGASPGTSSTGSPGASPGTSSTGSP
GTPGSGTASSSPGASPGTSSTGSPGASPGTSSTGSPGASPGTSSTGSPGASPGTSSTGSPGTPG
SGTASSSPGSSTPSGATGSPGTPGSGTASSSPGSSTPSGATGSPGTPGSGTASSSPGSSTPSGAT
GSPGSSTPSGATGSPGSSPSASTGTGPGSSPSASTGTGPGASPGTSSTGSPGTPGSGTASSSPGS
STPSGATGSPGSSPSASTGTGPGSSPSASTGTGPGASPGTSSTGSPGASPGTSSTGSPGSSTPSG
ATGSPGSSPSASTGTGPGASPGTSSTGSPGSSPSASTGTGPGTPGSGTASSSPGSSTPSGATGS
PGSSTPSGATGSPGASPGTSSTGSP
AM875
GTSTEPSEGSAPGSEPATSGSETPGSPAGSPTSTEEGSTSSTAESPGPGTSTPESGSASPGSTSE
202
SPSGTAPGSTSESPSGTAPGTSTPESGSASPGTSTPESGSASPGSEPATSGSETPGTSESATPES
GPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGS
PAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSTEP
SEGSAPGTSTEPSEGSAPGTSESATPESGPGTSTEPSEGSAPGSEPATSGSETPGSPAGSPTST
EEGSSTPSGATGSPGTPGSGTASSSPGSSTPSGATGSPGTSTEPSEGSAPGTSTEPSEGSAPGS
EPATSGSETPGSPAGSPTSTEEGSPAGSPTSTEEGTSTEPSEGSAPGASASGAPSTGGTSESAT
PESGPGSPAGSPTSTEEGSPAGSPTSTEEGSTSSTAESPGPGSTSESPSGTAPGTSPSGESSTAP
GTPGSGTASSSPGSSTPSGATGSPGSSPSASTGTGPGSEPATSGSETPGTSESATPESGPGSEP
ATSGSETPGSTSSTAESPGPGSTSSTAESPGPGTSPSGESSTAPGSEPATSGSETPGSEPATSGS
ETPGTSTEPSEGSAPGSTSSTAESPGPGTSTPESGSASPGSTSESPSGTAPGTSTEPSEGSAPG
TSTEPSEGSAPGTSTEPSEGSAPGSSTPSGATGSPGSSPSASTGTGPGASPGTSSTGSPGSEPA
TSGSETPGTSESATPESGPGSPAGSPTSTEEGSSTPSGATGSPGSSPSASTGTGPGASPGTSST
GSPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAP
AE912
MAEPAGSPTSTEEGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGSPGSPAGSPTSTEEGTS
203
ESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESAT
PESGPGSEPATSGSETPGSEPATSGSETPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSA
PGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGTS
TEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSTEPSEGSAPGTSTEPSEGSAPGTSESAT
PESGPGTSESATPESGPGSPAGSPTSTEEGTSESATPESGPGSEPATSGSETPGTSESATPESG
PGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTSTEPSEGSAPGTS
TEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGSEPATSGSETPGTSESAT
PESGPGSEPATSGSETPGTSESATPESGPGTSTEPSEGSAPGTSESATPESGPGSPAGSPTSTE
EGSPAGSPTSTEEGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGTSESATPESGPGSE
PATSGSETPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTSTEPSEGSAPGSPAGSP
TSTEEGTSESATPESGPGSEPATSGSETPGTSESATPESGPGSPAGSPTSTEEGSPAGSPTSTE
EGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSESATPESGPGSEPATSGSETPGSE
PATSGSETPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGSEPATSGSETPGTSESAT
PESGPGTSTEPSEGSAP
AM923
MAEPAGSPTSTEEGASPGTSSTGSPGSSTPSGATGSPGSSTPSGATGSPGTSTEPSEGSAPGSE
204
PATSGSETPGSPAGSPTSTEEGSTSSTAESPGPGTSTPESGSASPGSTSESPSGTAPGSTSESPS
GTAPGTSTPESGSASPGTSTPESGSASPGSEPATSGSETPGTSESATPESGPGSPAGSPTSTEE
GTSTEPSEGSAPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGSPAGSPTSTEEGTST
EPSEGSAPGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSTEPSEGSAPGTSTEPSE
GSAPGTSESATPESGPGTSTEPSEGSAPGSEPATSGSETPGSPAGSPTSTEEGSSTPSGATGSP
GTPGSGTASSSPGSSTPSGATGSPGTSTEPSEGSAPGTSTEPSEGSAPGSEPATSGSETPGSPA
GSPTSTEEGSPAGSPTSTEEGTSTEPSEGSAPGASASGAPSTGGTSESATPESGPGSPAGSPTS
TEEGSPAGSPTSTEEGSTSSTAESPGPGSTSESPSGTAPGTSPSGESSTAPGTPGSGTASSSPGS
STPSGATGSPGSSPSASTGTGPGSEPATSGSETPGTSESATPESGPGSEPATSGSETPGSTSST
AESPGPGSTSSTAESPGPGTSPSGESSTAPGSEPATSGSETPGSEPATSGSETPGTSTEPSEGS
APGSTSSTAESPGPGTSTPESGSASPGSTSESPSGTAPGTSTEPSEGSAPGTSTEPSEGSAPGT
STEPSEGSAPGSSTPSGATGSPGSSPSASTGTGPGASPGTSSTGSPGSEPATSGSETPGTSESA
TPESGPGSPAGSPTSTEEGSSTPSGATGSPGSSPSASTGTGPGASPGTSSTGSPGTSESATPES
GPGTSTEPSEGSAPGTSTEPSEGSAP
AM1318
GTSTEPSEGSAPGSEPATSGSETPGSPAGSPTSTEEGSTSSTAESPGPGTSTPESGSASPGSTSE
205
SPSGTAPGSTSESPSGTAPGTSTPESGSASPGTSTPESGSASPGSEPATSGSETPGTSESATPES
GPGSPAGSPTSTEEGTSTEPSEGSAPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGS
PAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGTSESATPESGPGTSTEP
SEGSAPGTSTEPSEGSAPGTSESATPESGPGTSTEPSEGSAPGSEPATSGSETPGSPAGSPTST
EEGSSTPSGATGSPGTPGSGTASSSPGSSTPSGATGSPGTSTEPSEGSAPGTSTEPSEGSAPGS
EPATSGSETPGSPAGSPTSTEEGSPAGSPTSTEEGTSTEPSEGSAPGPEPTGPAPSGGSEPATS
GSETPGTSESATPESGPGSPAGSPTSTEEGTSESATPESGPGSPAGSPTSTEEGSPAGSPTSTE
EGTSESATPESGPGSPAGSPTSTEEGSPAGSPTSTEEGSTSSTAESPGPGSTSESPSGTAPGTS
PSGESSTAPGSTSESPSGTAPGSTSESPSGTAPGTSPSGESSTAPGTSTEPSEGSAPGTSESATP
ESGPGTSESATPESGPGSEPATSGSETPGTSESATPESGPGTSESATPESGPGTSTEPSEGSAP
GTSESATPESGPGTSTEPSEGSAPGTSPSGESSTAPGTSPSGESSTAPGTSPSGESSTAPGTSTE
PSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGSSPSASTGTGPGSSTPSGATGSPGSSTPSGAT
GSPGSSTPSGATGSPGSSTPSGATGSPGASPGTSSTGSPGASASGAPSTGGTSPSGESSTAPGS
TSSTAESPGPGTSPSGESSTAPGTSESATPESGPGTSTEPSEGSAPGTSTEPSEGSAPGSSPSAS
TGTGPGSSTPSGATGSPGASPGTSSTGSPGTSTPESGSASPGTSPSGESSTAPGTSPSGESSTA
PGTSESATPESGPGSEPATSGSETPGTSTEPSEGSAPGSTSESPSGTAPGSTSESPSGTAPGTS
TPESGSASPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSESAT
PESGPGSEPATSGSETPGSSTPSGATGSPGASPGTSSTGSPGSSTPSGATGSPGSTSESPSGTAP
GTSPSGESSTAPGSTSSTAESPGPGSSTPSGATGSPGASPGTSSTGSPGTPGSGTASSSPGSPAG
SPTSTEEGSPAGSPTSTEEGTSTEPSEGSAP
BC864
GTSTEPSEPGSAGTSTEPSEPGSAGSEPATSGTEPSGSGASEPTSTEPGSEPATSGTEPSGSEP
206
ATSGTEPSGSEPATSGTEPSGSGASEPTSTEPGTSTEPSEPGSAGSEPATSGTEPSGTSTEPSE
PGSAGSEPATSGTEPSGSEPATSGTEPSGTSTEPSEPGSAGTSTEPSEPGSAGSEPATSGTEPS
GSEPATSGTEPSGTSEPSTSEPGAGSGASEPTSTEPGTSEPSTSEPGAGSEPATSGTEPSGSEP
ATSGTEPSGTSTEPSEPGSAGTSTEPSEPGSAGSGASEPTSTEPGSEPATSGTEPSGSEPATSG
TEPSGSEPATSGTEPSGSEPATSGTEPSGTSTEPSEPGSAGSEPATSGTEPSGSGASEPTSTEP
GTSTEPSEPGSAGSEPATSGTEPSGSGASEPTSTEPGTSTEPSEPGSAGSGASEPTSTEPGSEP
ATSGTEPSGSGASEPTSTEPGSEPATSGTEPSGSGASEPTSTEPGTSTEPSEPGSAGSEPATSG
TEPSGSGASEPTSTEPGTSTEPSEPGSAGSEPATSGTEPSGTSTEPSEPGSAGSEPATSGTEPS
GTSTEPSEPGSAGTSTEPSEPGSAGTSTEPSEPGSAGTSTEPSEPGSAGTSTEPSEPGSAGTST
EPSEPGSAGTSEPSTSEPGAGSGASEPTSTEPGTSTEPSEPGSAGTSTEPSEPGSAGTSTEPSE
PGSAGSEPATSGTEPSGSGASEPTSTEPGSEPATSGTEPSGSEPATSGTEPSGSEPATSGTEPS
GSEPATSGTEPSGTSEPSTSEPGAGSEPATSGTEPSGSGASEPTSTEPGTSTEPSEPGSAGSEP
ATSGTEPSGSGASEPTSTEPGTSTEPSEPGSA
BD864
GSETATSGSETAGTSESATSESGAGSTAGSETSTEAGTSESATSESGAGSETATSGSETAGSET
207
ATSGSETAGTSTEASEGSASGTSTEASEGSASGTSESATSESGAGSETATSGSETAGTSTEASE
GSASGSTAGSETSTEAGTSESATSESGAGTSESATSESGAGSETATSGSETAGTSESATSESGA
GTSTEASEGSASGSETATSGSETAGSETATSGSETAGTSTEASEGSASGSTAGSETSTEAGTSE
SATSESGAGTSTEASEGSASGSETATSGSETAGSTAGSETSTEAGSTAGSETSTEAGSETATSG
SETAGTSESATSESGAGTSESATSESGAGSETATSGSETAGTSESATSESGAGTSESATSESGA
GSETATSGSETAGSETATSGSETAGTSTEASEGSASGSTAGSETSTEAGSETATSGSETAGTSE
SATSESGAGSTAGSETSTEAGSTAGSETSTEAGSTAGSETSTEAGTSTEASEGSASGSTAGSET
STEAGSTAGSETSTEAGTSTEASEGSASGSTAGSETSTEAGSETATSGSETAGTSTEASEGSAS
GTSESATSESGAGSETATSGSETAGTSESATSESGAGTSESATSESGAGSETATSGSETAGTSE
SATSESGAGSETATSGSETAGTSTEASEGSASGTSTEASEGSASGSTAGSETSTEAGSTAGSET
STEAGSETATSGSETAGTSESATSESGAGTSESATSESGAGSETATSGSETAGSETATSGSETA
GSETATSGSETAGTSTEASEGSASGTSESATSESGAGSETATSGSETAGSETATSGSETAGTSE
SATSESGAGTSESATSESGAGSETATSGSETA

4. XTEN Segments

In one embodiment, the invention provides an isolated GPXTEN fusion protein wherein the cumulative length of the XTEN component is greater than about 100 to about 3000 amino acid residues containing at least one polypeptide sequence segment selected from Tables 5, 10, 11, 12, and 13 and wherein at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98% or more of the remainder of the XTEN sequence consists of hydrophilic amino acids and less than about 2% of the remainder of the XTEN by and large contains hydrophobic, aromatic or cysteine amino acids. In the foregoing embodiment, the XTEN can contain multiple segments wherein the segments are identical or different. In another embodiment, the invention provides an isolated GPXTEN fusion protein wherein the cumulative length of the XTEN component is greater than about 100 to about 3000 amino acid residues and comprises at least one sequence segment of at least about 100 to about 923, or at least about 100 to about 875, or at least about 100 to about 576, or at least about 100 to about 288, or at least about 100 to about 144 amino acid residues wherein the sequence segment(s) consists of at least three different types of amino acids and the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues in the sequence segment(s) constitutes at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% of the total amino acid sequence of the sequence segment and at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98% of the remainder of the XTEN sequence(s) consist of hydrophilic amino acids and less than about 2% of the remainder of the XTEN sequence(s) consists of hydrophobic, aromatic or cysteine amino acids. In another embodiment, the invention provides an isolated GPXTEN fusion protein wherein the cumulative length of the XTEN component is greater than about 100 to about 3000 amino acid residues and comprises at least one sequence segment of at least about 200 to about 923, or at least about 200 to about 875, or at least about 200 to about 576, or at least about 200 to about 288 amino acid residues wherein the sequence segment(s) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues in the sequence segment(s) constitutes at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% of the total amino acid sequence of the sequence segment and wherein the subsequence score of the segment is less than 12, more preferably less than 10, more preferably less than 9, more preferably less than 8, more preferably less than 7, more preferably less than 6, and most preferably less than 5, and at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98% of the remainder of the XTEN sequence(s) consist of hydrophilic amino acids and less than about 2% of the remainder of the XTEN sequence(s) consists of hydrophobic, aromatic or cysteine amino acids.

5. N-Terminal XTEN Expression-Enhancing Sequences

In some embodiments, the invention provides a short-length XTEN sequence as the N-terminal portion of the GPXTEN fusion protein. The expression of the fusion protein is enhanced in a host cell transformed with a suitable expression vector comprising an optimized N-terminal leader polynucleotide sequence (that encodes the N-terminal XTEN) incorporated into the polynucleotide encoding the binding fusion protein. It has been discovered, as described in Examples 14-17, that a host cell transformed with such an expression vector comprising an optimized N-terminal leader sequence (NTS) in the binding fusion protein gene results in greatly-enhanced expression of the fusion protein compared to the expression of a corresponding fusion protein from a polynucleotide not comprising the NTS, and can obviate the need for incorporation of a non-XTEN leader sequence used to enhance expression. In one embodiment, the invention provides GPXTEN fusion proteins comprising an NTS wherein the expression of the binding fusion protein from the encoding gene in a host cell is enhanced about 50%, or about 75%, or about 100%, or about 150%, or about 200%, or about 400% compared to expression of a GPXTEN fusion protein not comprising the N-terminal XTEN sequence (where the encoding gene lacks the NTS).

In one embodiment, the N-terminal XTEN polypeptide of the GPXTEN comprises a sequence that exhibits at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least 99%, or exhibits 100% sequence identity to the amino acid sequence of AE48 or AM48, the respective sequences of which are as follows:


AE48:
(SEQ ID NO: 208)
MAEPAGSPTSTEEGTPGSGTASSSPGSSTPSGATGSPGASPGTSSTGS
AM48:
(SEQ ID NO: 209)
MAEPAGSPTSTEEGASPGTSSTGSPGSSTPSGATGSPGSSTPSGATGS

In another embodiment, the short-length N-terminal XTEN can be linked to an XTEN of longer length to form the N-terminal region of the GPXTEN fusion protein, wherein the polynucleotide sequence encoding the short-length N-terminal XTEN confers the property of enhanced expression in the host cell, and wherein the long length of the expressed XTEN contributes to the enhanced properties of the XTEN carrier in the fusion protein, as described above. In the foregoing, the short-length XTEN can be linked to any of the XTEN disclosed herein (e.g., an XTEN of Table 5) and the resulting XTEN, in turn, is linked to the N-terminal of any of the GP disclosed herein (e.g., a GP of Tables 1-3) as a component of the fusion protein. Alternatively, polynucleotides encoding the short-length XTEN (or its complement) is linked to polynucleotides encoding any of the XTEN (or its complement) disclosed herein and the resulting gene encoding the N-terminal XTEN, in turn, is linked to the 5′ end of polynucleotides encoding any of the GP (or to the 3′ end of its complement) disclosed herein. In some embodiments, the N-terminal XTEN polypeptide with long length exhibits at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least 99%, or exhibits 100% sequence identity to an amino acid sequence selected from the group consisting of the sequences AE624, AE912, and AM923.

In any of the foregoing N-terminal XTEN embodiments described above, the N-terminal XTEN can have from about one to about six additional amino acid residues, preferably selected from GESTPA, to accommodate the restriction endonuclease restriction sites that would be employed to join the nucleotides encoding the N-terminal XTEN to the gene encoding the targeting moiety of the fusion protein. The methods for the generation of the N-terminal sequences and incorporation into the fusion proteins of the invention are described more fully in the Examples.

6. Net Charge

In other embodiments, the XTEN polypeptides have an unstructured characteristic imparted by incorporation of amino acid residues with a net charge and/or reducing the proportion of hydrophobic amino acids in the XTEN sequence. The overall net charge and net charge density is controlled by modifying the content of charged amino acids in the XTEN sequences. In some embodiments, the net charge density of the XTEN of the compositions may be above +0.1 or below −0.1 charges/residue. In other embodiments, the net charge of a XTEN can be about 0%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10% about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, or about 20% or more.

Since most tissues and surfaces in a human or animal have a net negative charge, in some embodiments, the XTEN sequences are designed to have a net negative charge to minimize non-specific interactions between the XTEN containing compositions and various surfaces such as blood vessels, healthy tissues, or various receptors. Not to be bound by a particular theory, the XTEN can adopt open conformations due to electrostatic repulsion between individual amino acids of the XTEN polypeptide that individually carry a net negative charge and that are distributed across the sequence of the XTEN polypeptide. Such a distribution of net negative charge in the extended sequence lengths of XTEN can lead to an unstructured conformation that, in turn, can result in an effective increase in hydrodynamic radius. In preferred embodiments, the negative charge is conferred by incorporation of glutamic acid residues. Accordingly, in one embodiment the invention provides XTEN in which the XTEN sequences contain about 8, 10, 15, 20, 25, or even about 30% glutamic acid. Generally, the glutamic residues would be spaced uniformly across the XTEN sequence. In some cases, the XTEN can contain about 10-80, or about 15-60, or about 20-50 glutamic residues per 20 kD of XTEN that can result in an XTEN with charged residues that would have very similar pKa, which can increase the charge homogeneity of the product and sharpen its isoelectric point, enhancing the physicochemical properties of the resulting GPXTEN fusion protein for, example, simplifying purification procedures.

The XTEN of the compositions of the present invention generally have no or a low content of positively charged amino acids. In some embodiments the XTEN may have less than about 10% amino acid residues with a positive charge, or less than about 7%, or less than about 5%, or less than about 2%, or less than about 1% amino acid residues with a positive charge. However, the invention contemplates constructs where a limited number of amino acids with a positive charge, such as lysine, are incorporated into XTEN to permit conjugation between the epsilon amine of the lysine and a reactive group on a peptide, a linker bridge, or a reactive group on a drug or small molecule to be conjugated to the XTEN backbone. In one embodiment of the foregoing, the XTEN has between about 1 to about 100 lysine residues, or about 1 to about 70 lysine residues, or about 1 to about 50 lysine residues, or about 1 to about 30 lysine residues, or about 1 to about 20 lysine residues, or about 1 to about 10 lysine residues, or about 1 to about 5 lysine residues, or alternatively only a single lysine residue. Using the foregoing lysine-containing XTEN, fusion proteins are constructed that comprises XTEN, a glucose regulating peptide, plus a chemotherapeutic agent useful in the treatment of glucose diseases or disorders, wherein the maximum number of molecules of the agent incorporated into the XTEN component is determined by the numbers of lysines or other amino acids with reactive side chains (e.g., cysteine) incorporated into the XTEN.

In some embodiments, the XTEN sequence comprises charged residues separated by other residues such as serine or glycine, which leads to better expression or purification behavior. Based on the net charge, some XTENs have an isoelectric point (pI) of 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, or even 6.5. In preferred embodiments, the XTEN will have an isoelectric point between 1.5 and 4.5. In these embodiments, the XTEN incorporated into the GPXTEN fusion protein compositions of the present invention carry a net negative charge under physiologic conditions that contribute to the unstructured conformation and reduced binding of the XTEN component to mammalian proteins and tissues.

As hydrophobic amino acids impart structure to a polypeptide, the invention provides that the content of hydrophobic amino acids in the XTEN will typically be less than 5%, or less than 2%, or less than 1% hydrophobic amino acid content. In one embodiment, the amino acid content of methionine and tryptophan in the XTEN component of a GPXTEN fusion protein is typically less than 5%, or less than 2%, and most preferably less than 1%. In another embodiment, the XTEN will have a sequence that has less than 10% amino acid residues with a positive charge, or less than about 7%, or less that about 5%, or less than about 2% amino acid residues with a positive charge, the sum of methionine and tryptophan residues will be less than 2%, and the sum of asparagine and glutamine residues will be less than 10% of the total XTEN sequence.

7. Low Immunogenicity

In another aspect, the invention provides compositions in which the XTEN sequences have a low degree of immunogenicity or are substantially non-immunogenic. Several factors can contribute to the low immunogenicity of XTEN, e.g., the non-repetitive sequence, the unstructured conformation, the high degree of solubility, the low degree or lack of self-aggregation, the low degree or lack of proteolytic sites within the sequence, and the low degree or lack of epitopes in the XTEN sequence.

Conformational epitopes are formed by regions of the protein surface that are composed of multiple discontinuous amino acid sequences of the protein antigen. The precise folding of the protein brings these sequences into a well-defined, stable spatial configurations, or epitopes, that can be recognized as “foreign” by the host humoral immune system, resulting in the production of antibodies to the protein or the activation of a cell-mediated immune response. In the latter case, the immune response to a protein in an individual is heavily influenced by T-cell epitope recognition that is a function of the peptide binding specificity of that individual's HLA-DR allotype. Engagement of a MHC Class II peptide complex by a cognate T-cell receptor on the surface of the T-cell, together with the cross-binding of certain other co-receptors such as the CD4 molecule, can induce an activated state within the T-cell. Activation leads to the release of cytokines further activating other lymphocytes such as B cells to produce antibodies or activating T killer cells as a full cellular immune response.

The ability of a peptide to bind a given MHC Class II molecule for presentation on the surface of an APC (antigen presenting cell) is dependent on a number of factors; most notably its primary sequence. In one embodiment, a lower degree of immunogenicity is achieved by designing XTEN sequences that resist antigen processing in antigen presenting cells, and/or choosing sequences that do not bind MHC receptors well. The invention provides GPXTEN fusion proteins with substantially non-repetitive XTEN polypeptides designed to reduce binding with MHC II receptors, as well as avoiding formation of epitopes for T-cell receptor or antibody binding, resulting in a low degree of immunogenicity. Avoidance of immunogenicity is, in part, a direct result of the conformational flexibility of XTEN sequences; i.e., the lack of secondary structure due to the selection and order of amino acid residues. For example, of particular interest are sequences having a low tendency to adapt compactly folded conformations in aqueous solution or under physiologic conditions that could result in conformational epitopes. The administration of fusion proteins comprising XTEN, using conventional therapeutic practices and dosing, would generally not result in the formation of neutralizing antibodies to the XTEN sequence, and also reduce the immunogenicity of the GP fusion partner in the GPXTEN compositions.

In one embodiment, the XTEN sequences utilized in the subject fusion proteins can be substantially free of epitopes recognized by human T cells. The elimination of such epitopes for the purpose of generating less immunogenic proteins has been disclosed previously; see for example WO 98/52976, WO 02/079232, and WO 00/3317 which are incorporated by reference herein. Assays for human T cell epitopes have been described (Stickler, M., et al. (2003) J Immunol Methods, 281: 95-108). Of particular interest are peptide sequences that can be oligomerized without generating T cell epitopes or non-human sequences. This is achieved by testing direct repeats of these sequences for the presence of T-cell epitopes and for the occurrence of 6 to 15-mer and, in particular, 9-mer sequences that are not human, and then altering the design of the XTEN sequence to eliminate or disrupt the epitope sequence. In some embodiments, the XTEN sequences are substantially non-immunogenic by the restriction of the numbers of epitopes of the XTEN predicted to bind MHC receptors. With a reduction in the numbers of epitopes capable of binding to MHC receptors, there is a concomitant reduction in the potential for T cell activation as well as T cell helper function, reduced B cell activation or upregulation and reduced antibody production. The low degree of predicted T-cell epitopes can be determined by epitope prediction algorithms such as, e.g., TEPITOPE (Sturniolo, T., et al. (1999) Nat Biotechnol, 17: 555-61), as shown in Example 45. The TEPITOPE score of a given peptide frame within a protein is the log of the Kd (dissociation constant, affinity, off-rate) of the binding of that peptide frame to multiple of the most common human MHC alleles, as disclosed in Sturniolo, T. et al. (1999) Nature Biotechnology 17:555). The score ranges over at least 20 logs, from about 10 to about −10 (corresponding to binding constraints of 10e10 Kd to 10e−10 Kd), and can be reduced by avoiding hydrophobic amino acids that serve as anchor residues during peptide display on MHC, such as M, I, L, V, F. In some embodiments, an XTEN component incorporated into a GPXTEN does not have a predicted T-cell epitope at a TEPITOPE score of about −5 or greater, or −6 or greater, or −7 or greater, or −8 or greater, or at a TEPITOPE score of −9 or greater. As used herein, a score of “−9 or greater” would encompass TEPITOPE scores of 10 to −9, inclusive, but would not encompass a score of −10, as −10 is less than −9.

In another embodiment, the inventive XTEN sequences, including those incorporated into the subject GPXTEN fusion proteins, are rendered substantially non-immunogenic by the restriction of known proteolytic sites from the sequence of the XTEN, reducing the processing of XTEN into small peptides that can bind to MHC II receptors. In another embodiment, the XTEN sequence is rendered substantially non-immunogenic by the use a sequence that is substantially devoid of secondary structure, conferring resistance to many proteases due to the high entropy of the structure. Accordingly, the reduced TEPITOPE score and elimination of known proteolytic sites from the XTEN render the XTEN compositions, including the XTEN of the GPXTEN fusion protein compositions, substantially unable to be bound by mammalian receptors, including those of the immune system. In one embodiment, an XTEN of a GPXTEN fusion protein can have >100 nM Kd binding to a mammalian receptor, or greater than 500 nM Kd, or greater than 1 μM Kd towards a mammalian cell surface or circulating polypeptide receptor.

Additionally, the non-repetitive sequence and corresponding lack of epitopes of XTEN limit the ability of B cells to bind to or be activated by XTEN. A repetitive sequence is recognized and can form multivalent contacts with even a few B cells and, as a consequence of the cross-linking of multiple T-cell independent receptors, can stimulate B cell proliferation and antibody production. In contrast, while a XTEN can make contacts with many different B cells over its extended sequence, each individual B cell may only make one or a small number of contacts with an individual XTEN due to the lack of repetitiveness of the sequence. Not being to be bound by any theory, XTENs typically have a much lower tendency to stimulate proliferation of B cells and thus an immune response. In one embodiment, the GPXTEN may have reduced immunogenicity as compared to the corresponding GP that is not fused. In one embodiment, the administration of up to three parenteral doses of a GPXTEN to a mammal result in detectable anti-GPXTEN IgG at a serum dilution of 1:100 but not at a dilution of 1:1000. In another embodiment, the administration of up to three parenteral doses of an GPXTEN to a mammal may result in detectable anti-GP IgG at a serum dilution of 1:100 but not at a dilution of 1:1000. In another embodiment, the administration of up to three parenteral doses of a GPXTEN to a mammal result in detectable anti-GP IgG at a serum dilution of 1:100 but not at a dilution of 1:1000. In another embodiment, the administration of up to three parenteral doses of a GPXTEN to a mammal results in detectable anti-XTEN IgG at a serum dilution of 1:100 but not at a dilution of 1:1000. In the foregoing embodiments, the mammal can be a mouse, a rat, a rabbit, or a cynomolgus monkey.

An additional feature of XTENs with non-repetitive sequences relative to sequences with a high degree of repetitiveness is non-repetitive XTENs form weaker contacts with antibodies. Antibodies are multivalent molecules. For instance, IgGs have two identical binding sites and IgMs contain 10 identical binding sites. Thus antibodies against repetitive sequences can form multivalent contacts with such repetitive sequences with high avidity, which can affect the potency and/or elimination of such repetitive sequences. In contrast, antibodies against non-repetitive XTENs may yield monovalent interactions, resulting in less likelihood of immune clearance such that the GPXTEN compositions can remain in circulation for an increased period of time.

8. Increased Hydrodynamic Radius

In another aspect, the present invention provides XTEN in which the XTEN polypeptides have a high hydrodynamic radius that confers a corresponding increased Apparent Molecular Weight to the GPXTEN fusion protein incorporating the XTEN. As detailed in Example 22, the linking of XTEN to GP sequences can result in GPXTEN compositions that can have increased hydrodynamic radii, increased Apparent Molecular Weight, and increased Apparent Molecular Weight Factor compared to a GP not linked to an XTEN. For example, in therapeutic applications in which prolonged half-life is desired, compositions in which a XTEN with a high hydrodynamic radius is incorporated into a fusion protein comprising one or more GP can effectively enlarge the hydrodynamic radius of the composition beyond the glomerular pore size of approximately 3-5 nm (corresponding to an apparent molecular weight of about 70 kDA) (Caliceti. 2003. Pharmacokinetic and biodistribution properties of poly(ethylene glycol)-protein conjugates. Adv Drug Deliv Rev 55:1261-1277), resulting in reduced renal clearance of circulating proteins. The hydrodynamic radius of a protein is determined by its molecular weight as well as by its structure, including shape or compactness. Not to be bound by a particular theory, the XTEN can adopt open conformations due to electrostatic repulsion between individual charges of the peptide or the inherent flexibility imparted by the particular amino acids in the sequence that lack potential to confer secondary structure. The open, extended and unstructured conformation of the XTEN polypeptide can have a greater proportional hydrodynamic radius compared to polypeptides of a comparable sequence length and/or molecular weight that have secondary and/or tertiary structure, such as typical globular proteins. Methods for determining the hydrodynamic radius are well known in the art, such as by the use of size exclusion chromatography (SEC), as described in U.S. Pat. Nos. 6,406,632 and 7,294,513. As the results of Example 22 demonstrate, the addition of increasing lengths of XTEN results in proportional increases in the parameters of hydrodynamic radius, Apparent Molecular Weight, and Apparent Molecular Weight Factor, permitting the tailoring of GPXTEN to desired characteristic cut-off Apparent Molecular Weights or hydrodynamic radii. Accordingly, in certain embodiments, the GPXTEN fusion protein can be configured with an XTEN such that the fusion protein can have a hydrodynamic radius of at least about 5 nm, or at least about 8 nm, or at least about 10 nm, or 12 nm, or at least about 15 nm. In the foregoing embodiments, the large hydrodynamic radius conferred by the XTEN in an GPXTEN fusion protein can lead to reduced renal clearance of the resulting fusion protein, leading to a corresponding increase in terminal half-life, an increase in mean residence time, and/or a decrease in renal clearance rate.

In another embodiment, an XTEN of a chosen length and sequence can be selectively incorporated into a GPXTEN to create a fusion protein that have, under physiologic conditions, an Apparent Molecular Weight of at least about 150 kDa, or at least about 300 kDa, or at least about 400 kDa, or at least about 500 kDA, or at least about 600 kDa, or at least about 700 kDA, or at least about 800 kDa, or at least about 900 kDa, or at least about 1000 kDa, or at least about 1200 kDa, or at least about 1500 kDa, or at least about 1800 kDa, or at least about 2000 kDa, or at least about 2300 kDa or more. In another embodiment, an XTEN of a chosen length and sequence can be selectively linked to a GP to result in a GPXTEN fusion protein that has, under physiologic conditions, an Apparent Molecular Weight Factor of at least three, alternatively of at least four, alternatively of at least five, alternatively of at least six, alternatively of at least eight, alternatively of at least 10, alternatively of at least 15, or an Apparent Molecular Weight Factor of at least 20 or greater. In another embodiment, the GPXTEN fusion protein has, under physiologic conditions, an Apparent Molecular Weight Factor that is about 4 to about 20, or is about 6 to about 15, or is about 8 to about 12, or is about 9 to about 10 relative to the actual molecular weight of the fusion protein.

V) GPXTEN Structural Configurations and Properties

The GP of the subject compositions are not limited to native, full-length polypeptides, but also include recombinant versions as well as biologically and/or pharmacologically active variants or fragments thereof. For example, it will be appreciated that various amino acid deletions, insertions and substitutions can be made in the GP to create variants without departing from the spirit of the invention with respect to the biological activity or pharmacologic properties of the GP. Examples of conservative substitutions for amino acids in polypeptide sequences are shown in Table 6. However, in embodiments of the GPXTEN in which the sequence identity of the GP is less than 100% compared to a specific sequence disclosed herein, the invention contemplates substitution of any of the other 19 natural L-amino acids for a given amino acid residue of the given GP, which may be at any position within the sequence of the GP, including adjacent amino acid residues. If any one substitution results in an undesirable change in biological activity, then one of the alternative amino acids can be employed and the construct evaluated by the methods described herein, or using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Pat. No. 5,364,934, the contents of which is incorporated by reference in its entirety, or using methods generally known in the art. In addition, variants can include, for instance, polypeptides wherein one or more amino acid residues are added or deleted at the N- or C-terminus of the full-length native amino acid sequence of a GP that retains some if not all of the biological activity of the native peptide.


TABLE 6
Exemplary conservative amino acid substitutions
Original Residue
Exemplary Substitutions
Ala (A)
val; leu; ile
Arg (R)
lys; gin; asn
Asn (N)
gin; his; Iys; arg
Asp (D)
glu
Cys (C)
ser
Gln (Q)
asn
Glu (E)
asp
Gly (G)
pro
His (H)
asn: gin: Iys: arg
xIle (I)
leu; val; met; ala; phe: norleucine
Leu (L)
norleucine: ile: val; met; ala: phe
Lys (K)
arg: gin: asn
Met (M)
leu; phe; ile
Phe (F)
leu: val: ile; ala
Pro (P)
gly
Ser (S)
thr
Thr (T)
ser
Trp (W)
tyr
Tyr (Y)
trp: phe: thr: ser
Val (V)
ile; leu; met; phe; ala; norleucine

a. GPXTEN Fusion Protein Configurations

The invention provides GPXTEN fusion protein compositions with the GP and XTEN components linked in specific N- to C-terminus configurations. In some embodiments, one or more GPs are linked to one or more XTENs, either at the N-terminus or at the C-terminus, with or without a spacer, to form a block copolymer, and the sequential arrangement of the GPs and the XTENs in the GPXTEN fusion protein are the same as the configuration known in the block copolymer chemistry. When there is more than one GP, XTEN, or spacer, each of the GP, the XTEN, or the spacer have the same or different sequences, and the GPs and/or XTENs are linked either continuous or alternately (regular or irregular). Thus, in all of the formulae provided herein, when there is more than one GP, XTEN, or spacer, each of the GP, XTEN, and spacer are the same or different. In some embodiments, the GPXTEN is a monomeric fusion protein with a GP linked to one XTEN polypeptide. In other cases, the GPXTEN is a monomeric fusion protein with a GP linked to two or more XTEN polypeptides. In still other embodiments, the GPXTEN is a monomeric fusion protein with two or more GP linked to one XTEN polypeptide. In still other embodiments, the GPXTEN is a monomeric fusion protein with two or more GP linked to two or more XTEN polypeptide. Table 7 provides non-limiting examples of configurations that are encompassed by the GPXTEN fusion proteins of the invention; numerous other variations will be apparent to the ordinarily skilled artisan, including the incorporation the spacer and cleavage sequences disclosed herein or known in the art.


TABLE 7
GPXTEN configurations
Components
Configuration*
Single GP; Single XTEN
GP-XTEN
XTEN-GP
Single GP; Multiple XTEN
XTEN-GP-XTEN
GP-XTEN-XTEN
XTEN-XTEN-GP
XTEN-GP-XTEN-XTEN
XTEN-XTEN-GP-XTEN
XTEN-XTEN-GP-XTEN
Multiple GP, Single XTEN
GP-XTEN-GP
XTEN-GP-GP
GP-GP-XTEN
GP-XTEN-GP-GP
Multiple GP, Multiple XTEN
GP-XTEN-GP-XTEN
XTEN-GP-XTEN-GP
XTEN-XTEN-GP-XTEN-GP
XTEN-XTEN-GP-GP
GP-XTEN-XTEN-GP
GP-GP-XTEN-XTEN
GP-GP-XTEN-XTEN-GP
GP-XTEN-GP-XTEN-GP
*Characterized as single for 1 component or multiple for 2 or more of that component
** Reflects N- to C-terminus configuration of the glucose regulating peptide and XTEN components

The invention contemplates GPXTEN fusion proteins compositions comprising, but not limited to GP selected from the sequences of Tables 1-3 (or fragments or sequence variants thereof), XTEN selected from Table 5 (or sequence variants thereof) that are in a configuration shown in Table 7. Generally, the resulting GPXTEN will retains at least a portion of the biological activity of the corresponding GP not linked to the XTEN. In other embodiments, the GP component either becomes biologically active or has an increase in activity upon its release from the XTEN by cleavage of an optional cleavage sequence incorporated within spacer sequences into the GPXTEN, described more fully below.

In one embodiment of the GPXTEN composition, the invention provides a fusion protein of formula I:

(XTEN)x-GP-(XTEN)y  I

wherein independently for each occurrence, GP is a is a glucose regulating peptide; x is either 0 or 1 and y is either 0 or 1 wherein x+y≥1; and XTEN is an extended recombinant polypeptide.

In another embodiment of the GPXTEN composition, the invention provides a fusion protein of formula II:

(XTEN)x-(GP)-(S)y-(XTEN)y  II

wherein independently for each occurrence, GP is a is a glucose regulating peptide a; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1 and y is either 0 or 1 wherein x+y≥1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula III:

(GP)-(S)x-(XTEN)-(S)y-(GP)-(S)z-(XTEN)z  III

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; z is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula IV:

(XTEN)x-(S)y-(GP)-(S)z-(XTEN)-(GP)  IV

wherein independently for each occurrence, GP is a is a glucose regulating peptide; S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; x is either 0 or 1; y is either 0 or 1; z is either 0 or 1; and XTEN is an extended recombinant polypeptide.

In another embodiment, the invention provides an isolated fusion protein, wherein the fusion protein is of formula VIII:

((S)m-(GP)x-(S)n-(XTEN)y-(S)0)t  VIII

wherein t is an integer that is greater than 0 (1, 2, 3, 4, etc. . . . ); independently each of m, n, o, x, and y is an integer (0, 1, 2, 3, 4, etc.), GP is a is a glucose regulating peptide; S is an spacer, optionally comprising a cleavage site; and XTEN is an extended recombinant polypeptide, with the proviso that: (1) x+y>1, (2) when t=1, x>0 and y>0, (3) when there is more than one GP, S, or XTEN, each GP, XTEN, or S are the same or independently different; and (4) when t>1, each m, n, o, x, or y within each subunit are the same or are independently different.

In some cases, administration of a therapeutically effective dose of a fusion protein of an embodiment of formulas I-VIII to a subject in need thereof can result in a gain in time of at least two-fold, or at least three-fold, or at least four-fold, or at least five-fold or more spent within a therapeutic window for the fusion protein compared to the corresponding GP not linked to the XTEN of and administered at a comparable dose to a subject. In other cases, administration of a therapeutically effective dose of a fusion protein of an embodiment of formulas I-VIII to a subject in need thereof can result in a gain in time between consecutive doses necessary to maintain a therapeutically effective dose regimen of at least 48 h, or at least 72 h, or at least about 96 h, or at least about 120 h, or at least about 7 days, or at least about 14 days, or at least about 21 days between consecutive doses compared to a GP not linked to XTEN and administered at a comparable dose.

Any spacer sequence group is optional in the fusion proteins encompassed by the invention. The spacer may be provided to enhance expression of the fusion protein from a host cell or to decrease steric hindrance such that the GP component may assume its desired tertiary structure and/or interact appropriately with its target receptor. For spacers and methods of identifying desirable spacers, see, for example, George, et al. (2003) Protein Engineering 15:871-879, specifically incorporated by reference herein. In one embodiment, the spacer comprises one or more peptide sequences that are between 1-50 amino acid residues in length, or about 1-25 residues, or about 1-10 residues in length. Spacer sequences, exclusive of cleavage sites, can comprise any of the 20 natural L amino acids, and will preferably comprise hydrophilic amino acids that are sterically unhindered that can include, but not be limited to, glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P). In some cases, the spacer can be polyglycines or polyalanines, or is predominately a mixture of combinations of glycine and alanine residues. The spacer polypeptide exclusive of a cleavage sequence is largely to substantially devoid of secondary structure; e.g., less than about 10%, or less than about 5% as determined by the Chou-Fasman and/or GOR algorithms. In one embodiment, one or both spacer sequences in a GPXTEN fusion protein composition may each further contain a cleavage sequence, which may be identical or may be different, wherein the cleavage sequence may be acted on by a protease to release the GP from the fusion protein.

In some cases, the incorporation of the cleavage sequence into the GPXTEN is designed to permit release of a GP that becomes active or more active upon its release from the XTEN. The cleavage sequences are located sufficiently close to the GP sequences, generally within 18, or within 12, or within 6, or within 2 amino acids of the GP sequence terminus, such that any remaining residues attached to the GP after cleavage do not appreciably interfere with the activity (e.g., such as binding to a receptor) of the GP, yet provide sufficient access to the protease to be able to effect cleavage of the cleavage sequence. In some embodiments, the cleavage site is a sequence that can be cleaved by a protease endogenous to the mammalian subject such that the GPXTEN can be cleaved after administration to a subject. In such cases, the GPXTEN can serve as a prodrug or a circulating depot for the GP. Examples of cleavage sites contemplated by the invention include, but are not limited to, a polypeptide sequence cleavable by a mammalian endogenous protease selected from FXIa, FXIIa, kallikrein, FVIIa, FIXa, FXa, FIIa (thrombin), Elastase-2, granzyme B, MMP-12, MMP-13, MMP-17 or MMP-20, or by non-mammalian proteases such as TEV, enterokinase, PreScission™ protease (rhinovirus 3C protease), and sortase A. Sequences known to be cleaved by the foregoing proteases and others are known in the art. Exemplary cleavage sequences and cut sites within the sequences are presented in Table 8, as well as sequence variants. For example, thrombin (activated clotting factor II) acts on the sequence LTPRSLLV (SEQ ID NO: 210) [Rawlings N. D., et al. (2008) Nucleic Acids Res., 36: D320], which would be cut after the arginine at position 4 in the sequence. Active FIIa is produced by cleavage of FII by FXa in the presence of phospholipids and calcium and is down stream from factor IX in the coagulation pathway. Once activated its natural role in coagulation is to cleave fibrinogen, which then in turn, begins clot formation. FIIa activity is tightly controlled and only occurs when coagulation is necessary for proper hemostasis. However, as coagulation is an on-going process in mammals, by incorporation of the LTPRSLLV (SEQ ID NO: 211) sequence into the GPXTEN between the GP and the XTEN, the XTEN domain would be removed from the adjoining GP concurrent with activation of either the extrinsic or intrinsic coagulation pathways when coagulation is required physiologically, thereby releasing GP over time. Similarly, incorporation of other sequences into GPXTEN that are acted upon by endogenous proteases would provide for sustained release of GP that may, in certain cases, provide a higher degree of activity for the GP from the “prodrug” form of the GPXTEN.

In some cases, only the two or three amino acids flanking both sides of the cut site (four to six amino acids total) would be incorporated into the cleavage sequence. In other cases, the known cleavage sequence can have one or more deletions or insertions or one or two or three amino acid substitutions for any one or two or three amino acids in the known sequence, wherein the deletions, insertions or substitutions result in reduced or enhanced susceptibility but not an absence of susceptibility to the protease, resulting in an ability to tailor the rate of release of the GP from the XTEN. Exemplary substitutions are shown in Table 8.


TABLE 8
Protease Cleavage Sequences
Exemplary
Protease Acting
Cleavage
SEQ ID
SEQ ID
Upon Sequence
Sequence
NO:
Minimal Cut Site*
NO:
FXIa
KLTR↓VVGG
212
KD/FL/T/R↓VA/VE/GT/GV
FXIIa
TMTR↓IVGG
213
NA
Kallikrein
SPFR↓STGG
214
—/—/FL/RY↓SR/RT/—/—
FVIIa
LQVR↓IVGG
215
NA
FIXa
PLGR↓IVGG
216
—/—/G/R↓—/—/—/—
FXa
IEGR↓TVGG
217
IA/E/GFP/R↓STI/VFS/—/G
FIIa (thrombin)
LTPR↓SLLV
218
—/—/PLA/R↓SAG/—/—/—
Elastase-2
LGPV↓SGVP
219
—/—/—/VIAT↓—/—/—/—
Granzyme-B
VAGD↓SLEE
220
V/—/—/D↓—/—/—/—
MMP-12
GPAG↓LGGA
221
G/PA/—/G↓L/—/G/—
222
MMP-13
GPAG↓LRGA
223
G/P/—/G↓L/—/GA/—
224
MMP-17
APLG↓LRLR
225
—/PS/—/—↓LQ/—/LT/—
MMP-20
PALP↓LVAQ
226
NA
TEV
ENLYFQ↓G
227
ENLYFQ↓G/S
228
Enterokinase
DDDK↓IVGG
229
DDDK↓IVGG
230
Protease 3C
LEVLFQ↓GP
231
LEVLFQ↓GP
232
(PreScission ™)
Sortase A
LPKT↓GSES
233
L/P/KEAD/T↓G/—/EKS/S
234
↓ indicates cleavage site
NA: not applicable
*the listing of multiple amino acids before, between, or after a slash indicate alternative amino acids that can be substituted at the position; “—” indicates that any amino acid may be substituted for the corresponding amino acid indicated in the middle column

In one embodiment, a GP incorporated into a GPXTEN fusion protein can have a sequence that exhibits at least about 80% sequence identity to a sequence from Tables 1-3, alternatively at least about 81%, or about 82%, or about 83%, or about 84%, or about 85%, or about 86%, or about 87%, or about 88%, or about 89%, or about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99%, or about 100% sequence identity as compared with a sequence from Tables 1-3. The GP of the foregoing embodiment can be evaluated for activity using assays or measured or determined parameters as described herein, and those sequences that retain at least about 40%, or about 50%, or about 55%, or about 60%, or about 70%, or about 80%, or about 90%, or about 95% or more activity compared to the corresponding native GP sequence would be considered suitable for inclusion in the subject GPXTEN. The GP found to retain a suitable level of activity can be linked to one or more XTEN polypeptides described hereinabove. In one embodiment, a GP found to retain a suitable level of activity can be linked to one or more XTEN polypeptides having at least about 80% sequence identity to a sequence from Table 5, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% sequence identity as compared with a sequence of Table 5, resulting in a chimeric fusion protein.

Non-limiting examples of sequences of GPXTEN fusion proteins containing a single GP linked to a single XTEN are presented in Table 36, and sequences of GPXTEN fusion proteins containing a single GP linked to two XTEN are presented in Table 37. In one embodiment, a GPXTEN composition would comprise a fusion protein having at least about 80% sequence identity to a GPXTEN from Tables 36-37, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% sequence identity as compared with a GPXTEN from Tables 36-37. However, the invention also contemplates substitution of other GP with sequences exhibiting at least about 90% sequence identity to a sequence selected from Tables 1-3 linked to one or two XTEN, which may be the same or different, exhibiting at least about 90% sequence identity selected from Table 5. In the foregoing fusion proteins hereinabove described in this paragraph, the GPXTEN fusion protein can further comprise a cleavage sequence from Table 8; the cleavage sequence being located between the GP and the XTEN or between adjacent GP (if more than one GP is included in the GPXTEN). In some cases, the GPXTEN comprising the cleavage sequences will also have one or more spacer sequence amino acids between the GP and the cleavage sequence or the XTEN and the cleavage sequence to facilitate access of the protease; the spacer amino acids comprising any natural amino acid, including glycine and alanine as preferred amino acids. Non-limiting examples of GPXTEN comprising GP, XTEN, cleavage sequence(s) and spacer amino acids are presented in Table 38. However, the invention also contemplates substitution of any of the GP sequences of Tables 1-3 for a GP sequence of Tables 36-38, substitution of any XTEN sequence of Table 5 for an XTEN sequence of Tables 36-38, and substitution of any cleavage sequence of Table 8 for a cleavage sequence of Table 38.

b. Pharmacokinetic Properties of GPXTEN

The invention provides GPXTEN fusion proteins with enhanced pharmacokinetics compared to the GP not linked to XTEN that, when used at the dose determined for the composition by the methods described herein, can achieve a circulating concentration resulting in a pharmacologic effect, yet stay within the safety range for biologically active component of the composition for an extended period of time compared to a comparable dose of the GP not linked to XTEN. In such cases, the GPXTEN remains within the therapeutic window for the fusion protein composition for the extended period of time. As used herein, a “comparable dose” means a dose with an equivalent moles/kg for the active GP pharmacophore that is administered to a subject in a comparable fashion. It will be understood in the art that a “comparable dosage” of GPXTEN fusion protein would represent a greater weight of agent but would have essentially the same mole-equivalents of GP in the dose of the fusion protein and/or would have the same approximate molar concentration relative to the GP.

The pharmacokinetic properties of a GP that can be enhanced by linking a given XTEN to the GP include terminal half-life, area under the curve (AUC), Cmax volume of distribution, and bioavailability providing enhanced utility in the treatment of glucose regulating peptide-related disorders, diseases and related conditions. The GP of the GPXTEN compositions exhibiting enhanced PK properties can be a sequence that exhibits at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a protein sequence selected from Tables 1-3, linked to one or more XTEN that exhibit at least about 80% sequence identity, or alternatively 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a protein sequence selected from Table 5, and can be in a configuration selected from the configurations of Table 7.

As described more fully in the Examples pertaining to pharmacokinetic characteristics of fusion proteins comprising XTEN, it was surprisingly discovered that increasing the length of the XTEN sequence could confer a disproportionate increase in the terminal half-life of a fusion protein comprising the XTEN. Accordingly, the invention provides GPXTEN fusion proteins comprising XTEN wherein the XTEN can be selected to provide a targeted half-life for the GPXTEN composition administered to a subject. In some embodiments, the invention provides monomeric fusion proteins comprising XTEN wherein the XTEN is selected to confer an increase in the terminal half-life for the GPXTEN administered to a subject, compared to the corresponding GP not linked to the fusion protein and administered at a comparable dose, of at least about two-fold longer, or at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about seven-fold, or at least about eight-fold, or at least about nine-fold, or at least about ten-fold, or at least about 15-fold, or at least a 20-fold, or at least a 40-fold, or at least a 80-fold, or at least a 100-fold or greater an increase in terminal half-life compared to the GP not linked to the fusion protein. Exogenously administered exendin-4 has been reported to have a terminal half-life in humans of 2.4 h and glucagon has a half-life of less than 20 minutes, whereas various GPXTEN compositions disclosed herein that have been experimentally administered to various animals species, as described in the Examples, have resulted in terminal half-life values of several hours. Similarly, the GPXTEN fusion proteins can have an increase in AUC of at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about a 100%, or at least about 150%, or at least about 200%, or at least about 300%, or at least about 500%, or at least about 1000%, or at least about a 2000% increase in AUC compared to the corresponding GP not linked to the fusion protein and administered to a subject at a comparable dose. The pharmacokinetic parameters of a GPXTEN can be determined by standard methods involving dosing, the taking of blood samples at times intervals, and the assaying of the protein using ELISA, HPLC, radioassay, or other methods known in the art or as described herein, followed by standard calculations of the data to derive the half-life and other PK parameters.

The invention further provides GPXTEN comprising a first and a second GP molecule, optionally separated by a spacer sequence that may further comprise a cleavage sequence, or separated by a second XTEN sequence. In one embodiment, the GP has less activity when linked to the fusion protein compared to a corresponding GP not linked to the fusion protein. In such case, as illustrated in FIG. 38, the GPXTEN can be designed such that upon administration to a subject, the GP component is gradually released by cleavage of the cleavage sequence(s), whereupon it regains activity or the ability to bind to its target receptor or ligand. Accordingly, the GPXTEN of the foregoing serves as a prodrug or a circulating depot, resulting in a longer terminal half-life compared to GP not linked to the fusion protein.

c. Pharmacology and Pharmaceutical Properties of GPXTEN

The present invention provides GPXTEN compositions comprising GP covalently linked to XTEN that can have enhanced properties compared to GP not linked to XTEN, as well as methods to enhance the therapeutic and/or biologic activity or effect of the respective two GP components of the compositions. In addition, the invention provides GPXTEN compositions with enhanced properties compared to those art-known fusion proteins containing immunoglobulin polypeptide partners, polypeptides of shorter length and/or polypeptide partners with repetitive sequences. In addition, GPXTEN fusion proteins provide significant advantages over chemical conjugates, such as pegylated constructs, notably the fact that recombinant GPXTEN fusion proteins can be made in bacterial cell expression systems, which can reduce time and cost at both the research and development and manufacturing stages of a product, as well as result in a more homogeneous, defined product with less toxicity for both the product and metabolites of the GPXTEN compared to pegylated conjugates.

As therapeutic agents, the GPXTEN may possess a number of advantages over therapeutics not comprising XTEN including one or more of the following non-limiting exemplary enhance properties; increased solubility, increased thermal stability, reduced immunogenicity, increased apparent molecular weight, reduced renal clearance, reduced proteolysis, reduced metabolism, enhanced therapeutic efficiency, a lower effective therapeutic dose, increased bioavailability, increased time between dosages capable of maintain blood levels within the therapeutic window for the GP, a “tailored” rate of absorption, enhanced lyophilization stability, enhanced serum/plasma stability, increased terminal half-life, increased solubility in blood stream, decreased binding by neutralizing antibodies, decreased receptor-mediated clearance, reduced side effects, retention of receptor/ligand binding affinity or receptor/ligand activation, stability to degradation, stability to freeze-thaw, stability to proteases, stability to ubiquitination, ease of administration, compatibility with other pharmaceutical excipients or carriers, persistence in the subject, increased stability in storage (e.g., increased shelf-life), reduced toxicity in an organism or environment and the like. The net effect of the enhanced properties is that the GPXTEN may result in enhanced therapeutic and/or biologic effect or improved patient compliance when administered to a subject with a glucose regulating peptide-related disease or disorder.

In other cases where, where enhancement of the pharmaceutical or physicochemical properties of the GP is desirable, (such as the degree of aqueous solubility or stability), the length and/or the motif family composition of the first and the second XTEN sequences of the first and the second fusion protein may each be selected to confer a different degree of solubility and/or stability on the respective fusion proteins such that the overall pharmaceutical properties of the GPXTEN composition are enhanced. The GPXTEN fusion proteins can be constructed and assayed, using methods described herein, to confirm the physicochemical properties and the XTEN adjusted, as needed, to result in the desired properties. In one embodiment, the XTEN sequence of the GPXTEN is selected such that the fusion protein has an aqueous solubility that is within at least about 25% greater compared to a GP not linked to the fusion protein, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 75%, or at least about 100%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500%, or at least about 1000% greater than the corresponding GP not linked to the fusion protein. In the embodiments hereinabove described in this paragraph, the XTEN of the fusion proteins can have at least about 80% sequence identity, or about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99%, to about 100% sequence identity to an XTEN selected from Table 5.

In one embodiment, the invention provides GPXTEN compositions that can maintain the GP component within a therapeutic window for a greater period of time compared to comparable dosages of the corresponding GP not linked to XTEN. It will be understood in the art that a “comparable dosage” of GPXTEN fusion protein would represent a greater weight of agent but would have the same approximate mole-equivalents of GP in the dose of the fusion protein and/or would have the same approximate molar concentration relative to the GP.

The invention also provides methods to select the XTEN appropriate for conjugation to provide the desired pharmacokinetic properties that, when matched with the selection of dose, enables increased efficacy of the administered composition by maintaining the circulating concentrations of the GP within the therapeutic window for an enhanced period of time. As used herein, “therapeutic window” means that the amount of drug or biologic as a blood or plasma concentration range, which provides efficacy or a desired pharmacologic effect over time for the disease or condition without unacceptable toxicity; the range of the circulating blood concentrations between the minimal amount to achieve any positive therapeutic effect and the maximum amount which results in a response that is the response immediately before toxicity to the subject (at a higher dose or concentration). Additionally, therapeutic window generally encompasses an aspect of time; the maximum and minimum concentration that results in a desired pharmacologic effect over time that does not result in unacceptable toxicity or adverse events. A dosed composition that stays within the therapeutic window for the subject could also be said to be within the “safety range.”

The characteristics of GPXTEN compositions of the invention, including functional characteristics or biologic and pharmacologic activity and parameters that result, may be determined by any suitable screening assay known in the art for measuring the desired characteristic. The invention provides methods to assay the GPXTEN fusion proteins of differing composition or configuration in order to provide GPXTEN with the desired degree of biologic and/or therapeutic activity, as well as safety profile. Specific in vivo and ex vivo biological assays may be used to assess the activity of each configured GPXTEN and/or GP component to be incorporated into GPXTEN, including but not limited to the assays of the Examples, those assays of Table 35, as well as the following assays or other such assays known in the art for assaying the properties and effects of GP. Assays can be conducted that allow determination of binding characteristics of the GPXTEN for GP receptors or a ligand, including binding constant (Kd), EC50 values, as well as their half-life of dissociation of the ligand-receptor complex (T1/2). Binding affinity can be measured, for example, by a competition-type binding assay that detects changes in the ability to specifically bind to a receptor (see, e.g., Examples). Additionally, techniques such as flow cytometry or surface plasmon resonance can be used to detect binding events. The assays may comprise soluble receptor molecules, or may determine the binding to cell-expressed receptors. Such assays may include cell-based assays, including assays for calcium flux, signal transduction, and cell proliferation. Other possible assays may determine receptor binding of expressed polypeptides, wherein the assay may comprise soluble receptor molecules, or may determine the binding to cell-expressed receptors. The binding affinity of a GPXTEN for the target receptors of the corresponding GP can be assayed using binding or competitive binding assays, such as Biacore assays with chip-bound receptors or binding proteins or ELISA assays, as described in U.S. Pat. No. 5,534,617, assays described in the Examples herein, radio-receptor assays, or other assays known in the art. In addition, GP sequence variants (assayed as single components or as GPXTEN fusion proteins) can be compared to the native GP using a competitive ELISA binding assay to determine whether they have the same binding specificity and affinity as the native GP, or some fraction thereof such that they are suitable for inclusion in GPXTEN. Functional assays can include insulin concentrations and/or generation within target cells as a result of exposure to GPXTEN, and/or the resulting stimulatory effects of beta cells, glucose uptake and/or homeostasis, HbA1c concentrations, insulin concentrations, stimulated C peptide, fasting plasma glucose (FPG), serum cytokine levels, CRP levels, insulin secretion and Insulin-sensitivity index derived from an oral glucose tolerance test (OGTT), as well as body weight, food consumption, and other accepted diabetic markers known in the art would be suitable parameters to assess the activity of GP for inclusion in the GPXTEN fusion protein or the resulting GPXTEN.

Dose optimization is important for all drugs, especially for those with a narrow therapeutic window. For example, a standardized single dose of GP for all patients presenting with a diverse symptoms or abnormal clinical parameters may not always be effective. A consideration of these factors is well within the purview of the ordinarily skilled clinician for the purpose of determining the therapeutically or pharmacologically effective amount of the GPXTEN, versus that amount that would result in unacceptable toxicity and place it outside of the safety range, or insufficient potency such that clinical improvement is not achieved.

In many cases, the therapeutic window for GP in subjects of different ages or degree of disease have been established and are available in published literature or are stated on the drug label for approved products containing the GP. In other cases, the therapeutic window can be established. The methods for establishing the therapeutic window for a given composition are known to those of skill in the art (see, e.g., Goodman & Gilman's The Pharmacological Basis of Therapeutics, 11th Edition, McGraw-Hill (2005)). For example, by using dose-escalation studies in subjects with the target disease or disorder to determine efficacy or a desirable pharmacologic effect, appearance of adverse events, and determination of circulating blood levels, the therapeutic window for a given subject or population of subjects can be determined for a given drug or biologic, or combinations of biologics or drugs. The dose escalation studies can evaluate the activity of a GPXTEN through metabolic studies in a subject or group of subjects that monitor physiological or biochemical parameters, as known in the art or as described herein for one or more parameters associated with the metabolic disease or disorder, or clinical parameters associated with a beneficial outcome for the particular indication, together with observations and/or measured parameters to determine the no effect dose, adverse events, maximum tolerated dose and the like, together with measurement of pharmacokinetic parameters that establish the determined or derived circulating blood levels. The results can then be correlated with the dose administered and the blood concentrations of the therapeutic that are coincident with the foregoing determined parameters or effect levels. By these methods, a range of doses and blood concentrations can be correlated to the minimum effective dose as well as the maximum dose and blood concentration at which a desired effect occurs and above which toxicity occurs, thereby establishing the therapeutic window for the dosed therapeutic. Blood concentrations of the fusion protein (or as measured by the GP component) above the maximum would be considered outside the therapeutic window or safety range. Thus, by the foregoing methods, a Cmin blood level would be established, below which the GPXTEN fusion protein would not have the desired pharmacologic effect, and a Cmax blood level would be established that would represent the highest circulating concentration before reaching a concentration that would elicit unacceptable side effects, toxicity or adverse events, placing it outside the safety range for the GPXTEN. With such concentrations established, the frequency of dosing and the dosage can be further refined by measurement of the Cmax and Cmin to provide the appropriate dose and dose frequency to keep the fusion protein(s) within the therapeutic window. One of skill in the art can, by the means disclosed herein or by other methods known in the art, confirm that the administered GPXTEN remains in the therapeutic window for the desired interval or requires adjustment in dose or length or sequence of XTEN. Further, the determination of the appropriate dose and dose frequency to keep the GPXTEN within the therapeutic window establishes the therapeutically effective dose regimen; the schedule for administration of multiple consecutive doses using a therapeutically effective dose of the fusion protein to a subject in need thereof resulting in consecutive Cmax peaks and/or Cmin troughs that remain within the therapeutic window and results in an improvement in at least one measured parameter relevant for the target disease, disorder or condition. In some cases, the GPXTEN administered at an appropriate dose to a subject may result in blood concentrations of the GPXTEN fusion protein that remains within the therapeutic window for a period at least about two-fold longer compared to the corresponding GP not linked to XTEN and administered at a comparable dose; alternatively at least about three-fold longer; alternatively at least about four-fold longer; alternatively at least about five-fold longer; alternatively at least about six-fold longer; alternatively at least about seven-fold longer; alternatively at least about eight-fold longer; alternatively at least about nine-fold longer or at least about ten-fold longer or greater compared to the corresponding GP not linked to XTEN and administered at a comparable dose. As used herein, an “appropriate dose” means a dose of a drug or biologic that, when administered to a subject, would result in a desirable therapeutic or pharmacologic effect and a blood concentration within the therapeutic window.

In one embodiment, the GPXTEN administered at a therapeutically effective dose regimen results in a gain in time of at least about three-fold longer; alternatively at least about four-fold longer; alternatively at least about five-fold longer; alternatively at least about six-fold longer; alternatively at least about seven-fold longer; alternatively at least about eight-fold longer; alternatively at least about nine-fold longer or at least about ten-fold longer between at least two consecutive Cmax peaks and/or Cmin troughs for blood levels of the fusion protein compared to the corresponding biologically active protein of the fusion protein not linked to the fusion protein and administered at a comparable dose regimen to a subject. In another embodiment, the GPXTEN administered at a therapeutically effective dose regimen results in a comparable improvement in one, or two, or three or more measured parameter using less frequent dosing or a lower total dosage in moles of the fusion protein of the pharmaceutical composition compared to the corresponding biologically active protein component(s) not linked to the fusion protein and administered to a subject using a therapeutically effective dose regimen for the GP. The measured parameters may include any of the clinical, biochemical, or physiological parameters disclosed herein, or others known in the art for assessing subjects with glucose- or insulin-related disorders.

The activity of the GPXTEN compositions of the invention, including functional characteristics or biologic and pharmacologic activity and parameters that result, may be determined by any suitable screening assay known in the art for measuring the desired characteristic. The activity and structure of the GPXTEN polypeptides comprising GP components may be assessed by measuring parameters described herein, by use of one or more assays selected from Table 35, assays of the Examples, or by methods known in the art to ascertain the degree of solubility, structure and retention of biologic activity. Assays can be conducted that allow determination of binding characteristics of the GPXTEN for GP receptors or a ligand, including binding constant (Kd), EC50 values, as well as their half-life of dissociation of the ligand-receptor complex (T1/2). Binding affinity can be measured, for example, by a competition-type binding assay that detects changes in the ability to specifically bind to a receptor or ligand (see, e.g., Examples). Additionally, techniques such as flow cytometry or surface plasmon resonance can be used to detect binding events. The assays may comprise soluble receptor molecules, or may determine the binding to cell-expressed receptors. Such assays may include cell-based assays, including assays for proliferation, cell death, apoptosis and cell migration. Other possible assays may determine receptor binding of expressed polypeptides, wherein the assay may comprise soluble receptor molecules, or may determine the binding to cell-expressed receptors. The binding affinity of a GPXTEN for the target receptors or ligands of the corresponding GP can be assayed using binding or competitive binding assays, such as Biacore assays with chip-bound receptors or binding proteins or ELISA assays, as described in U.S. Pat. No. 5,534,617, assays described in the Examples herein, radio-receptor assays, or other assays known in the art. In addition, GP sequence variants (assayed as single components or as GPXTEN fusion proteins) can be compared to the native GP using a competitive ELISA binding assay to determine whether they have the same binding specificity and affinity as the native GP, or some fraction thereof such that they are suitable for inclusion in GPXTEN.

The invention provides isolated GPXTEN in which the binding affinity for GP target receptors or ligands by the GPXTEN can be at least about 10%, or at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95%, or at least about 99%, or at least about 100% or more of the affinity of a native GP not bound to XTEN for the target receptor or ligand. In some cases, the binding affinity Kd between the subject GPXTEN and a native receptor or ligand of the GPXTEN is at least about 10−4M, alternatively at least about 10−5M, alternatively at least about 10−6M, or at least about 10−7M, or at least about 10−8M, or at least about 10−9M of the affinity between the GPXTEN and a native receptor or ligand.

In other cases, the invention provides isolated GPXTEN fusion proteins specifically designed to have reduced binding affinity to the GP receptor. In one em, such as fusion proteins comprising an XTEN fused to the C-terminus of the GP component. In some cases, the GPXTEN can be configured to have reduced binding affinity wherein the binding affinity is assessed by an in vitro cell receptor binding assay wherein the binding is reduced by about 10%, or about 20%, or about 40%, or about 60%, or about 80%, or about 90% compared to native GP. In other cases, the GPXTEN can be configured to have reduced binding affinity wherein the binding affinity is assessed by signal transduction wherein the GPXTEN fusion protein elicits less than about 80%, or less than about 60%, or less than about 40%, or less than about 20%, or less than 10%, or less than about 5% activation of the signaling pathways of the cell with bound GPXTEN in comparison to those evoked by the native GP ligand. In the foregoing cases, the binding affinity is “substantially reduced.” Non-limiting examples of specific constructs of such GPXTEN with reduced binding affinity include fusion proteins with at least about 80% sequence identity, or at least about 85% sequence identity, or at least about 90% sequence identity, or at least about 95% sequence identity, or at least about 97% sequence identity, or at least about 99% sequence identity to GP fusion proteins selected from AE912-GP-AE144, AE912-GP-AF144, AE912-GP-AE288, AM923-GP-AE144, AM923-GP-AF144, AM923-GP-AE288.

In some cases, the GPXTEN fusion proteins of the invention retain at least about 10%, or about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% percent of the biological activity of the corresponding GP not linked to the fusion protein with regard to an in vitro biologic activity or an in vivo pharmacologic effect known or associated with the use of the native GP in the treatment and prevention of metabolic conditions and disorders. Non-limiting examples of activities or pharmacologic effects that can be assayed to assess the retained activity of the GPXTEN fusion proteins include including assays for calcium flux and/or signal transduction in response to receptor binding, insulin concentrations and/or generation within target cells as a result of exposure to GPXTEN, and/or the resulting stimulatory effects of beta cells, glucose uptake and/or homeostasis, HbA1c concentrations, insulin concentrations, stimulated C peptide, fasting plasma glucose (FPG), serum cytokine levels, CRP levels, insulin secretion and Insulin-sensitivity index derived from an oral glucose tolerance test (OGTT), as well as body weight, food consumption, and other accepted diabetic markers known in the art would be suitable parameters to assess the activity of GP for inclusion in the GPXTEN fusion protein or the resulting GPXTEN.

In some cases of the foregoing embodiment, the activity of the GP component may be manifest by the intact GPXTEN fusion protein, while in other cases the activity of the GP component would be primarily manifested upon cleavage and release of the GP from the fusion protein by action of a protease that acts on a cleavage sequence incorporated into the GPXTEN fusion protein. In the foregoing, the GPXTEN can be designed to reduce the binding affinity of the GP component for the receptor or ligand when linked to the XTEN but have increased affinity when released from XTEN through the cleavage of cleavage sequence(s) incorporated into the GPXTEN sequence, as described more fully above.

In other cases, the GPXTEN can be designed to reduce the binding affinity of the GP component to the GP receptor to increase the terminal half-life of GPXTEN administered to a subject by reducing receptor-mediated clearance; e.g., by adding an XTEN to the C-terminus of the GP component of the fusion protein. In other cases, the GPXTEN are designed to reduce the binding affinity of the GP component to the GP receptor to reduce toxicity or side effects due to the administered composition.

Accordingly, the invention provides a method for increasing the terminal half-life of a GPXTEN by producing a single-chain fusion protein construct with a specific N- to C-terminus configuration of the components comprising at least a first GP and a first and a second XTEN, wherein the fusion protein in a first N- to C-terminus configuration of the GP and XTEN components has reduced receptor-mediated clearance (RMC) and a corresponding increase in terminal half-life compared to a GPXTEN in a second N- to C-terminus configuration. In one embodiment of the foregoing, the GPXTEN is configured, N- to C-terminus as XTEN-GP-XTEN, which has reduced receptor binding compared to a GPXTEN configures, N- to C-terminus XTEN-GP. In another embodiment of the foregoing, the GPXTEN is configured GP-XTEN. In the foregoing embodiments, the two XTEN molecules can be identical or they can be of a different sequence composition or length. Non-limiting examples of the foregoing embodiment with two XTEN linked to a single GP include the constructs AE912-GP-AE144, AE912-GP-AE288, AE864-GP-AE144, AM923-GP-AE144, and AM923-GP-AE288. The invention contemplates other such constructs in which a GP from Tables 1-3 and XTEN from Table 5 are substituted for the respective components of the foregoing examples, and can be produced, for example, in a configuration from Table 7 such that the construct has reduced receptor mediated clearance compared to an alternate configuration of the respective components. In some cases, the foregoing method for increasing the terminal half-life provides configured GPXTEN that can result in an increase in the terminal half-life of at least about 50%, or about 75%, or about 100%, or about 150%, or about 200%, or about 300%, or about 400% or more compared to the half-life of a GPXTEN in a second configuration where receptor binding is not reduced. The invention takes advantage of the fact that certain ligands wherein reduced binding affinity to a receptor, either as a result of a decreased on-rate or an increased off-rate, may be effected by the obstruction of either the N- or C-terminus, and using that terminus as the linkage to another polypeptide of the composition, whether another molecule of a GP, an XTEN, or a spacer sequence results in the reduced binding affinity. The choice of the particular configuration of the GPXTEN fusion protein can reduce the degree of binding affinity to the receptor such that a reduced rate of receptor-mediated clearance can be achieved. Generally, activation of the receptor is coupled to RMC such that binding of a polypeptide to its receptor without activation does not lead to RMC, while activation of the receptor leads to RMC. However, in some cases, particularly where the ligand has an increased off rate, the ligand may nevertheless be able to bind sufficiently to initiate cell signaling without triggering receptor mediated clearance, with the net result that the GPXTEN remains bioavailable. In such cases, the configured GPXTEN has an increased half-life compared to those configurations that lead to a higher degree of RMC.

In cases where a reduction in binding affinity to a glucose regulating peptide receptor is desired in order to reduce receptor-mediated clearance but retention of at least a portion of the biological activity is desired, it will be clear that sufficient binding affinity to obtain the desired receptor activation must nevertheless be maintained e.g., by initiation of signal transduction. Thus, in one embodiment, the invention provides a GPXTEN configured such that the binding affinity of the GPXTEN for a target receptor is in the range of about 0.01%-40%, or about 0.1%-30%, or about 1%-20% of the binding affinity compared to a corresponding GPXTEN in a configuration wherein the binding affinity is not reduced. The binding affinity of the configured BXTEN is thus preferably reduced by at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95%, or at least about 99%, or at least about 99.99% as compared to the binding affinity of a corresponding GPXTEN in a configuration wherein the binding affinity of the GP component to the target receptor is not reduced or compared to the GP not linked to the fusion protein, determined under comparable conditions. Expressed differently, the GP component of the configured GPXTEN may have a binding affinity that is as small as about 0.01%, or at least about 0.1%, or at least about 1%, or at least about 2%, or at least about 3%, or at least about 4%, or at least about 5%, or at least about 10%, or at least about 20%, or at least about 30%, or at least 40% of that of the corresponding GP component of a GPXTEN in a configuration wherein the binding affinity of the GP component is not reduced. In the foregoing embodiments hereinabove described in this paragraph, the binding affinity of the configured GPXTEN for the target receptor would be “substantially reduced” compared to a corresponding native GP or a GPXTEN with a configuration in which the binding affinity of the corresponding GP component is not reduced. Accordingly, the present invention provides compositions and methods to produce compositions with reduced RMC by configuring the GPXTEN, examples of which were provided above, so as to be able to bind and activate a sufficient number of receptors to obtain a desired in vivo biological response yet avoid activation of more receptors than is required for obtaining such response. In the foregoing embodiments hereinabove described in this paragraph, the increased half-life can permit higher dosages and reduced frequency of dosing compared to GP not linked to XTEN or compared to GPXTEN configurations wherein the GP component retains sufficient biological or pharmacological activity to result in a composition with clinical efficacy maintained despite reduced dosing frequency.

VI) Uses of the Compositions of the Present Invention

In another aspect, the invention provides a method for achieving a beneficial effect in a disease, disorder or condition mediated by GP. The present invention addresses disadvantages and/or limitations of GP that have a relatively short terminal half-life and/or a narrow therapeutic window between the minimum effective dose and the maximum tolerated dose.

Most processes involved in glucose homoeostasis are regulated by multiple peptides and hormones, and such peptides and hormones, as well as analogues thereof, have found utility in the treatment of glucose regulating peptide-related diseases, disorders and conditions. However, the use of commercially-available glucose regulating peptides, has met with less than optimal success in the management of subjects afflicted with such diseases, disorders and conditions. In particular, dose optimization and frequency of dosing is important for peptide and hormone biologics used in the treatment of glucose regulating peptide-related diseases and disorders. The fact that many glucose regulating peptides have a short half-life, necessitates frequent dosing in order to achieve clinical benefit, which results in difficulties in the management of such patients.

In one embodiment, the invention provides a method for achieving a beneficial affect in a subject with a glucose regulating peptide-related disease, disorder or condition comprising the step of administering to the subject a therapeutically- or prophylactically-effective amount of a GPXTEN wherein said administration results in the improvement of one or more biochemical or physiological parameters or clinical endpoints associated with a glucose regulating peptide-related disease, disorder or condition. The effective amount can produce a beneficial effect in helping to treat (e.g., cure or reduce the severity) or prevent (e.g., reduce the likelihood of onset or severity) a glucose regulating peptide-related disease, disorder or condition. In some cases, the method for achieving a beneficial effect can include administering a therapeutically effective amount of a GPXTEN fusion protein composition to treat a subject with a glucose regulating peptide-related disease, disorder, or condition, including, but not limited to, juvenile diabetes, type I diabetes, type II diabetes, obesity, acute hypoglycemia, acute hyperglycemia, nocturnal hypoglycemia, chronic hyperglycemia, glucagonomas, secretory disorders of the airway, arthritis, osteoporosis, central nervous system disease, restenosis, neurodegenerative disease, renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, hypertension, and disorders wherein the reduction of food intake is desired, stroke, irritable bowel syndrome, myocardial infarction (e.g., reducing the morbidity and/or mortality associated therewith), stroke, acute coronary syndrome (e.g., characterized by an absence of Q-wave) myocardial infarction, post-surgical catabolic changes, hibernating myocardium or diabetic cardiomyopathy, insufficient urinary sodium excretion, excessive urinary potassium concentration, conditions or disorders associated with toxic hypervolemia, (e.g., renal failure, congestive heart failure, nephrotic syndrome, cirrhosis, pulmonary edema, and hypertension), polycystic ovary syndrome, respiratory distress, nephropathy, left ventricular systolic dysfunction, (e.g., with abnormal left ventricular ejection fraction), gastrointestinal disorders such as diarrhea, postoperative dumping syndrome and irritable bowel syndrome, (i.e., via inhibition of antro-duodenal motility), critical illness polyneuropathy (CIPN), dyslipidemia, organ tissue injury caused by reperfusion of blood flow following ischemia, and coronary heart disease risk factor (CHDRF) syndrome, and any other indication for which the unmodified glucose-regulating peptide (e.g. exendin-4, GLP-1 or glucagon) is utilized, or any other indication for which GP can be utilized (but for which endogenous glucose regulating peptide levels in a subject are not necessarily deficient).

In another embodiment, the invention provides a method of stimulating insulin secretion in subjects with a glucose regulating peptide-related disease, disorder or deficiency. The method comprises the step of administering therapeutically effective amount of GPXTEN to a subject that results in the increased blood levels and/or duration in increased blood levels of insulin compared to a subject receiving a GP not linked to an XTEN and administered at a comparable dose. In some cases, the increase in insulin secretion and/or area under the curve is at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 75%, or at least about 100%, or at least about 200%, or at least about 300% compared to a subject receiving a GP not linked to an XTEN and administered at a comparable dose.

As a result of the enhanced PK parameters of GPXTEN, as described herein, the GP may be administered using longer intervals between doses compared to the corresponding GP not linked to XTEN to prevent, treat, alleviate, reverse or ameliorate symptoms or clinical abnormalities of the glucose regulating peptide-related disease, disorder or condition or prolong the survival of the subject being treated.

The methods of the invention may include administration of consecutive doses of a therapeutically effective amount of the GPXTEN for a period of time sufficient to achieve and/or maintain the desired parameter or clinical effect, and such consecutive doses of a therapeutically effective amount establishes the therapeutically effective dose regimen for the GPXTEN; i.e., the schedule for consecutively administered doses of the fusion protein composition, wherein the doses are given in therapeutically effective amounts to result in a sustained beneficial effect on any clinical sign or symptom, aspect, measured parameter or characteristic of a metabolic disease state or condition, including, but not limited to, those described herein. In one embodiment, the method comprises administering a therapeutically-effective amount of a pharmaceutical composition comprising a GPXTEN fusion protein composition comprising a GP linked to an XTEN sequence(s) and at least one pharmaceutically acceptable carrier to a subject in need thereof that results in greater improvement in at least one parameter, physiologic condition, or clinical outcome mediated by the GP component(s) (non-limiting examples of which are described above) compared to the effect mediated by administration of a pharmaceutical composition comprising a GP not linked to XTEN and administered at a comparable dose. In one embodiment, the pharmaceutical composition is administered at a therapeutically effective dose. In another embodiment, the pharmaceutical composition is administered using multiple consecutive doses using a therapeutically effective dose regimen (as defined herein) for the length of the dosing period.

A therapeutically effective amount of the GPXTEN may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the antibody or antibody portion to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the GPXTEN are outweighed by the therapeutically beneficial effects. A prophylactically effective amount refers to an amount of GPXTEN required for the period of time necessary to achieve the desired prophylactic result.

For the inventive methods, longer acting GPXTEN compositions are preferred, so as to improve patient convenience, to increase the interval between doses and to reduce the amount of drug required to achieve a sustained effect. In one embodiment, a method of treatment comprises administration of a therapeutically effective dose of a GPXTEN to a subject in need thereof that results in a gain in time spent within a therapeutic window established for the fusion protein of the composition compared to the corresponding GP component(s) not linked to the fusion protein and administered at a comparable dose to a subject. In some cases, the gain in time spent within the therapeutic window is at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about eight-fold, or at least about 10-fold, or at least about 20-fold, or at least about 40-fold compared to the corresponding GP component not linked to the fusion protein and administered at a comparable dose to a subject. The methods further provide that administration of multiple consecutive doses of a GPXTEN administered using a therapeutically effective dose regimen to a subject in need thereof can result in a gain in time between consecutive Cmax peaks and/or Cmin troughs for blood levels of the fusion protein compared to the corresponding GP not linked to the fusion protein and administered using a dose regimen established for that GP. In the foregoing embodiment, the gain in time spent between consecutive Cmax peaks and/or Cmin troughs can be at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold, or at least about eight-fold, or at least about 10-fold, or at least about 20-fold, or at least about 40-fold compared to the corresponding GP component not linked to the fusion protein and administered using a dose regimen established for that GP. In the embodiments hereinabove described in this paragraph the administration of the fusion protein can result in an improvement in at least one of the parameters (disclosed herein as being useful for assessing the subject diseases, conditions or disorders) using a lower unit dose in moles of fusion protein compared to the corresponding GP component not linked to the fusion protein and administered at a comparable unit dose or dose regimen to a subject.

The method of treatment comprises administration of a GPXTEN using a therapeutically effective dose regimen to effect improvements in one or more parameters associated with glucose regulating peptide diseases, disorders or conditions. In some cases, administration of the GPXTEN to a subject can result in an improvement in one or more of the biochemical, physiologic, or clinical parameters that is of greater magnitude than that of the corresponding GP component not linked to XTEN, determined using the same assay or based on a measured clinical parameter. In other cases, administration of the GPXTEN to a subject can result in activity in one or more of the biochemical, physiologic, or clinical parameters that is of longer duration than the activity of one of the single GP components not linked to XTEN, determined using that same assay or based on a measured clinical parameter. In one embodiment of the foregoing, the administration of the GPXTEN to a subject can result in an improvement in peak concentrations and area under the curve of blood GP levels of at least about 10%, or about 20%, or about 30%, or about 40%, or about 50% or more in the subject compared to a comparable dose of GP not linked to XTEN administered to a subject. In another embodiment of the foregoing, the administration of the GPXTEN to a subject can result in an improvement in one or more parameters selected from, but not limited to HbA1c concentrations, insulin concentrations, stimulated C peptide, fasting plasma glucose (FPG), serum cytokine levels, CRP levels, insulin secretion and Insulin-sensitivity index derived from an oral glucose tolerance test (OGTT), body weight, and food consumption.

The invention further contemplates that GPXTEN used in accordance with the methods provided herein may be administered in conjunction with other treatment methods and pharmaceutical compositions useful for treating glucose regulating peptide-related diseases, disorders, and conditions, or conditions for which glucose regulating peptide is adjunctive therapy; e.g., insulin resistance and poor glycemic control. Such compositions, may include for example, DPP-IV inhibitors, insulin, insulin analogues, PPAR gamma agonists, dual-acting PPAR agonists, GLP-1 agonists or analogues, PTP1B inhibitors, SGLT inhibitors, insulin secretagogues, RXR agonists, glycogen synthase kinase-3 inhibitors, insulin sensitizers, immune modulators, beta-3 adrenergic receptor agonists, Pan-PPAR agonists, 11beta-HSD1 inhibitors, biguanides, alpha-glucosidase inhibitors, meglitinides, thiazolidinediones, sulfonylureas and other diabetes medicants known in the art, or anti-hypertensive drugs, calcium channel blockers, and related products. In some cases, the administration of a GPXTEN may permit use of lower dosages of the co-administered pharmaceutical composition to achieve a comparable clinical effect or measured parameter for the disease, disorder or condition in the subject.

In another aspect, the invention provides a method of designing the GPXTEN compositions with desired pharmacologic or pharmaceutical properties. The GPXTEN fusion proteins are designed and prepared with various objectives in mind (compared to the GP components not linked to the fusion protein), including improving the therapeutic efficacy for the treatment of glucose regulating peptide-related diseases, disorders, and conditions, enhancing the pharmacokinetic characteristics of the fusion proteins compared to the GP, lowering the dose or frequency of dosing required to achieve a pharmacologic effect, enhancing the pharmaceutical properties, and to enhance the ability of the GP components to remain within the therapeutic window for an extended period of time.

In general, the steps in the design and production of the fusion proteins and the inventive compositions may, as illustrated in FIGS. 4-6, include: (1) the selection of GPs (e.g., native proteins, analogs or derivatives with activity) to treat the particular disease, disorder or condition; (2) selecting the XTEN that will confer the desired PK and physicochemical characteristics on the resulting GPXTEN (e.g., the administration of the composition to a subject results in the fusion protein being maintained within the therapeutic window for a greater period compared to GP not linked to XTEN); (3) establishing a desired N- to C-terminus configuration of the GPXTEN to achieve the desired efficacy or PK parameters; (4) establishing the design of the expression vector encoding the configured GPXTEN; (5) transforming a suitable host with the expression vector; and (6) expression and recovery of the resultant fusion protein. For those GPXTEN for which an increase in half-life (greater than 24 h) or an increased period of time spent within a therapeutic window is desired, the XTEN chosen for incorporation will generally have at least about 500, or about 576, or about 864, or about 875, or about 912, or about 923 amino acid residues where a single XTEN is to be incorporated into the GPXTEN. In another embodiment, the GPXTEN can comprise a first XTEN of the foregoing lengths, and a second XTEN of about 144, or about 288, or about 576, or about 864, or about 875, or about 912, or about 923 amino acid residues.

In other cases, where in increase in half-life is not required, but an increase in a pharmaceutical property (e.g., solubility) is desired, a GPXTEN can be designed to include XTEN of shorter lengths. In some embodiments of the foregoing, the GPXTEN can comprise a GP linked to an XTEN having at least about 24, or about 36, or about 48, or about 60, or about 72, or about 84, or about 96 amino acid residues, in which the solubility of the fusion protein under physiologic conditions is at least three-fold greater than the corresponding GP not linked to XTEN, or alternatively, at least four-fold, or five-fold, or six-fold, or seven-fold, or eight-fold, or nine-fold, or at least 10-fold, or at least 20-fold, or at least 30-fold, or at least 50-fold, or at least 60-fold or greater than GP not linked to XTEN. In one embodiment of the foregoing, the GP is glucagon.

In another aspect, the invention provides methods of making GPXTEN compositions to improve ease of manufacture, result in increased stability, increased water solubility, and/or ease of formulation, as compared to the native GP. In one embodiment, the invention includes a method of increasing the water solubility of a GP comprising the step of linking the GP to one or more XTEN such that a higher concentration in soluble form of the resulting GPXTEN can be achieved, under physiologic conditions, compared to the GP in an un-fused state. Factors that contribute to the property of XTEN to confer increased water solubility of GPs when incorporated into a fusion protein include the high solubility of the XTEN fusion partner and the low degree of self-aggregation between molecules of XTEN in solution. In some embodiments, the method results in a GPXTEN fusion protein wherein the water solubility is at least about 20%, or at least about 30% greater, or at least about 50% greater, or at least about 75% greater, or at least about 90% greater, or at least about 100% greater, or at least about 150% greater, or at least about 200% greater, or at least about 400% greater, or at least about 600% greater, or at least about 800% greater, or at least about 1000% greater, or at least about 2000% greater, or at least about 4000% greater, or at least about 6000% greater under physiologic conditions, compared to the un-fused GP.

In another embodiment, the invention includes a method of enhancing the shelf-life of a GP comprising the step of linking the GP with one or more XTEN selected such that the shelf-life of the resulting GPXTEN is extended compared to the GP in an un-fused state. As used herein, shelf-life refers to the period of time over which the functional activity of a GP or GPXTEN that is in solution or in some other storage formulation remains stable without undue loss of activity. As used herein, “functional activity” refers to a pharmacologic effect or biological activity, such as the ability to bind a receptor or ligand, or an enzymatic activity, or to display one or more known functional activities associated with a GP, as known in the art. A GP that degrades or aggregates generally has reduced functional activity or reduced bioavailability compared to one that remains in solution. Factors that contribute to the ability of the method to extend the shelf life of GPs when incorporated into a fusion protein include the increased water solubility, reduced self-aggregation in solution, and increased heat stability of the XTEN fusion partner. In particular, the low tendency of XTEN to aggregate facilitates methods of formulating pharmaceutical preparations containing higher drug concentrations of GPs, and the heat-stability of XTEN contributes to the property of GPXTEN fusion proteins to remain soluble and functionally active for extended periods. In one embodiment, the method results in GPXTEN fusion proteins with “prolonged” or “extended” shelf-life that exhibit greater activity relative to a standard that has been subjected to the same storage and handling conditions. The standard may be the un-fused full-length GP. In one embodiment, the method includes the step of formulating the isolated GPXTEN with one or more pharmaceutically acceptable excipients that enhance the ability of the XTEN to retain its unstructured conformation and for the GPXTEN to remain soluble in the formulation for a time that is greater than that of the corresponding un-fused GP. In one embodiment, the method comprises linking a GP to one or more XTEN to create a GPXTEN fusion protein results in a solution that retains greater than about 100% of the functional activity, or greater than about 105%, 110%, 120%, 130%, 150% or 200% of the functional activity of a standard when compared at a given time point and when subjected to the same storage and handling conditions as the standard, thereby enhancing its shelf-life.

Shelf-life may also be assessed in terms of functional activity remaining after storage, normalized to functional activity when storage began. GPXTEN fusion proteins of the invention with prolonged or extended shelf-life as exhibited by prolonged or extended functional activity may retain about 50% more functional activity, or about 60%, 70%, 80%, or 90% more of the functional activity of the equivalent GP not linked to XTEN when subjected to the same conditions for the same period of time. For example, a GPXTEN fusion protein of the invention comprising exendin-4 fused to one or more XTEN sequences may retain about 80% or more of its original activity in solution for periods of up to 2 weeks, or 4 weeks, or 6 weeks or longer under various temperature conditions. In some embodiments, the GPXTEN retains at least about 50%, or about 60%, or at least about 70%, or at least about 80%, and most preferably at least about 90% or more of its original activity in solution when heated at 80° C. for 10 min. In other embodiments, the GPXTEN retains at least about 50%, preferably at least about 60%, or at least about 70%, or at least about 80%, or alternatively at least about 90% or more of its original activity in solution when heated or maintained at 37° C. for about 7 days. In another embodiment, GPXTEN fusion protein retains at least about 80% or more of its functional activity after exposure to a temperature of about 30° C. to about 70° C. over a period of time of about one hour to about 18 hours. In the foregoing embodiments hereinabove described in this paragraph, the retained activity of the GPXTEN would be at least about two-fold, or at least about three-fold, or at least about four-fold, or at least about five-fold, or at least about six-fold greater at a given time point than that of the corresponding GP not linked to the fusion protein.

VII) The Nucleic Acids Sequences of the Invention

The present invention provides isolated polynucleic acids encoding GPXTEN chimeric fusion proteins and sequences complementary to polynucleic acid molecules encoding GPXTEN chimeric fusion proteins, including homologous variants thereof. In another aspect, the invention encompasses methods to produce polynucleic acids encoding GPXTEN chimeric fusion proteins and sequences complementary to polynucleic acid molecules encoding GPXTEN chimeric fusion protein, including homologous variants thereof. In general, and as illustrated in FIGS. 4-6, the methods of producing a polynucleotide sequence coding for a GPXTEN fusion protein and expressing the resulting gene product include assembling nucleotides encoding GP and XTEN, ligating the components in frame, incorporating the encoding gene into an expression vector appropriate for and that can be recognized by a host cell, transforming the appropriate host cell with the expression vector, and culturing the host cell under conditions causing or permitting the fusion protein to be expressed in the transformed host cell, thereby producing the biologically-active GPXTEN polypeptide, which can be recovered as an isolated fusion protein by standard protein purification methods known in the art. Standard recombinant techniques in molecular biology can be used to make the polynucleotides and expression vectors of the present invention, and can be applied in the methods to create the polynucleotides, genes and expression vectors encoding the GPXTEN disclosed herein.

In accordance with the invention, nucleic acid sequences that encode GPXTEN (or its complement) may be used to generate recombinant DNA molecules that direct the expression of GPXTEN fusion proteins in appropriate host cells. Several cloning strategies are envisioned to be suitable for performing the present invention, many of which can be used to generate a construct that comprises a gene coding for a fusion protein of the GPXTEN composition of the present invention, or its complement. In some cases, the cloning strategy would be used to create a gene that encodes a monomeric GPXTEN that comprises at least a first GP and at least a first XTEN polypeptide, or their complement. In one embodiment of the foregoing, the gene would comprise a sequence encoding a GP or sequence variant. In other cases, the cloning strategy would be used to create a gene that encodes a monomeric GPXTEN that comprises nucleotides encoding at least a first molecule of GP or its complement and a first and at least a second XTEN or their complement that would be used to transform a host cell for expression of the fusion protein of the GPXTEN composition. In the foregoing embodiments hereinabove described in this paragraph, the genes can further comprise nucleotides encoding spacer sequences that may also encode cleavage sequence(s).

In designing a desired XTEN sequences, it was discovered that the non-repetitive nature of the XTEN of the inventive compositions can be achieved despite use of a “building block” molecular approach in the creation of the XTEN-encoding sequences. This was achieved by the use of a library of polynucleotides encoding peptide sequence motifs, described above, that are then ligated and/or multimerized to create the genes encoding the XTEN sequences (see FIGS. 4 and 5 and Examples). Thus, while the XTEN(s) of the expressed fusion protein may consist of multiple units of as few as four different sequence motifs, because the motifs themselves consist of non-repetitive amino acid sequences, the overall XTEN sequence is rendered non-repetitive. Accordingly, in one embodiment, the XTEN-encoding polynucleotides comprise multiple polynucleotides that encode non-repetitive sequences, or motifs, operably linked in frame and in which the resulting expressed XTEN amino acid sequences are non-repetitive.

In one approach, a construct is first prepared containing the DNA sequence corresponding to GPXTEN fusion protein. DNA encoding the GP of the compositions may be obtained from a cDNA library prepared using standard methods from tissue or isolated cells believed to possess GP mRNA and to express it at a detectable level. Libraries can be screened with probes containing, for example, about 20 to 100 bases designed to identify the GP gene of interest by hybridization using conventional molecular biology techniques. The best candidates for probes are those that represent sequences that are highly homologous for the given glucose regulating peptide, and should be of sufficient length and sufficiently unambiguous that false positives are minimized, but may be degenerate at one or more positions. If necessary, the coding sequence can be obtained using conventional primer extension procedures as described in Sambrook, et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. One can then use polymerase chain reaction (PCR) methodology to amplify the target DNA or RNA coding sequence to obtain sufficient material for the preparation of the GPXTEN constructs containing the GP gene(s). Assays can then be conducted to confirm that hybridizing full-length genes are the desired GP gene(s). By these conventional methods, DNA can be conveniently obtained from a cDNA library prepared from such sources. The GP encoding gene(s) may also be obtained from a genomic library or created by standard synthetic procedures known in the art (e.g., automated nucleic acid synthesis using, for example one of the methods described in Engels et al. (Agnew. Chem. Int. Ed. Engl., 28:716-734 1989!)), using DNA sequences obtained from publicly available databases, patents, or literature references. Such procedures are well known in the art and well described in the scientific and patent literature. For example, sequences can be obtained from Chemical Abstracts Services (CAS) Registry Numbers (published by the American Chemical Society) and/or GenBank Accession Numbers (e.g., Locus ID, NP_XXXXX, and XP_XXXXX) Model Protein identifiers available through the National Center for Biotechnology Information (NCBI) webpage, available on the world wide web at ncbi.nlm.nih.gov that correspond to entries in the CAS Registry or GenBank database that contain an amino acid sequence of the protein of interest or of a fragment or variant of the protein. For such sequence identifiers provided herein, the summary pages associated with each of these CAS and GenBank and GenSeq Accession Numbers as well as the cited journal publications (e.g., PubMedID number (PMID)) are each incorporated by reference in their entireties, particularly with respect to the amino acid sequences described therein. In one embodiment, the GP encoding gene encodes a protein from any one of Tables 1-3, or a fragment or variant thereof.

A gene or polynucleotide encoding the GP portion of the subject GPXTEN protein, in the case of an expressed fusion protein that will comprise a single GP can be then be cloned into a construct, which can be a plasmid or other vector under control of appropriate transcription and translation sequences for high level protein expression in a biological system. In a later step, a second gene or polynucleotide coding for the XTEN is genetically fused to the nucleotides encoding the N- and/or C-terminus of the GP gene by cloning it into the construct adjacent and in frame with the gene(s) coding for the GP. This second step can occur through a ligation or multimerization step. In the foregoing embodiments hereinabove described in this paragraph, it is to be understood that the gene constructs that are created can alternatively be the complement of the respective genes that encode the respective fusion proteins.

The gene encoding for the XTEN can be made in one or more steps, either fully synthetically or by synthesis combined with enzymatic processes, such as restriction enzyme-mediated cloning, PCR and overlap extension, including methods more fully described in the Examples. The methods disclosed herein can be used, for example, to ligate short sequences of polynucleotides encoding XTEN into longer XTEN genes of a desired length and sequence. In one embodiment, the method ligates two or more codon-optimized oligonucleotides encoding XTEN motif or segment sequences of about 9 to 14 amino acids, or about 12 to 20 amino acids, or about 18 to 36 amino acids, or about 48 to about 144 amino acids, or about 144 to about 288 or longer, or any combination of the foregoing ranges of motif or segment lengths.

Alternatively, the disclosed method can be used to multimerize XTEN-encoding sequences into longer sequences of a desired length; e.g., a gene encoding 36 amino acids of XTEN can be dimerized into a gene encoding 72 amino acids, then 144, then 288, etc. Even with multimerization, XTEN polypeptides can be constructed such that the XTEN-encoding gene has low or virtually no repetitiveness through design of the codons selected for the motifs of the shortest unit used, which can reduce recombination and increase stability of the encoding gene in the transformed host. Genes encoding XTEN with non-repetitive sequences can be assembled from oligonucleotides using standard techniques of gene synthesis. The gene design can be performed using algorithms that optimize codon usage and amino acid composition. In one method of the invention, a library of relatively short XTEN-encoding polynucleotide constructs is created and then assembled, as illustrated in FIGS. 4 and 5. This can be a pure codon library such that each library member has the same amino acid sequence but many different coding sequences are possible. Such libraries can be assembled from partially randomized oligonucleotides and used to generate large libraries of XTEN segments comprising the sequence motifs. The randomization scheme can be optimized to control amino acid choices for each position as well as codon usage. Exemplary methods to achieve the foregoing are disclosed in the Examples.

a. Polynucleotide Libraries

In another aspect, the invention provides libraries of polynucleotides that encode XTEN sequences that can be used to assemble genes that encode XTEN of a desired length and sequence.

In certain embodiments, the XTEN-encoding library constructs comprise polynucleotides that encode polypeptide segments of a fixed length. As an initial step, a library of oligonucleotides that encode motifs of 9-14 amino acid residues can be assembled. In a preferred embodiment, libraries of oligonucleotides that encode motifs of 12 amino acids are assembled.

The XTEN-encoding sequence segments can be dimerized or multimerized into longer encoding sequences. Dimerization or multimerization can be performed by ligation, overlap extension, PCR assembly or similar cloning techniques known in the art. This process of can be repeated multiple times until the resulting XTEN-encoding sequences have reached the organization of sequence and desired length, providing the XTEN-encoding genes. As will be appreciated, a library of polynucleotides that encodes, e.g., 12 amino acid motifs can be dimerized and/or ligated into a library of polynucleotides that encode 36 amino acids. Libraries encoding motifs of different lengths; e.g., 9-14 amino acid motifs leading to libraries encoding 27 to 42 amino acids are contemplated by the invention. In turn, the library of polynucleotides that encode 27 to 42 amino acids, and preferably 36 amino acids (as described in the Examples) can be serially dimerized into a library containing successively longer lengths of polynucleotides that encode XTEN sequences of a desired length for incorporation into the gene encoding the GPXTEN fusion protein, as disclosed herein. In some embodiments, libraries can be assembled of polynucleotides that encode amino acids that are limited to specific sequence XTEN families; e.g., AD, AE, AF, AG, AM, or AQ sequences of Table 1. In other embodiments, libraries can comprises sequences that encode two or more of the motif family sequences from Table 1. The names and sequences of representative, non-limiting polynucleotide sequences of libraries that encode 36 mers are presented in Tables 10-13, and the methods used to create them are described more fully in the Examples. In other cases, libraries that encode XTEN can be constructed from segments of polynucleotide codons linked in a randomized sequence that encode amino acids wherein at least about 80%, or at least about 90%, or at least about 91%, or at least about 92%, or at least about 93%, or at least about 94%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% of the codons are selected from the group consisting of condons for glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) amino acids. The libraries can be used, in turn, for serial dimerization or ligation to achieve polynucleotide sequence libraries that encode XTEN sequences, for example, of 48, 72, 144, 288, 576, 864, 912, 923, 1318 amino acids, or up to a total length of about 3000 amino acids, as well as intermediate lengths, in which the encoded XTEN can have one or more of the properties disclosed herein, when expressed as a component of a GPXTEN fusion protein. In some cases, the polynucleotide library sequences may also include additional bases used as “sequencing islands,” described more fully below.

FIG. 5 is a schematic flowchart of representative, non-limiting steps in the assembly of a XTEN polynucleotide construct and a GPXTEN polynucleotide construct in the embodiments of the invention. Individual oligonucleotides 501 can be annealed into sequence motifs 502 such as a 12 amino acid motif (“12-mer”), which is subsequently ligated with an oligo containing BbsI, and KpnI restriction sites 503. Additional sequence motifs from a library are annealed to the 12-mer until the desired length of the XTEN gene 504 is achieved. The XTEN gene is cloned into a stuffer vector. The vector can optionally encode a Flag sequence 506 followed by a stuffer sequence that is flanked by BsaI, BbsI, and KpnI sites 507 and, in this case, a single GP gene (encoding Ex4 in this example) 508, resulting in the gene encoding a GPXTEN comprising a single GP 500. A non-exhaustive list of the XTEN names for polynucleotides encoding XTEN and precursor sequences is provided in Table 9.


TABLE 9
DNA nucleotide sequences of XTEN and precursor sequences
XTEN
SEQ ID
Name
DNA Nucleotide Sequence
NO:
AE48
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTACCCCGGGTAGCGGTACTGCT
235
TCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTCTCCGGGCA
CCAGCTCTACCGGTTCT
AM48
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTGCATCCCCGGGCACCAGCTCTA
236
CCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTACCCCGTC
TGGTGCTACTGGCTCT
AE144
GGTAGCGAACCGGCAACTTCCGGCTCTGAAACCCCAGGTACTTCTGAAAGCGCTACTCCTGAG
237
TCTGGCCCAGGTAGCGAACCTGCTACCTCTGGCTCTGAAACCCCAGGTAGCCCGGCAGGCTCTC
CGACTTCCACCGAGGAAGGTACCTCTACTGAACCTTCTGAGGGTAGCGCTCCAGGTAGCGAAC
CGGCAACCTCTGGCTCTGAAACCCCAGGTAGCGAACCTGCTACCTCCGGCTCTGAAACTCCAGG
TAGCGAACCGGCTACTTCCGGTTCTGAAACTCCAGGTACCTCTACCGAACCTTCCGAAGGCAG
CGCACCAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTAGCGAACCGGCTACTTC
TGGCTCTGAGACTCCAGGTACTTCTACCGAACCGTCCGAAGGTAGCGCACCA
AF144
GGTACTTCTACTCCGGAAAGCGGTTCCGCATCTCCAGGTACTTCTCCTAGCGGTGAATCTTCT
238
ACTGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACTGCTCCAGGTTCTACCAGCTCTACCG
CTGAATCTCCTGGCCCAGGTTCTACCAGCGAATCCCCGTCTGGCACCGCACCAGGTTCTACTAG
CTCTACCGCAGAATCTCCGGGTCCAGGTACTTCCCCTAGCGGTGAATCTTCTACTGCTCCAGGT
ACCTCTACTCCGGAAAGCGGCTCCGCATCTCCAGGTTCTACTAGCTCTACTGCTGAATCTCCTG
GTCCAGGTACCTCCCCTAGCGGCGAATCTTCTACTGCTCCAGGTACCTCTCCTAGCGGCGAATC
TTCTACCGCTCCAGGTACCTCCCCTAGCGGTGAATCTTCTACCGCACCA
AE288
GGTACCTCTGAAAGCGCAACTCCTGAGTCTGGCCCAGGTAGCGAACCTGCTACCTCCGGCTCTG
239
AGACTCCAGGTACCTCTGAAAGCGCAACCCCGGAATCTGGTCCAGGTAGCGAACCTGCAACCT
CTGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCAGGTACTTCTAC
TGAACCGTCCGAGGGCAGCGCACCAGGTAGCCCTGCTGGCTCTCCAACCTCCACCGAAGAAGG
TACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGCGAACCGGCAACCTCCGGTTCTGA
AACCCCAGGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCG
ACTTCCACCGAGGAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGTACTTCTACC
GAACCTTCCGAGGGCAGCGCACCAGGTACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCAGGT
ACTTCTGAAAGCGCTACTCCTGAATCCGGTCCAGGTACTTCTGAAAGCGCTACCCCGGAATCT
GGCCCAGGTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAGCGAACCGGCTACCTCC
GGTTCTGAAACTCCAGGTAGCCCAGCAGGCTCTCCGACTTCCACTGAGGAAGGTACTTCTACT
GAACCTTCCGAAGGCAGCGCACCAGGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCAGGT
AGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCTGAATCT
GGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
AE576
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAAGGTACTTCTGAAAGCGCTACTCCTGAG
240
TCTGGTCCAGGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCAGGTAGCCCAGCAGGCTCTC
CGACTTCCACTGAGGAAGGTACTTCTACTGAACCTTCCGAAGGCAGCGCACCAGGTACCTCTA
CTGAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAATCTGGCCCAG
GTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAGCGAACCGGCTACCTCCGGTTCTG
AAACTCCAGGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAAGGTACTTCTGAAAGCGCAA
CCCCGGAGTCCGGCCCAGGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCAGGTACTTCTAC
CGAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGG
TACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTACTGAACCTTCTGAGGGCAG
CGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGTACTTCTACTGAACCGTCC
GAAGGTAGCGCACCAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTAGCGAACCG
GCTACTTCTGGCTCTGAGACTCCAGGTACTTCTACCGAACCGTCCGAAGGTAGCGCACCAGGT
ACTTCTACTGAACCGTCTGAAGGTAGCGCACCAGGTACTTCTGAAAGCGCAACCCCGGAATCC
GGCCCAGGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTAGCCCTGCTGGCTCTCCAA
CCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGCGAACCGG
CAACCTCCGGTTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCAGGTAC
CTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACTTCTACTGAACCGTCCGAAGGTAGCGC
ACCAGGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGTACCTCTACTGAACCTTCCGAG
GGCAGCGCTCCAGGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCAGGTACTTCTACCGAA
CCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACT
TCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTGAAAGCGCAACTCCTGAGTCTGGC
CCAGGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCAGGTACCTCTGAAAGCGCAACCCCGG
AATCTGGTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGCG
CTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCAGGTACTTC
TGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCGACTTCCACCGAGGAA
GGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGTAGCCCGGCAGGCTCTCCGACCTCTA
CTGAGGAAGGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTACCTCTACCGAACCGT
CTGAGGGCAGCGCACCA
AF576
GGTTCTACTAGCTCTACCGCTGAATCTCCTGGCCCAGGTTCCACTAGCTCTACCGCAGAATCTC
241
CGGGCCCAGGTTCTACTAGCGAATCCCCTTCTGGTACCGCTCCAGGTTCTACTAGCTCTACCGC
TGAATCTCCGGGTCCAGGTTCTACCAGCTCTACTGCAGAATCTCCTGGCCCAGGTACTTCTACT
CCGGAAAGCGGTTCCGCTTCTCCAGGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCAGGTA
CCTCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGC
ACCAGGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCAGGTACCTCTCCTAGCGGCGAATCT
TCTACCGCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACCAGCGAAT
CTCCTTCTGGCACCGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTTCTAC
TAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCA
GGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCAGGTACCTCTACCCCTGAAAGCGGTTCCG
CTTCTCCAGGTTCTACTAGCGAATCTCCTTCTGGTACCGCTCCAGGTACTTCTACCCCTGAAAG
CGGCTCCGCTTCTCCAGGTTCCACTAGCTCTACCGCTGAATCTCCGGGTCCAGGTTCTACTAGC
TCTACTGCAGAATCTCCTGGCCCAGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTA
CTTCTACCCCTGAAAGCGGTTCTGCATCTCCAGGTTCTACTAGCGAATCCCCGTCTGGTACCGC
ACCAGGTACTTCTACCCCGGAAAGCGGCTCTGCTTCTCCAGGTACTTCTACCCCGGAAAGCGGC
TCCGCATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGTACCGCTCCAGGTTCTACCAGCGAAT
CCCCGTCTGGTACTGCTCCAGGTTCTACCAGCGAATCTCCTTCTGGTACTGCACCAGGTTCTAC
TAGCTCTACTGCAGAATCTCCTGGCCCAGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCA
GGTACTTCTACCCCTGAAAGCGGTTCTGCATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCA
CTGCACCAGGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCAGGTACCTCTACCCCTGAAAG
CGGTTCCGCTTCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACCAGC
GAATCTCCGTCTGGCACTGCACCAGGTACCTCTACCCCTGAAAGCGGTTCCGCTTCTCCAGGTA
CTTCTCCGAGCGGTGAATCTTCTACCGCACCAGGTTCTACTAGCTCTACCGCTGAATCTCCGGG
CCCAGGTACTTCTCCGAGCGGTGAATCTTCTACTGCTCCAGGTTCCACTAGCTCTACTGCTGAA
TCTCCTGGCCCAGGTACTTCTACTCCGGAAAGCGGTTCCGCTTCTCCAGGTTCTACTAGCGAAT
CTCCGTCTGGCACCGCACCAGGTTCTACTAGCTCTACTGCAGAATCTCCTGGCCCAGGTACCTC
TACTCCGGAAAGCGGCTCTGCATCTCCAGGTACTTCTACCCCTGAAAGCGGTTCTGCATCTCCA
AM875
GGTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGTAGCGAACCGGCTACTTCCGGTTCT
242
GAAACCCCAGGTAGCCCAGCAGGTTCTCCAACTTCTACTGAAGAAGGTTCTACCAGCTCTACC
GCAGAATCTCCTGGTCCAGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTTCTACTA
GCGAATCTCCTTCTGGCACTGCACCAGGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCCAGG
TACTTCTACTCCTGAAAGCGGTTCCGCTTCTCCAGGTACCTCTACTCCGGAAAGCGGTTCTGCA
TCTCCAGGTAGCGAACCGGCAACCTCCGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTC
CTGAATCCGGCCCAGGTAGCCCGGCAGGTTCTCCGACTTCCACTGAGGAAGGTACCTCTACTG
AACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGTA
CTTCTACTGAACCGTCCGAAGGTAGCGCACCAGGTACTTCTACCGAACCGTCCGAGGGTAGCG
CACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACTTCTACCGAACCGTCCGA
GGGTAGCGCACCAGGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGGTACTTCTGAAAG
CGCTACCCCTGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTCCTGAATCCGGTCCAGGTACC
TCTACTGAACCTTCCGAAGGCAGCGCTCCAGGTACCTCTACCGAACCGTCCGAGGGCAGCGCAC
CAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTACTTCTACTGAACCTTCCGAAG
GTAGCGCTCCAGGTAGCGAACCTGCTACTTCTGGTTCTGAAACCCCAGGTAGCCCGGCTGGCTC
TCCGACCTCCACCGAGGAAGGTAGCTCTACCCCGTCTGGTGCTACTGGTTCTCCAGGTACTCCG
GGCAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCTACTGGCTCTCCAG
GTACCTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTACTGAACCGTCTGAGGGTA
GCGCTCCAGGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCCAGGTAGCCCTGCTGGCTCTCC
GACTTCTACTGAGGAAGGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAAGGTACTTCTAC
CGAACCTTCCGAAGGTAGCGCTCCAGGTGCAAGCGCAAGCGGCGCGCCAAGCACGGGAGGTAC
TTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCGACTTCCACCGAG
GAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGTTCTACCAGCTCTACCGCTGAA
TCTCCTGGCCCAGGTTCTACTAGCGAATCTCCGTCTGGCACCGCACCAGGTACTTCCCCTAGCG
GTGAATCTTCTACTGCACCAGGTACCCCTGGCAGCGGTACCGCTTCTTCCTCTCCAGGTAGCTC
TACCCCGTCTGGTGCTACTGGCTCTCCAGGTTCTAGCCCGTCTGCATCTACCGGTACCGGCCCA
GGTAGCGAACCGGCAACCTCCGGCTCTGAAACTCCAGGTACTTCTGAAAGCGCTACTCCGGAA
TCCGGCCCAGGTAGCGAACCGGCTACTTCCGGCTCTGAAACCCCAGGTTCCACCAGCTCTACTG
CAGAATCTCCGGGCCCAGGTTCTACTAGCTCTACTGCAGAATCTCCGGGTCCAGGTACTTCTCC
TAGCGGCGAATCTTCTACCGCTCCAGGTAGCGAACCGGCAACCTCTGGCTCTGAAACTCCAGG
TAGCGAACCTGCAACCTCCGGCTCTGAAACCCCAGGTACTTCTACTGAACCTTCTGAGGGCAG
CGCACCAGGTTCTACCAGCTCTACCGCAGAATCTCCTGGTCCAGGTACCTCTACTCCGGAAAGC
GGCTCTGCATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTACTTCTACCG
AACCGTCCGAAGGCAGCGCTCCAGGTACCTCTACTGAACCTTCCGAGGGCAGCGCTCCAGGTA
CCTCTACCGAACCTTCTGAAGGTAGCGCACCAGGTAGCTCTACTCCGTCTGGTGCAACCGGCTC
CCCAGGTTCTAGCCCGTCTGCTTCCACTGGTACTGGCCCAGGTGCTTCCCCGGGCACCAGCTCT
ACTGGTTCTCCAGGTAGCGAACCTGCTACCTCCGGTTCTGAAACCCCAGGTACCTCTGAAAGC
GCAACTCCGGAGTCTGGTCCAGGTAGCCCTGCAGGTTCTCCTACCTCCACTGAGGAAGGTAGC
TCTACTCCGTCTGGTGCAACCGGCTCCCCAGGTTCTAGCCCGTCTGCTTCCACTGGTACTGGCC
CAGGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTACCTCTGAAAGCGCTACTCCGGA
GTCTGGCCCAGGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACTTCTACTGAACC
GTCCGAAGGTAGCGCACCA
AE864
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAAGGTACTTCTGAAAGCGCTACTCCTGAG
243
TCTGGTCCAGGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCAGGTAGCCCAGCAGGCTCTC
CGACTTCCACTGAGGAAGGTACTTCTACTGAACCTTCCGAAGGCAGCGCACCAGGTACCTCTA
CTGAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAATCTGGCCCAG
GTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAGCGAACCGGCTACCTCCGGTTCTG
AAACTCCAGGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAAGGTACTTCTGAAAGCGCAA
CCCCGGAGTCCGGCCCAGGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCAGGTACTTCTAC
CGAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGG
TACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTACTGAACCTTCTGAGGGCAG
CGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGTACTTCTACTGAACCGTCC
GAAGGTAGCGCACCAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTAGCGAACCG
GCTACTTCTGGCTCTGAGACTCCAGGTACTTCTACCGAACCGTCCGAAGGTAGCGCACCAGGT
ACTTCTACTGAACCGTCTGAAGGTAGCGCACCAGGTACTTCTGAAAGCGCAACCCCGGAATCC
GGCCCAGGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTAGCCCTGCTGGCTCTCCAA
CCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGCGAACCGG
CAACCTCCGGTTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCAGGTAC
CTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACTTCTACTGAACCGTCCGAAGGTAGCGC
ACCAGGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGTACCTCTACTGAACCTTCCGAG
GGCAGCGCTCCAGGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCAGGTACTTCTACCGAA
CCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACT
TCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTGAAAGCGCAACTCCTGAGTCTGGC
CCAGGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCAGGTACCTCTGAAAGCGCAACCCCGG
AATCTGGTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGCG
CTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCAGGTACTTC
TGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCGACTTCCACCGAGGAA
GGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGTAGCCCGGCAGGCTCTCCGACCTCTA
CTGAGGAAGGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTACCTCTACCGAACCGT
CTGAGGGCAGCGCACCAGGTACCTCTGAAAGCGCAACTCCTGAGTCTGGCCCAGGTAGCGAAC
CTGCTACCTCCGGCTCTGAGACTCCAGGTACCTCTGAAAGCGCAACCCCGGAATCTGGTCCAGG
TAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCTGAATC
TGGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCAGGTAGCCCTGCTGGCTCTCCA
ACCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGCGAACCG
GCAACCTCCGGTTCTGAAACCCCAGGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTA
GCCCGGCTGGCTCTCCGACTTCCACCGAGGAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGA
AGAAGGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGGTACTTCTGAAAGCGCTACCCC
TGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTCCTGAATCCGGTCCAGGTACTTCTGAAAG
CGCTACCCCGGAATCTGGCCCAGGTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAG
CGAACCGGCTACCTCCGGTTCTGAAACTCCAGGTAGCCCAGCAGGCTCTCCGACTTCCACTGAG
GAAGGTACTTCTACTGAACCTTCCGAAGGCAGCGCACCAGGTACCTCTACTGAACCTTCTGAG
GGCAGCGCTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGC
GCTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
AF864
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTA
244
CCGCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACTAGCGAATCCCC
GTCTGGTACTGCTCCAGGTACTTCTACTCCTGAAAGCGGTTCCGCTTCTCCAGGTACCTCTACT
CCGGAAAGCGGTTCTGCATCTCCAGGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCAGGTT
CTACTAGCGAATCCCCGTCTGGTACCGCACCAGGTACTTCTCCTAGCGGCGAATCTTCTACCGC
ACCAGGTTCTACTAGCGAATCTCCGTCTGGCACTGCTCCAGGTACTTCTCCTAGCGGTGAATCT
TCTACCGCTCCAGGTACTTCCCCTAGCGGCGAATCTTCTACCGCTCCAGGTTCTACTAGCTCTA
CTGCAGAATCTCCGGGCCCAGGTACCTCTCCTAGCGGTGAATCTTCTACCGCTCCAGGTACTTC
TCCGAGCGGTGAATCTTCTACCGCTCCAGGTTCTACTAGCTCTACTGCAGAATCTCCTGGCCCA
GGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTACTTCTACCCCTGAAAGCGGTTCTG
CATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACCAGCGAATCTCC
GTCTGGCACTGCACCAGGTACCTCTACCCCTGAAAGCGGTTCCGCTTCTCCAGGTTCTACCAGC
TCTACCGCAGAATCTCCTGGTCCAGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTT
CTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTACTTCTCCGAGCGGTGAATCTTCTACCGC
ACCAGGTTCTACTAGCTCTACCGCTGAATCTCCGGGCCCAGGTACTTCTCCGAGCGGTGAATCT
TCTACTGCTCCAGGTACCTCTACTCCTGAAAGCGGTTCTGCATCTCCAGGTTCCACTAGCTCTA
CCGCAGAATCTCCGGGCCCAGGTTCTACTAGCTCTACTGCTGAATCTCCTGGCCCAGGTTCTAC
TAGCTCTACTGCTGAATCTCCGGGTCCAGGTTCTACCAGCTCTACTGCTGAATCTCCTGGTCCA
GGTACCTCCCCGAGCGGTGAATCTTCTACTGCACCAGGTTCTACTAGCGAATCTCCTTCTGGCA
CTGCACCAGGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCAGGTACCTCTACCCCTGAAAG
CGGTCCXXXXXXXXXXXXTGCAAGCGCAAGCGGCGCGCCAAGCACGGGAXXXXXXXXTAGCGAA
TCTCCTTCTGGTACCGCTCCAGGTTCTACCAGCGAATCCCCGTCTGGTACTGCTCCAGGTTCTA
CCAGCGAATCTCCTTCTGGTACTGCACCAGGTTCTACTAGCGAATCTCCTTCTGGTACCGCTCC
AGGTTCTACCAGCGAATCCCCGTCTGGTACTGCTCCAGGTTCTACCAGCGAATCTCCTTCTGGT
ACTGCACCAGGTACTTCTACTCCGGAAAGCGGTTCCGCATCTCCAGGTACTTCTCCTAGCGGTG
AATCTTCTACTGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACTGCTCCAGGTTCTACCAG
CTCTACTGCTGAATCTCCGGGTCCAGGTACTTCCCCGAGCGGTGAATCTTCTACTGCACCAGGT
ACTTCTACTCCGGAAAGCGGTTCCGCTTCTCCAGGTTCTACCAGCGAATCTCCTTCTGGCACCG
CTCCAGGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCAGGTACTTCTCCTAGCGGCGAATC
TTCTACCGCACCAGGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCAGGTACTTCTACCCCG
GAAAGCGGCTCTGCTTCTCCAGGTACTTCTACCCCGGAAAGCGGCTCCGCATCTCCAGGTTCTA
CTAGCGAATCTCCTTCTGGTACCGCTCCAGGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTCC
AGGTTCCACTAGCTCTACCGCTGAATCTCCGGGTCCAGGTTCTACCAGCGAATCTCCTTCTGGC
ACCGCTCCAGGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCAGGTACTTCTCCTAGCGGCG
AATCTTCTACCGCACCAGGTTCTACCAGCTCTACTGCTGAATCTCCGGGTCCAGGTACTTCCCC
GAGCGGTGAATCTTCTACTGCACCAGGTACTTCTACTCCGGAAAGCGGTTCCGCTTCTCCAGG
TACCTCCCCTAGCGGCGAATCTTCTACTGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACC
GCTCCAGGTACCTCCCCTAGCGGTGAATCTTCTACCGCACCAGGTTCTACTAGCTCTACTGCTG
AATCTCCGGGTCCAGGTTCTACCAGCTCTACTGCTGAATCTCCTGGTCCAGGTACCTCCCCGAG
CGGTGAATCTTCTACTGCACCAGGTTCTAGCCCTTCTGCTTCCACCGGTACCGGCCCAGGTAGC
TCTACTCCGTCTGGTGCAACTGGCTCTCCAGGTAGCTCTACTCCGTCTGGTGCAACCGGCTCCC
CA
XXXX was inserted in two areas where no sequence information is available.
AG864
GGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTTCTAGCCCGTCTGCTTCTACTGGTA
245
CTGGTCCAGGTTCTAGCCCTTCTGCTTCCACTGGTACTGGTCCAGGTACCCCGGGTAGCGGTAC
CGCTTCTTCTTCTCCAGGTAGCTCTACTCCGTCTGGTGCTACCGGCTCTCCAGGTTCTAACCCT
TCTGCATCCACCGGTACCGGCCCAGGTGCTTCTCCGGGCACCAGCTCTACTGGTTCTCCAGGTA
CCCCGGGCAGCGGTACCGCATCTTCTTCTCCAGGTAGCTCTACTCCTTCTGGTGCAACTGGTTC
TCCAGGTACTCCTGGCAGCGGTACCGCTTCTTCTTCTCCAGGTGCTTCTCCTGGTACTAGCTCT
ACTGGTTCTCCAGGTGCTTCTCCGGGCACTAGCTCTACTGGTTCTCCAGGTACCCCGGGTAGCG
GTACTGCTTCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTC
TCCGGGCACCAGCTCTACCGGTTCTCCAGGTACCCCGGGTAGCGGTACCGCTTCTTCTTCTCCA
GGTAGCTCTACTCCGTCTGGTGCTACCGGCTCTCCAGGTTCTAACCCTTCTGCATCCACCGGTA
CCGGCCCAGGTTCTAGCCCTTCTGCTTCCACCGGTACTGGCCCAGGTAGCTCTACCCCTTCTGG
TGCTACCGGCTCCCCAGGTAGCTCTACTCCTTCTGGTGCAACTGGCTCTCCAGGTGCATCTCCG
GGCACTAGCTCTACTGGTTCTCCAGGTGCATCCCCTGGCACTAGCTCTACTGGTTCTCCAGGTG
CTTCTCCTGGTACCAGCTCTACTGGTTCTCCAGGTACTCCTGGCAGCGGTACCGCTTCTTCTTC
TCCAGGTGCTTCTCCTGGTACTAGCTCTACTGGTTCTCCAGGTGCTTCTCCGGGCACTAGCTCT
ACTGGTTCTCCAGGTGCTTCCCCGGGCACTAGCTCTACCGGTTCTCCAGGTTCTAGCCCTTCTG
CATCTACTGGTACTGGCCCAGGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCAGGTGCATC
TCCGGGCACTAGCTCTACTGGTTCTCCAGGTGCATCCCCTGGCACTAGCTCTACTGGTTCTCCA
GGTGCTTCTCCTGGTACCAGCTCTACTGGTTCTCCAGGTAGCTCTACTCCGTCTGGTGCAACCG
GTTCCCCAGGTAGCTCTACTCCTTCTGGTGCTACTGGCTCCCCAGGTGCATCCCCTGGCACCAG
CTCTACCGGTTCTCCAGGTACCCCGGGCAGCGGTACCGCATCTTCCTCTCCAGGTAGCTCTACC
CCGTCTGGTGCTACCGGTTCCCCAGGTAGCTCTACCCCGTCTGGTGCAACCGGCTCCCCAGGTA
GCTCTACTCCGTCTGGTGCAACCGGCTCCCCAGGTTCTAGCCCGTCTGCTTCCACTGGTACTGG
CCCAGGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTGCATCCCCGGGTACCAGCTCT
ACCGGTTCTCCAGGTACTCCTGGCAGCGGTACTGCATCTTCCTCTCCAGGTGCTTCTCCGGGCA
CCAGCTCTACTGGTTCTCCAGGTGCATCTCCGGGCACTAGCTCTACTGGTTCTCCAGGTGCATC
CCCTGGCACTAGCTCTACTGGTTCTCCAGGTGCTTCTCCTGGTACCAGCTCTACTGGTTCTCCA
GGTACCCCTGGTAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTACTCCGTCTGGTGCTACCG
GTTCTCCAGGTACCCCGGGTAGCGGTACCGCATCTTCTTCTCCAGGTAGCTCTACCCCGTCTGG
TGCTACTGGTTCTCCAGGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTACC
CCTTCTGGTGCTACTGGCTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACTGGCTCCCCAGGTT
CTAGCCCTTCTGCATCCACCGGTACCGGTCCAGGTTCTAGCCCGTCTGCATCTACTGGTACTGG
TCCAGGTGCATCCCCGGGCACTAGCTCTACCGGTTCTCCAGGTACTCCTGGTAGCGGTACTGCT
TCTTCTTCTCCAGGTAGCTCTACTCCTTCTGGTGCTACTGGTTCTCCAGGTTCTAGCCCTTCTG
CATCCACCGGTACCGGCCCAGGTTCTAGCCCGTCTGCTTCTACCGGTACTGGTCCAGGTGCTTC
TCCGGGTACTAGCTCTACTGGTTCTCCAGGTGCATCTCCTGGTACTAGCTCTACTGGTTCTCCA
GGTAGCTCTACTCCGTCTGGTGCAACCGGCTCTCCAGGTTCTAGCCCTTCTGCATCTACCGGTA
CTGGTCCAGGTGCATCCCCTGGTACCAGCTCTACCGGTTCTCCAGGTTCTAGCCCTTCTGCTTC
TACCGGTACCGGTCCAGGTACCCCTGGCAGCGGTACCGCATCTTCCTCTCCAGGTAGCTCTACT
CCGTCTGGTGCAACCGGTTCCCCAGGTAGCTCTACTCCTTCTGGTGCTACTGGCTCCCCAGGTG
CATCCCCTGGCACCAGCTCTACCGGTTCTCCA
AM923
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTGCATCCCCGGGCACCAGCTCTA
246
CCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTACCCCGTC
TGGTGCTACTGGCTCTCCAGGTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGTAGCGA
ACCGGCTACTTCCGGTTCTGAAACCCCAGGTAGCCCAGCAGGTTCTCCAACTTCTACTGAAGA
AGGTTCTACCAGCTCTACCGCAGAATCTCCTGGTCCAGGTACCTCTACTCCGGAAAGCGGCTCT
GCATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCAGGTTCTACTAGCGAATCCC
CGTCTGGTACTGCTCCAGGTACTTCTACTCCTGAAAGCGGTTCCGCTTCTCCAGGTACCTCTAC
TCCGGAAAGCGGTTCTGCATCTCCAGGTAGCGAACCGGCAACCTCCGGCTCTGAAACCCCAGG
TACCTCTGAAAGCGCTACTCCTGAATCCGGCCCAGGTAGCCCGGCAGGTTCTCCGACTTCCACT
GAGGAAGGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACC
CCGGAGTCCGGTCCAGGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCAGGTACTTCTACC
GAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGT
ACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACTTCTACCGAACCTTCCGAGGGCAGC
GCACCAGGTACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTC
CTGAATCCGGTCCAGGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCAGGTACCTCTACCGA
ACCGTCCGAGGGCAGCGCACCAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTAC
TTCTACTGAACCTTCCGAAGGTAGCGCTCCAGGTAGCGAACCTGCTACTTCTGGTTCTGAAAC
CCCAGGTAGCCCGGCTGGCTCTCCGACCTCCACCGAGGAAGGTAGCTCTACCCCGTCTGGTGCT
ACTGGTTCTCCAGGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTACCCCTT
CTGGTGCTACTGGCTCTCCAGGTACCTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTC
TACTGAACCGTCTGAGGGTAGCGCTCCAGGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCC
AGGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAAGGTAGCCCGGCTGGTTCTCCGACTTCT
ACTGAGGAAGGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCAGGTGCAAGCGCAAGCGGC
GCGCCAAGCACGGGAGGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCT
GGCTCTCCGACTTCCACCGAGGAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGT
TCTACCAGCTCTACCGCTGAATCTCCTGGCCCAGGTTCTACTAGCGAATCTCCGTCTGGCACCG
CACCAGGTACTTCCCCTAGCGGTGAATCTTCTACTGCACCAGGTACCCCTGGCAGCGGTACCGC
TTCTTCCTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCAGGTTCTAGCCCGTCT
GCATCTACCGGTACCGGCCCAGGTAGCGAACCGGCAACCTCCGGCTCTGAAACTCCAGGTACTT
CTGAAAGCGCTACTCCGGAATCCGGCCCAGGTAGCGAACCGGCTACTTCCGGCTCTGAAACCCC
AGGTTCCACCAGCTCTACTGCAGAATCTCCGGGCCCAGGTTCTACTAGCTCTACTGCAGAATCT
CCGGGTCCAGGTACTTCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTAGCGAACCGGCAACCT
CTGGCTCTGAAACTCCAGGTAGCGAACCTGCAACCTCCGGCTCTGAAACCCCAGGTACTTCTAC
TGAACCTTCTGAGGGCAGCGCACCAGGTTCTACCAGCTCTACCGCAGAATCTCCTGGTCCAGG
TACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTTCTACTAGCGAATCTCCTTCTGGCACT
GCACCAGGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGTACCTCTACTGAACCTTCCG
AGGGCAGCGCTCCAGGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCAGGTAGCTCTACTC
CGTCTGGTGCAACCGGCTCCCCAGGTTCTAGCCCGTCTGCTTCCACTGGTACTGGCCCAGGTGC
TTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTAGCGAACCTGCTACCTCCGGTTCTGAAACC
CCAGGTACCTCTGAAAGCGCAACTCCGGAGTCTGGTCCAGGTAGCCCTGCAGGTTCTCCTACCT
CCACTGAGGAAGGTAGCTCTACTCCGTCTGGTGCAACCGGCTCCCCAGGTTCTAGCCCGTCTGC
TTCCACTGGTACTGGCCCAGGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTACCTCT
GAAAGCGCTACTCCGGAGTCTGGCCCAGGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
AE912
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTACCCCGGGTAGCGGTACTGCT
247
TCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTCTCCGGGCA
CCAGCTCTACCGGTTCTCCAGGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAAGGTACTTC
TGAAAGCGCTACTCCTGAGTCTGGTCCAGGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCC
AGGTAGCCCAGCAGGCTCTCCGACTTCCACTGAGGAAGGTACTTCTACTGAACCTTCCGAAGG
CAGCGCACCAGGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGC
TACCCCGGAATCTGGCCCAGGTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAGCGA
ACCGGCTACCTCCGGTTCTGAAACTCCAGGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAA
GGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTACCTCTACCGAACCGTCTGAGGGC
AGCGCACCAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCT
CCTACCTCCACCGAGGAAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTA
CTGAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAG
GTACTTCTACTGAACCGTCCGAAGGTAGCGCACCAGGTACTTCTGAAAGCGCAACCCCTGAAT
CCGGTCCAGGTAGCGAACCGGCTACTTCTGGCTCTGAGACTCCAGGTACTTCTACCGAACCGTC
CGAAGGTAGCGCACCAGGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCAGGTACTTCTGA
AAGCGCAACCCCGGAATCCGGCCCAGGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGT
AGCCCTGCTGGCTCTCCAACCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATCCG
GCCCAGGTAGCGAACCGGCAACCTCCGGTTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCC
GGAGTCTGGCCCAGGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACTTCTACTGA
ACCGTCCGAAGGTAGCGCACCAGGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGTAC
CTCTACTGAACCTTCCGAGGGCAGCGCTCCAGGTACCTCTACCGAACCTTCTGAAGGTAGCGCA
CCAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGGTTCTCCTACCT
CCACCGAGGAAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTGAAAGCG
CAACTCCTGAGTCTGGCCCAGGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCAGGTACCTC
TGAAAGCGCAACCCCGGAATCTGGTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCC
AGGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAGGG
CAGCGCACCAGGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCT
CCGACTTCCACCGAGGAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGAAGGTAGCCCG
GCAGGCTCTCCGACCTCTACTGAGGAAGGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
GGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCAGGTACCTCTGAAAGCGCAACTCCTGAG
TCTGGCCCAGGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCAGGTACCTCTGAAAGCGCA
ACCCCGGAATCTGGTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTG
AAAGCGCTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCAG
GTAGCCCTGCTGGCTCTCCAACCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATC
CGGCCCAGGTAGCGAACCGGCAACCTCCGGTTCTGAAACCCCAGGTACTTCTGAAAGCGCTAC
TCCTGAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCGACTTCCACCGAGGAAGGTAGCCCGGCT
GGCTCTCCAACTTCTACTGAAGAAGGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGGT
ACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTCCTGAATCCG
GTCCAGGTACTTCTGAAAGCGCTACCCCGGAATCTGGCCCAGGTAGCGAACCGGCTACTTCTG
GTTCTGAAACCCCAGGTAGCGAACCGGCTACCTCCGGTTCTGAAACTCCAGGTAGCCCAGCAG
GCTCTCCGACTTCCACTGAGGAAGGTACTTCTACTGAACCTTCCGAAGGCAGCGCACCAGGTA
CCTCTACTGAACCTTCTGAGGGCAGCGCTCCAGGTAGCGAACCTGCAACCTCTGGCTCTGAAAC
CCCAGGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCAGGTACTTCTACTGAACCGTCCGAG
GGCAGCGCACCA
AM1318
GGTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGTAGCGAACCGGCTACTTCCGGTTCT
248
GAAACCCCAGGTAGCCCAGCAGGTTCTCCAACTTCTACTGAAGAAGGTTCTACCAGCTCTACC
GCAGAATCTCCTGGTCCAGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTCCAGGTTCTACTA
GCGAATCTCCTTCTGGCACTGCACCAGGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCCAGG
TACTTCTACTCCTGAAAGCGGTTCCGCTTCTCCAGGTACCTCTACTCCGGAAAGCGGTTCTGCA
TCTCCAGGTAGCGAACCGGCAACCTCCGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTC
CTGAATCCGGCCCAGGTAGCCCGGCAGGTTCTCCGACTTCCACTGAGGAAGGTACCTCTACTG
AACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGTA
CTTCTACTGAACCGTCCGAAGGTAGCGCACCAGGTACTTCTACCGAACCGTCCGAGGGTAGCG
CACCAGGTAGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACTTCTACCGAACCGTCCGA
GGGTAGCGCACCAGGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGGTACTTCTGAAAG
CGCTACCCCTGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTCCTGAATCCGGTCCAGGTACC
TCTACTGAACCTTCCGAAGGCAGCGCTCCAGGTACCTCTACCGAACCGTCCGAGGGCAGCGCAC
CAGGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGTACTTCTACTGAACCTTCCGAAG
GTAGCGCTCCAGGTAGCGAACCTGCTACTTCTGGTTCTGAAACCCCAGGTAGCCCGGCTGGCTC
TCCGACCTCCACCGAGGAAGGTAGCTCTACCCCGTCTGGTGCTACTGGTTCTCCAGGTACTCCG
GGCAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCTACTGGCTCTCCAG
GTACCTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTACCTCTACTGAACCGTCTGAGGGTA
GCGCTCCAGGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCCAGGTAGCCCTGCTGGCTCTCC
GACTTCTACTGAGGAAGGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAAGGTACTTCTAC
CGAACCTTCCGAAGGTAGCGCTCCAGGTCCAGAACCAACGGGGCCGGCCCCAAGCGGAGGTAG
CGAACCGGCAACCTCCGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACTCCTGAATCCGGC
CCAGGTAGCCCGGCAGGTTCTCCGACTTCCACTGAGGAAGGTACTTCTGAAAGCGCTACTCCT
GAGTCCGGCCCAGGTAGCCCGGCTGGCTCTCCGACTTCCACCGAGGAAGGTAGCCCGGCTGGCT
CTCCAACTTCTACTGAAGAAGGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGTAGCC
CGGCTGGCTCTCCGACTTCCACCGAGGAAGGTAGCCCGGCTGGCTCTCCAACTTCTACTGAAGA
AGGTTCTACCAGCTCTACCGCTGAATCTCCTGGCCCAGGTTCTACTAGCGAATCTCCGTCTGGC
ACCGCACCAGGTACTTCCCCTAGCGGTGAATCTTCTACTGCACCAGGTTCTACCAGCGAATCTC
CTTCTGGCACCGCTCCAGGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCAGGTACTTCTCC
TAGCGGCGAATCTTCTACCGCACCAGGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGG
TACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCAGGTACTTCTGAAAGCGCTACTCCTGAATCC
GGTCCAGGTAGCGAACCGGCAACCTCTGGCTCTGAAACCCCAGGTACCTCTGAAAGCGCTACT
CCGGAATCTGGTCCAGGTACTTCTGAAAGCGCTACTCCGGAATCCGGTCCAGGTACCTCTACT
GAACCTTCTGAGGGCAGCGCTCCAGGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGT
ACTTCTACTGAACCGTCCGAAGGTAGCGCACCAGGTACCTCCCCTAGCGGCGAATCTTCTACTG
CTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTACCTCCCCTAGCGGTGAATC
TTCTACCGCACCAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTAGCCCAGCAGG
TTCTCCTACCTCCACCGAGGAAGGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTTCT
AGCCCTTCTGCTTCCACCGGTACCGGCCCAGGTAGCTCTACTCCGTCTGGTGCAACTGGCTCTC
CAGGTAGCTCTACTCCGTCTGGTGCAACCGGCTCCCCAGGTAGCTCTACCCCGTCTGGTGCTAC
CGGCTCTCCAGGTAGCTCTACCCCGTCTGGTGCAACCGGCTCCCCAGGTGCATCCCCGGGTACT
AGCTCTACCGGTTCTCCAGGTGCAAGCGCAAGCGGCGCGCCAAGCACGGGAGGTACTTCTCCG
AGCGGTGAATCTTCTACCGCACCAGGTTCTACTAGCTCTACCGCTGAATCTCCGGGCCCAGGTA
CTTCTCCGAGCGGTGAATCTTCTACTGCTCCAGGTACCTCTGAAAGCGCTACTCCGGAGTCTGG
CCCAGGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACTTCTACTGAACCGTCCGA
AGGTAGCGCACCAGGTTCTAGCCCTTCTGCATCTACTGGTACTGGCCCAGGTAGCTCTACTCCT
TCTGGTGCTACCGGCTCTCCAGGTGCTTCTCCGGGTACTAGCTCTACCGGTTCTCCAGGTACTT
CTACTCCGGAAAGCGGTTCCGCATCTCCAGGTACTTCTCCTAGCGGTGAATCTTCTACTGCTCC
AGGTACCTCTCCTAGCGGCGAATCTTCTACTGCTCCAGGTACTTCTGAAAGCGCAACCCCTGA
ATCCGGTCCAGGTAGCGAACCGGCTACTTCTGGCTCTGAGACTCCAGGTACTTCTACCGAACC
GTCCGAAGGTAGCGCACCAGGTTCTACCAGCGAATCCCCTTCTGGTACTGCTCCAGGTTCTACC
AGCGAATCCCCTTCTGGCACCGCACCAGGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTCCAG
GTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAAGGTACTTCTGAAAGCGCAACCCCGGAGT
CCGGCCCAGGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCAGGTAGCCCTGCTGGCTCTCC
AACCTCCACCGAAGAAGGTACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGCGAACC
GGCAACCTCCGGTTCTGAAACCCCAGGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCAGGT
GCTTCTCCTGGTACTAGCTCTACCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACTGGCT
CTCCAGGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCCAGGTACTTCCCCTAGCGGTGAATC
TTCTACTGCTCCAGGTTCTACCAGCTCTACCGCAGAATCTCCGGGTCCAGGTAGCTCTACCCCT
TCTGGTGCAACCGGCTCTCCAGGTGCATCCCCGGGTACCAGCTCTACCGGTTCTCCAGGTACTC
CGGGTAGCGGTACCGCTTCTTCCTCTCCAGGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGA
AGGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAAGGTACTTCTACCGAACCTTCCGAAGG
TAGCGCTCCA
BC864
GGTACTTCCACCGAACCATCCGAACCAGGTAGCGCAGGTACTTCCACCGAACCATCCGAACCTG
249
GCAGCGCAGGTAGCGAACCGGCAACCTCTGGTACTGAACCATCAGGTAGCGGCGCATCCGAGC
CTACCTCTACTGAACCAGGTAGCGAACCGGCTACCTCCGGTACTGAGCCATCAGGTAGCGAAC
CGGCAACTTCCGGTACTGAACCATCAGGTAGCGAACCGGCAACTTCCGGCACTGAACCATCAG
GTAGCGGTGCATCTGAGCCGACCTCTACTGAACCAGGTACTTCTACTGAACCATCTGAGCCGG
GCAGCGCAGGTAGCGAACCAGCTACTTCTGGCACTGAACCATCAGGTACTTCTACTGAACCAT
CCGAACCAGGTAGCGCAGGTAGCGAACCTGCTACCTCTGGTACTGAGCCATCAGGTAGCGAAC
CGGCTACCTCTGGTACTGAACCATCAGGTACTTCTACCGAACCATCCGAGCCTGGTAGCGCAG
GTACTTCTACCGAACCATCCGAGCCAGGCAGCGCAGGTAGCGAACCGGCAACCTCTGGCACTG
AGCCATCAGGTAGCGAACCAGCAACTTCTGGTACTGAACCATCAGGTACTAGCGAGCCATCTA
CTTCCGAACCAGGTGCAGGTAGCGGCGCATCCGAACCTACTTCCACTGAACCAGGTACTAGCG
AGCCATCCACCTCTGAACCAGGTGCAGGTAGCGAACCGGCAACTTCCGGCACTGAACCATCAG
GTAGCGAACCGGCTACCTCTGGTACTGAACCATCAGGTACTTCTACCGAACCATCCGAGCCTG
GTAGCGCAGGTACTTCTACCGAACCATCCGAGCCAGGCAGCGCAGGTAGCGGTGCATCCGAGC
CGACCTCTACTGAACCAGGTAGCGAACCAGCAACTTCTGGCACTGAGCCATCAGGTAGCGAAC
CAGCTACCTCTGGTACTGAACCATCAGGTAGCGAACCGGCTACTTCCGGCACTGAACCATCAG
GTAGCGAACCAGCAACCTCCGGTACTGAACCATCAGGTACTTCCACTGAACCATCCGAACCGG
GTAGCGCAGGTAGCGAACCGGCAACTTCCGGCACTGAACCATCAGGTAGCGGTGCATCTGAGC
CGACCTCTACTGAACCAGGTACTTCTACTGAACCATCTGAGCCGGGCAGCGCAGGTAGCGAAC
CTGCAACCTCCGGCACTGAGCCATCAGGTAGCGGCGCATCTGAACCAACCTCTACTGAACCAG
GTACTTCCACCGAACCATCTGAGCCAGGCAGCGCAGGTAGCGGCGCATCTGAACCAACCTCTA
CTGAACCAGGTAGCGAACCAGCAACTTCTGGTACTGAACCATCAGGTAGCGGCGCATCTGAGC
CTACTTCCACTGAACCAGGTAGCGAACCGGCAACTTCCGGCACTGAACCATCAGGTAGCGGTG
CATCTGAGCCGACCTCTACTGAACCAGGTACTTCTACTGAACCATCTGAGCCGGGCAGCGCAG
GTAGCGAACCGGCAACTTCCGGCACTGAACCATCAGGTAGCGGTGCATCTGAGCCGACCTCTA
CTGAACCAGGTACTTCTACTGAACCATCTGAGCCGGGCAGCGCAGGTAGCGAACCAGCTACTT
CTGGCACTGAACCATCAGGTACTTCTACTGAACCATCCGAACCAGGTAGCGCAGGTAGCGAAC
CTGCTACCTCTGGTACTGAGCCATCAGGTACTTCTACTGAACCATCCGAGCCGGGTAGCGCAG
GTACTTCCACTGAACCATCTGAACCTGGTAGCGCAGGTACTTCCACTGAACCATCCGAACCAG
GTAGCGCAGGTACTTCTACTGAACCATCCGAGCCGGGTAGCGCAGGTACTTCCACTGAACCAT
CTGAACCTGGTAGCGCAGGTACTTCCACTGAACCATCCGAACCAGGTAGCGCAGGTACTAGCG
AACCATCCACCTCCGAACCAGGCGCAGGTAGCGGTGCATCTGAACCGACTTCTACTGAACCAG
GTACTTCCACTGAACCATCTGAGCCAGGTAGCGCAGGTACTTCCACCGAACCATCCGAACCAG
GTAGCGCAGGTACTTCCACCGAACCATCCGAACCTGGCAGCGCAGGTAGCGAACCGGCAACCT
CTGGTACTGAACCATCAGGTAGCGGTGCATCCGAGCCGACCTCTACTGAACCAGGTAGCGAAC
CAGCAACTTCTGGCACTGAGCCATCAGGTAGCGAACCAGCTACCTCTGGTACTGAACCATCAG
GTAGCGAACCGGCAACCTCTGGCACTGAGCCATCAGGTAGCGAACCAGCAACTTCTGGTACTG
AACCATCAGGTACTAGCGAGCCATCTACTTCCGAACCAGGTGCAGGTAGCGAACCTGCAACCT
CCGGCACTGAGCCATCAGGTAGCGGCGCATCTGAACCAACCTCTACTGAACCAGGTACTTCCA
CCGAACCATCTGAGCCAGGCAGCGCAGGTAGCGAACCTGCAACCTCCGGCACTGAGCCATCAG
GTAGCGGCGCATCTGAACCAACCTCTACTGAACCAGGTACTTCCACCGAACCATCTGAGCCAG
GCAGCGCA
BD864
GGTAGCGAAACTGCTACTTCCGGCTCTGAGACTGCAGGTACTAGTGAATCCGCAACTAGCGAA
250
TCTGGCGCAGGTAGCACTGCAGGCTCTGAGACTTCCACTGAAGCAGGTACTAGCGAGTCCGCA
ACCAGCGAATCCGGCGCAGGTAGCGAAACTGCTACCTCTGGCTCCGAGACTGCAGGTAGCGAA
ACTGCAACCTCTGGCTCTGAAACTGCAGGTACTTCCACTGAAGCAAGTGAAGGCTCCGCATCA
GGTACTTCCACCGAAGCAAGCGAAGGCTCCGCATCAGGTACTAGTGAGTCCGCAACTAGCGAA
TCCGGTGCAGGTAGCGAAACCGCTACCTCTGGTTCCGAAACTGCAGGTACTTCTACCGAGGCT
AGCGAAGGTTCTGCATCAGGTAGCACTGCTGGTTCCGAGACTTCTACTGAAGCAGGTACTAGC
GAATCTGCTACTAGCGAATCCGGCGCAGGTACTAGCGAATCCGCTACCAGCGAATCCGGCGCA
GGTAGCGAAACTGCAACCTCTGGTTCCGAGACTGCAGGTACTAGCGAGTCCGCTACTAGCGAA
TCTGGCGCAGGTACTTCCACTGAAGCTAGTGAAGGTTCTGCATCAGGTAGCGAAACTGCTACT
TCTGGTTCCGAAACTGCAGGTAGCGAAACCGCTACCTCTGGTTCCGAAACTGCAGGTACTTCT
ACCGAGGCTAGCGAAGGTTCTGCATCAGGTAGCACTGCTGGTTCCGAGACTTCTACTGAAGCA
GGTACTAGCGAGTCCGCTACTAGCGAATCTGGCGCAGGTACTTCCACTGAAGCTAGTGAAGGT
TCTGCATCAGGTAGCGAAACTGCTACTTCTGGTTCCGAAACTGCAGGTAGCACTGCTGGCTCC
GAGACTTCTACCGAAGCAGGTAGCACTGCAGGTTCCGAAACTTCCACTGAAGCAGGTAGCGAA
ACTGCTACCTCTGGCTCTGAGACTGCAGGTACTAGCGAATCTGCTACTAGCGAATCCGGCGCA
GGTACTAGCGAATCCGCTACCAGCGAATCCGGCGCAGGTAGCGAAACTGCAACCTCTGGTTCC
GAGACTGCAGGTACTAGCGAATCTGCTACTAGCGAATCCGGCGCAGGTACTAGCGAATCCGCT
ACCAGCGAATCCGGCGCAGGTAGCGAAACTGCAACCTCTGGTTCCGAGACTGCAGGTAGCGAA
ACCGCTACCTCTGGTTCCGAAACTGCAGGTACTTCTACCGAGGCTAGCGAAGGTTCTGCATCA
GGTAGCACTGCTGGTTCCGAGACTTCTACTGAAGCAGGTAGCGAAACTGCTACTTCCGGCTCT
GAGACTGCAGGTACTAGTGAATCCGCAACTAGCGAATCTGGCGCAGGTAGCACTGCAGGCTCT
GAGACTTCCACTGAAGCAGGTAGCACTGCTGGTTCCGAAACCTCTACCGAAGCAGGTAGCACT
GCAGGTTCTGAAACCTCCACTGAAGCAGGTACTTCCACTGAGGCTAGTGAAGGCTCTGCATCA
GGTAGCACTGCTGGTTCCGAAACCTCTACCGAAGCAGGTAGCACTGCAGGTTCTGAAACCTCC
ACTGAAGCAGGTACTTCCACTGAGGCTAGTGAAGGCTCTGCATCAGGTAGCACTGCAGGTTCT
GAGACTTCCACCGAAGCAGGTAGCGAAACTGCTACTTCTGGTTCCGAAACTGCAGGTACTTCC
ACTGAAGCTAGTGAAGGTTCCGCATCAGGTACTAGTGAGTCCGCAACCAGCGAATCCGGCGCA
GGTAGCGAAACCGCAACCTCCGGTTCTGAAACTGCAGGTACTAGCGAATCCGCAACCAGCGAA
TCTGGCGCAGGTACTAGTGAGTCCGCAACCAGCGAATCCGGCGCAGGTAGCGAAACCGCAACC
TCCGGTTCTGAAACTGCAGGTACTAGCGAATCCGCAACCAGCGAATCTGGCGCAGGTAGCGAA
ACTGCTACTTCCGGCTCTGAGACTGCAGGTACTTCCACCGAAGCAAGCGAAGGTTCCGCATCA
GGTACTTCCACCGAGGCTAGTGAAGGCTCTGCATCAGGTAGCACTGCTGGCTCCGAGACTTCT
ACCGAAGCAGGTAGCACTGCAGGTTCCGAAACTTCCACTGAAGCAGGTAGCGAAACTGCTACC
TCTGGCTCTGAGACTGCAGGTACTAGCGAATCTGCTACTAGCGAATCCGGCGCAGGTACTAGC
GAATCCGCTACCAGCGAATCCGGCGCAGGTAGCGAAACTGCAACCTCTGGTTCCGAGACTGCA
GGTAGCGAAACTGCTACTTCCGGCTCCGAGACTGCAGGTAGCGAAACTGCTACTTCTGGCTCC
GAAACTGCAGGTACTTCTACTGAGGCTAGTGAAGGTTCCGCATCAGGTACTAGCGAGTCCGCA
ACCAGCGAATCCGGCGCAGGTAGCGAAACTGCTACCTCTGGCTCCGAGACTGCAGGTAGCGAA
ACTGCAACCTCTGGCTCTGAAACTGCAGGTACTAGCGAATCTGCTACTAGCGAATCCGGCGCA
GGTACTAGCGAATCCGCTACCAGCGAATCCGGCGCAGGTAGCGAAACTGCAACCTCTGGTTCC
GAGACTGCA

One may clone the library of XTEN-encoding genes into one or more expression vectors known in the art. To facilitate the identification of well-expressing library members, one can construct the library as fusion to a reporter protein. Non-limiting examples of suitable reporter genes are green fluorescent protein, luciferace, alkaline phosphatase, and beta-galactosidase. By screening, one can identify short XTEN sequences that can be expressed in high concentration in the host organism of choice. Subsequently, one can generate a library of random XTEN dimers and repeat the screen for high level of expression. Subsequently, one can screen the resulting constructs for a number of properties such as level of expression, protease stability, or binding to antiserum.

One aspect of the invention is to provide polynucleotide sequences encoding the components of the fusion protein wherein the creation of the sequence has undergone codon optimization. Of particular interest is codon optimization with the goal of improving expression of the polypeptide compositions and to improve the genetic stability of the encoding gene in the production hosts. For example, codon optimization is of particular importance for XTEN sequences that are rich in glycine or that have very repetitive amino acid sequences. Codon optimization can be performed using computer programs (Gustafsson, C., et al. (2004) Trends Biotechnol, 22: 346-53), some of which minimize ribosomal pausing (Coda Genomics Inc.). In one embodiment, one can perform codon optimization by constructing codon libraries where all members of the library encode the same amino acid sequence but where codon usage is varied. Such libraries can be screened for highly expressing and genetically stable members that are particularly suitable for the large-scale production of XTEN-containing products. When designing XTEN sequences one can consider a number of properties. One can minimize the repetitiveness in the encoding DNA sequences. In addition, one can avoid or minimize the use of codons that are rarely used by the production host (e.g. the AGG and AGA arginine codons and one leucine codon in E. coli). In the case of E. coli, two glycine codons, GGA and GGG, are rarely used in highly expressed proteins. Thus codon optimization of the gene encoding XTEN sequences can be very desirable. DNA sequences that have a high level of glycine tend to have a high GC content that can lead to instability or low expression levels. Thus, when possible, it is preferred to choose codons such that the GC-content of XTEN-encoding sequence is suitable for the production organism that will be used to manufacture the XTEN.

Optionally, the full-length XTEN-encoding gene may comprise one or more sequencing islands. In this context, sequencing islands are short-stretch sequences that are distinct from the XTEN library construct sequences and that include a restriction site not present or expected to be present in the full-length XTEN-encoding gene. In one embodiment, a sequencing island is the sequence

5′-AGGTGCAAGCGCAAGCGGCGCGCCAAGCACGGGAGGT-3′ (SEQ ID NO: 251). In another embodiment, a sequencing island is the sequence

5′-AGGTCCAGAACCAACGGGGCCGGCCCCAAGCGGAGGT-3′ (SEQ ID NO: 252).

As an alternative, one can construct codon libraries where all members of the library encode the same amino acid sequence but where codon usage for the respective amino acids in the sequence is varied. Such libraries can be screened for highly expressing and genetically stable members that are particularly suitable for the large-scale production of XTEN-containing products.

Optionally, one can sequence clones in the library to eliminate isolates that contain undesirable sequences. The initial library of short XTEN sequences can allow some variation in amino acid sequence. For instance one can randomize some codons such that a number of hydrophilic amino acids can occur in a particular position. During the process of iterative multimerization one can screen the resulting library members for other characteristics like solubility or protease resistance in addition to a screen for high-level expression.

Once the gene that encodes the XTEN of desired length and properties is selected, the method provides that it can be genetically fused to the nucleotides encoding the N- and/or the C-terminus of the GP gene(s) by cloning it into the construct adjacent and in frame with the gene coding for GP or, optionally, adjacent to a spacer sequence. The invention provides various permutations of the foregoing, depending on the GPXTEN to be encoded. For example, a gene encoding a GPXTEN fusion protein comprising a GP and two XTEN, such as embodied by formula VI, as depicted above, the gene would have polynucleotides encoding GP, encoding two XTEN, which can be identical or different in composition and sequence length. In one non-limiting embodiment of the foregoing, the GP polynucleotides would encode exendin-4 and the polynucleotides encoding the N-terminus XTEN would encode AE912 and the polynucleotides encoding the C-terminus XTEN would encode AE144. The step of cloning the GP genes into the XTEN construct can occur through a ligation or multimerization step. As shown in FIG. 2, the constructs encoding GPXTEN fusion proteins can be designed in different configurations of the components XTEN 202, GP 203, and spacer sequences 204. In one embodiment, as illustrated in FIG. 2A, the construct comprises polynucleotide sequences complementary to, or those that encode a monomeric polypeptide of components in the following order (5′ to 3′) GP 203 and XTEN 202, or the reverse order. In another embodiment, as illustrated in FIG. 2B, the construct comprises polynucleotide sequences complementary to, or those that encode a monomeric polypeptide of components in the following order (5′ to 3′) GP 203, spacer sequence 204, and XTEN 202, or the reverse order. In another embodiment, as illustrated in FIG. 2C, the construct 201 encodes a monomeric GPXTEN comprising polynucleotide sequences complementary to, or those that encode components in the following order (5′ to 3′): two molecules of GP 203 and XTEN 202, or the reverse order. In another embodiment, as illustrated in FIG. 2D, the construct comprises polynucleotide sequences complementary to, or those that encode a monomeric polypeptide of components in the following order (5′ to 3′): two molecules of GP 203, spacer sequence 204, and XTEN 202, or the reverse order. In another embodiment, as illustrated in FIG. 2E, the construct comprises polynucleotide sequences complementary to, or those that encode a monomeric polypeptide of components in the following order (5′ to 3′): GP 203, spacer sequence 204, a second molecule of GP 203, and XTEN 202, or the reverse order. In another embodiment, as illustrated in FIG. 2F, the construct comprises polynucleotide sequences complementary to, or those that encode a monomeric polypeptide of components in the following order (5′ to 3′): GP 203, XTEN 202, GP 203, and a second XTEN 202, or the reverse sequence. The spacer polynucleotides can optionally comprise sequences encoding cleavage sequences. As will be apparent to those of skill in the art, other permutations of the foregoing are possible.

The invention also encompasses polynucleotides comprising XTEN-encoding polynucleotide variants that have a high percentage of sequence identity to (a) a polynucleotide sequence from Table 9, or (b) sequences that are complementary to the polynucleotides of (a). A polynucleotide with a high percentage of sequence identity is one that has at least about an 80% nucleic acid sequence identity, alternatively at least about 81%, alternatively at least about 82%, alternatively at least about 83%, alternatively at least about 84%, alternatively at least about 85%, alternatively at least about 86%, alternatively at least about 87%, alternatively at least about 88%, alternatively at least about 89%, alternatively at least about 90%, alternatively at least about 91%, alternatively at least about 92%, alternatively at least about 93%, alternatively at least about 94%, alternatively at least about 95%, alternatively at least about 96%, alternatively at least about 97%, alternatively at least about 98%, and alternatively at least about 99% nucleic acid sequence identity to (a) or (b) of the foregoing, or that can hybridize with the target polynucleotide or its complement under stringent conditions.

Homology, sequence similarity or sequence identity of nucleotide or amino acid sequences may also be determined conventionally by using known software or computer programs such as the BestFit or Gap pairwise comparison programs (GCG Wisconsin Package, Genetics Computer Group, 575 Science Drive, Madison, Wis. 53711). BestFit uses the local homology algorithm of Smith and Waterman (Advances in Applied Mathematics. 1981. 2: 482-489), to find the best segment of identity or similarity between two sequences. Gap performs global alignments: all of one sequence with all of another similar sequence using the method of Needleman and Wunsch, (Journal of Molecular Biology. 1970. 48:443-453). When using a sequence alignment program such as BestFit, to determine the degree of sequence homology, similarity or identity, the default setting may be used, or an appropriate scoring matrix may be selected to optimize identity, similarity or homology scores.

Nucleic acid sequences that are “complementary” are those that are capable of base-pairing according to the standard Watson-Crick complementarity rules. As used herein, the term “complementary sequences” means nucleic acid sequences that are substantially complementary, as may be assessed by the same nucleotide comparison set forth above, or as defined as being capable of hybridizing to the polynucleotides that encode the GPXTEN sequences under stringent conditions, such as those described herein.

The resulting polynucleotides encoding the GPXTEN chimeric fusion proteins can then be individually cloned into an expression vector. The nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan. Such techniques are well known in the art and well described in the scientific and patent literature.

Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage. The invention provides for the use of plasmid vectors containing replication and control sequences that are compatible with and recognized by the host cell, and are operably linked to the GPXTEN gene for controlled expression of the GPXTEN fusion proteins. The vector ordinarily carries a replication site, as well as sequences that encode proteins that are capable of providing phenotypic selection in transformed cells. For example, E. coli may be transformed using pBR322, a plasmid derived from an E. coli species (Mandel et al., J Mol. Biol., 53: 154 (1970)). Plasmid pBR322 contains genes for ampicillin and tetracycline resistance and thus provides easy means for selection. Such vector sequences are well known for a variety of bacteria, yeast, and viruses. Useful expression vectors that can be used include, for example, segments of chromosomal, non-chromosomal and synthetic DNA sequences. “Expression vector” refers to a DNA construct containing a DNA sequence that is operably linked to a suitable control sequence capable of effecting the expression of the DNA encoding the fusion protein in a suitable host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences that control termination of transcription and translation. Other suitable vectors include, but are not limited to, derivatives of SV40 and pcDNA and known bacterial plasmids such as col EI, pCR1, pBR322, pMa1-C2, pET, pGEX as described by Smith, et al., Gene 57:31-40 (1988), pMB9 and derivatives thereof, plasmids such as RP4, phage DNAs such as the numerous derivatives of phage I such as NM98 9, as well as other phage DNA such as M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2 micron plasmid or derivatives of the 2 m plasmid, as well as centomeric and integrative yeast shuttle vectors; vectors useful in eukaryotic cells such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or the expression control sequences; and the like. The requirements are that the vectors are replicable and viable in the host cell of choice. Low- or high-copy number vectors may be used as desired.

Promoters suitable for use in expression vectors with prokaryotic hosts include the β-lactamase and lactose promoter systems [Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)], all would be operably linked to the DNA encoding GPXTEN polypeptides. Promoters for use in bacterial systems can also contain a Shine-Dalgarno (S.D.) sequence, operably linked to the DNA encoding GPXTEN polypeptides.

The invention contemplates use of other expression systems including, for example, a baculovirus expression system with both non-fusion transfer vectors, such as, but not limited to pVL941 (BamHI cloning site, available from Summers, et al., Virology 84:390-402 (1978)), pVL1393 (BamHI, Sma1, Xba1, EcoRI, IVot1, Xma111, BgIII and Pst1 cloning sites; Invitrogen), pVL1392 (BgIII, Pst1, NotI, XmaIII, EcoRI, Xba11, Sma1 and BamHI cloning site; Summers, et al., Virology 84:390-402 (1978) and Invitrogen) and pBlueBacIII (BamHI, BgIII, Pst1, Nco1 and Hindi II cloning site, with blue/white recombinant screening, Invitrogen), and fusion transfer vectors such as, but not limited to, pAc7 00 (BamHI and Kpn1 cloning sites, in which the BamHI recognition site begins with the initiation codon; Summers, et al., Virology 84:390-402 (1978)), pAc701 and pAc70-2 (same as pAc700, with different reading frames), pAc360 [BamHI cloning site 36 base pairs downstream of a polyhedrin initiation codon; Invitrogen (1995)) and pBlueBacHisA, B, C (three different reading frames with BamH I, BgI II, Pst1, Nco 1 and Hind III cloning site, an N-terminal peptide for ProBond purification and blue/white recombinant screening of plaques; Invitrogen (220) can be used.

Mammalian expression vectors can comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements. Mammalian expression vectors contemplated for use in the invention include vectors with inducible promoters, such as the dihydrofolate reductase promoters, any expression vector with a DHFR expression cassette or a DHFR/methotrexate co-amplification vector such as pED (Pst1, Sai1, Sba1, Sma1 and EcoRI cloning sites, with the vector expressing both the cloned gene and DHFR; Randal J. Kaufman, 1991, Randal J. Kaufman, Current Protocols in Molecular Biology, 16,12 (1991)). Alternatively a glutamine synthetase/methionine sulfoximine co-amplification vector, such as pEE14 (Hind111, Xba11, Sma1, Sba1, EcoRI and Se11 cloning sites in which the vector expresses glutamine synthetase and the cloned gene; Celltech). A vector that directs episomal expression under the control of the Epstein Barr Virus (EBV) or nuclear antigen (EBNA) can be used such as pREP4 (BamHI r SfH, Xho1, NotI, Nhe1, Hindi II, NheI, PvuII and Kpn1 cloning sites, constitutive RSV-LTR promoter, hygromycin selectable marker; Invitrogen), pCEP4 (BamHI, SfH, Xho1, NotI, Nhe1, Hind111, Nhe1, PvuII and Kpn1 cloning sites, constitutive hCMV immediate early gene promoter, hygromycin selectable marker; Invitrogen), pMEP4 (.Kpn1, Pvu1, Nhe1, Hind111, NotI, Xho1, Sfi1, BamHI cloning sites, inducible methallothionein H a gene promoter, hygromycin selectable marker, Invitrogen), pREP8 (BamHI, Xho1, NotI, Hind111, Nhe1 and Kpn1 cloning sites, RSV-LTR promoter, histidinol selectable marker; Invitrogen), pREP9 (Kpn1, Nhe1, Hind 111, NotI, Xho 1, Sfi 1, BamH I cloning sites, RSV-LTR promoter, G418 selectable marker; Invitrogen), and pEBVHis (RSV-LTR promoter, hygromycin selectable marker, N-terminal peptide purifiable via ProBond resin and cleaved by enterokinase; Invitrogen).

Selectable mammalian expression vectors for use in the invention include, but are not limited to, pRc/CMV (Hind 111, BstXI, NotI, Sba1 and Apa1 cloning sites, G418 selection, Invitrogen), pRc/RSV (Hind II, Spe1, BstXI, NotI, Xba1 cloning sites, G418 selection, Invitrogen) and the like. Vaccinia virus mammalian expression vectors (see, for example, Randall J. Kaufman, Current Protocols in Molecular Biology 16.12 (Frederick M. Ausubel, et al., eds. Wiley 1991) that can be used in the present invention include, but are not limited to, pSC11 (Sma1 cloning site, TK- and beta-gal selection), pMJ601 (Sal 1, Sma 1, A f1I, Nar1, BspM1I, BamHI, Apa1, Nhe1, SacII, Kpn1 and Hind111 cloning sites; TK- and -gal selection), pTKgptF1S (EcoRI, Pst1, SaIII, Acc1, HindII, Sba1, BamHI and Hpa cloning sites, TK or XPRT selection) and the like.

Yeast expression systems that can also be used in the present invention include, but are not limited to, the non-fusion pYES2 vector (XJba1, Sph1, Sho1, NotI, GstXI, EcoRI, BstXI, BamHI, Sad, Kpn1 and Hind111 cloning sites, Invitrogen), the fusion pYESHisA, B, C (Xba11, Sph1, Sho1, NotI, BstXI, EcoRI, BamHI, Sad, Kpn1 and Hindi II cloning sites, N-terminal peptide purified with ProBond resin and cleaved with enterokinase; Invitrogen), pRS vectors and the like.

In addition, the expression vector containing the chimeric GPXTEN fusion protein-encoding polynucleotide molecule may include drug selection markers. Such markers aid in cloning and in the selection or identification of vectors containing chimeric DNA molecules. For example, genes that confer resistance to neomycin, puromycin, hygromycin, dihydrofolate reductase (DHFR) inhibitor, guanine phosphoribosyl transferase (GPT), zeocin, and histidinol are useful selectable markers. Alternatively, enzymes such as herpes simplex virus thymidine kinase (tk) or chloramphenicol acetyltransferase (CAT) may be employed. Immunologic markers also can be employed. Any known selectable marker may be employed so long as it is capable of being expressed simultaneously with the nucleic acid encoding a gene product. Further examples of selectable markers are well known to one of skill in the art and include reporters such as enhanced green fluorescent protein (EGFP), beta-galactosidase (β-gal) or chloramphenicol acetyltransferase (CAT).

In one embodiment, the polynucleotide encoding a GPXTEN fusion protein composition can be fused C-terminally to an N-terminal signal sequence appropriate for the expression host system. Signal sequences are typically proteolytically removed from the protein during the translocation and secretion process, generating a defined N-terminus. A wide variety of signal sequences have been described for most expression systems, including bacterial, yeast, insect, and mammalian systems. A non-limiting list of preferred examples for each expression system follows herein. Preferred signal sequences are OmpA, PhoA, and DsbA for E. coli expression. Signal peptides preferred for yeast expression are ppL-alpha, DEX4, invertase signal peptide, acid phosphatase signal peptide, CPY, or INU1. For insect cell expression the preferred signal sequences are sexta adipokinetic hormone precursor, CP1, CP2, CP3, CP4, TPA, PAP, or gp67. For mammalian expression the preferred signal sequences are IL2L, SV40, IgG kappa and IgG lambda.

In another embodiment, a leader sequence, potentially comprising a well-expressed, independent protein domain, can be fused to the N-terminus of the GPXTEN sequence, separated by a protease cleavage site. While any leader peptide sequence which does not inhibit cleavage at the designed proteolytic site can be used, sequences in preferred embodiments will comprise stable, well-expressed sequences such that expression and folding of the overall composition is not significantly adversely affected, and preferably expression, solubility, and/or folding efficiency are significantly improved. A wide variety of suitable leader sequences have been described in the literature. A non-limiting list of suitable sequences includes maltose binding protein, cellulose binding domain, glutathione S-transferase, 6×His tag (SEQ ID NO: 253), FLAG tag, hemaglutinin tag, and green fluorescent protein. The leader sequence can also be further improved by codon optimization, especially in the second codon position following the ATG start codon, by methods well described in the literature and hereinabove.

Various in vitro enzymatic methods for cleaving proteins at specific sites are known. Such methods include use of enterokinase (DDDK (SEQ ID NO: 254)), Factor Xa (IDGR (SEQ ID NO: 255)), thrombin (LVPRGS (SEQ ID NO: 256)), PreScission™ (LEVLFQGP (SEQ ID NO: 257)), TEV protease (EQLYFQG (SEQ ID NO: 258)), 3C protease (ETLFQGP (SEQ ID NO: 259)), Sortase A (LPETG (SEQ ID NO: 260)), Granzyme B (D/X, N/X, M/N or S/X), inteins, SUMO, DAPase (TAGZyme™), Aeromonas aminopeptidase, Aminopeptidase M, and carboxypeptidases A and B. Additional methods are disclosed in Arnau, et al., Protein Expression and Purification 48: 1-13 (2006).

In other cases, the invention provides polynucleotide constructs and methods of making constructs (e.g., as described in the Examples) comprising an optimized polynucleotide sequence encoding at least about 20 to about 60 amino acids with XTEN characteristics can be included at the N-terminus of the XTEN-encoding sequence to promote the initiation of translation to allow for expression of XTEN fusions at the N-terminus of proteins without the presence of a helper domain. In an advantage of the foregoing, the sequence does not require subsequent cleavage of a helper domain, thereby reducing the number of steps to manufacture XTEN-containing compositions. As described in more detail in the Examples, the optimized N-terminal sequence has attributes of an unstructured protein, but may include nucleotide bases encoding amino acids selected for their ability to promote initiation of translation and enhanced expression. In one embodiment of the foregoing, the optimized polynucleotide encodes an XTEN sequence with at least about 90% sequence identity to AE912. In another embodiment of the foregoing, the optimized polynucleotide encodes an XTEN sequence with at least about 90% sequence identity to AM923. In another embodiment of the foregoing, the optimized polynucleotide encodes an XTEN sequence with at least about 90% sequence identity to AE624. In another embodiment of the foregoing, the optimized polynucleotide encodes an XTEN sequence with at least about 90% sequence identity to AE48. In another embodiment of the foregoing, the optimized polynucleotide encodes an XTEN sequence with at least about 90% sequence identity to AM48. In one embodiment, the optimized polynucleotide NTS comprises a sequence that exhibits at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%, sequence identity to a sequence or its complement selected from AE 48: 5′-ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTACCCCGGGTAGCGGTACTGCTT CTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTCTCCGGGCACC AGCTCTACCGGTTCTCCA-3′ (SEQ ID NO: 261) and AM 48: 5′-ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTGCATCCCCGGGCACCAGCTCTA CCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTACCCCGTCT GGTGCTACTGGCTCTCCA-3′ (SEQ ID NO: 262)

In another embodiment, the protease site of the leader sequence construct is chosen such that it is recognized by an in vivo protease. In this embodiment, the protein is purified from the expression system while retaining the leader by avoiding contact with an appropriate protease. The full-length construct is then injected into a patient. Upon injection, the construct comes into contact with the protease specific for the cleavage site and is cleaved by the protease. In the case where the uncleaved protein is substantially less active than the cleaved form, this method has the beneficial effect of allowing higher initial doses while avoiding toxicity, as the active form is generated slowly in vivo. Some non-limiting examples of in vivo proteases which are useful for this application include tissue kallikrein, plasma kallikrein, trypsin, pepsin, chymotrypsin, thrombin, and matrix metalloproteinases, or the proteases of Table 8.

In this manner, a chimeric DNA molecule coding for a monomeric GPXTEN fusion protein is generated within the construct. Optionally, this chimeric DNA molecule may be transferred or cloned into another construct that is a more appropriate expression vector. At this point, a host cell capable of expressing the chimeric DNA molecule can be transformed with the chimeric DNA molecule. The vectors containing the DNA segments of interest can be transferred into the host cell by well-known methods, depending on the type of cellular host. For example, calcium chloride transfection is commonly utilized for prokaryotic cells, whereas calcium phosphate treatment, lipofection, or electroporation may be used for other cellular hosts. Other methods used to transform mammalian cells include the use of polybrene, protoplast fusion, liposomes, electroporation, and microinjection. See, generally, Sambrook, et al., supra.

The transformation may occur with or without the utilization of a carrier, such as an expression vector. Then, the transformed host cell is cultured under conditions suitable for expression of the chimeric DNA molecule encoding of GPXTEN.

The present invention also provides a host cell for expressing the monomeric fusion protein compositions disclosed herein. Examples of suitable eukaryotic host cells include, but are not limited to mammalian cells, such as VERO cells, HELA cells such as ATCC No. CCL2, CHO cell lines, COS cells, WI38 cells, BHK cells, HepG2 cells, 3T3 cells, A549 cells, PC12 cells, K562 cells, 293 cells, Sf9 cells and CvI cells. Examples of suitable non-mammalian eukaryotic cells include eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for encoding vectors. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. Others include Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 [1981]; EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Pat. No. 4,943,529; Fleer et al., Bio/Technology, 9:968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 737 [1983]), K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al., Bio/Technology, 8:135 (1990)), K. thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic Microbiol., 28:265-278 [1988]); Candida; Trichoderma reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76:5259-5263 [1979]); Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538 published 31 Oct. 1990); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 Jan. 1991), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res. Commun., 112:284-289 [1983]; Tilburn et al., Gene, 26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA, 81: 1470-1474 [1984]) and A. niger (Kelly and Hynes, EMBO J., 4:475-479 [1985]). Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).

Other suitable cells that can be used in the present invention include, but are not limited to, prokaryotic host cells strains such as Escherichia coli, (e.g., strain DH5-α), Bacillus subtilis, Salmonella typhimurium, or strains of the genera of Pseudomonas, Streptomyces and Staphylococcus. Non-limiting examples of suitable prokaryotes include those from the genera: Actinoplanes; Archaeoglobus; Bdellovibrio; Borrelia; Chloroflexus; Enterococcus; Escherichia; Lactobacillus; Listeria; Oceanobacillus; Paracoccus; Pseudomonas; Staphylococcus; Streptococcus; Streptomyces; Thermoplasma; and Vibrio. Non-limiting examples of specific strains include: Archaeoglobus fulgidus; Bdellovibrio bacteriovorus; Borrelia burgdorferi; Chloroflexus aurantiacus; Enterococcus faecalis; Enterococcus faecium; Lactobacillus johnsonii; Lactobacillus plantarum; Lactococcus lactis; Listeria innocua; Listeria monocytogenes; Oceanobacillus iheyensis; Paracoccus zeaxanthinifaciens; Pseudomonas mevalonii; Staphylococcus aureus; Staphylococcus epidermidis; Staphylococcus haemolyticus; Streptococcus agalactiae; Streptomyces griseolosporeus; Streptococcus mutans; Streptococcus pneumoniae; Streptococcus pyogenes; Thermoplasma acidophilum; Thermoplasma volcanium; Vibrio cholerae; Vibrio parahaemolyticus; and Vibrio vulnificus.

Host cells containing the polynucleotides of interest can be cultured in conventional nutrient media (e.g., Ham's nutrient mixture) modified as appropriate for activating promoters, selecting transformants or amplifying genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. For compositions secreted by the host cells, supernatant from centrifugation is separated and retained for further purification. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, all of which are well known to those skilled in the art. Embodiments that involve cell lysis may entail use of a buffer that contains protease inhibitors that limit degradation after expression of the chimeric DNA molecule. Suitable protease inhibitors include, but are not limited to leupeptin, pepstatin or aprotinin. The supernatant then may be precipitated in successively increasing concentrations of saturated ammonium sulfate.

Gene expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

Gene expression, alternatively, may be measured by immunological of fluorescent methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids or the detection of selectable markers, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal Conveniently, the antibodies may be prepared against a native sequence GP polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to GP and encoding a specific antibody epitope. Examples of selectable markers are well known to one of skill in the art and include reporters such as enhanced green fluorescent protein (EGFP), beta-galactosidase (β-gal) or chloramphenicol acetyltransferase (CAT).

Expressed GPXTEN polypeptide product(s) may be purified via methods known in the art or by methods disclosed herein. Procedures such as gel filtration, affinity purification, salt fractionation, ion exchange chromatography, size exclusion chromatography, hydroxyapatite adsorption chromatography, hydrophobic interaction chromatography and gel electrophoresis may be used; each tailored to recover and purify the fusion protein produced by the respective host cells. Some expressed GPXTEN may require refolding during isolation and purification. Methods of purification are described in Robert K. Scopes, Protein Purification: Principles and Practice, Charles R. Castor (ed.), Springer-Verlag 1994, and Sambrook, et al., supra. Multi-step purification separations are also described in Baron, et al., Crit. Rev. Biotechnol. 10:179-90 (1990) and Below, et al., J. Chromatogr. A. 679:67-83 (1994).

VIII) Pharmaceutical Compositions

The present invention provides pharmaceutical compositions comprising GPXTEN. In one embodiment, the pharmaceutical composition comprises the GPXTEN fusion protein and at least me pharmaceutically acceptable carrier. GPXTEN polypeptides of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby the polypeptide is combined in admixture with a pharmaceutically acceptable carrier vehicle, such as aqueous solutions or buffers, pharmaceutically acceptable suspensions and emulsions. Examples of non-aqueous solvents include propyl ethylene glycol, polyethylene glycol and vegetable oils. Therapeutic formulations are prepared for storage by mixing the active ingredient having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers, as described in Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980), in the form of lyophilized formulations or aqueous solutions.

The pharmaceutical compositions can be administered orally, intranasally, parenterally or by inhalation therapy, and may take the form of tablets, lozenges, granules, capsules, pills, ampoules, suppositories or aerosol form. They may also take the form of suspensions, solutions and emulsions of the active ingredient in aqueous or nonaqueous diluents, syrups, granulates or powders. In addition, the pharmaceutical compositions can also contain other pharmaceutically active compounds or a plurality of compounds of the invention.

More particularly, the present pharmaceutical compositions may be administered for therapy by any suitable route including oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parenteral (including subcutaneous, subcutaneous by infusion pump, intramuscular, intravenous and intradermal), intravitreal, and pulmonary. It will also be appreciated that the preferred route will vary with the condition and age of the recipient, and the disease being treated.

In one embodiment, the pharmaceutical composition is administered subcutaneously. In this embodiment, the composition may be supplied as a lyophilized powder to be reconstituted prior to administration. The composition may also be supplied in a liquid form, which can be administered directly to a patient. In one embodiment, the composition is supplied as a liquid in a pre-filled syringe such that a patient can easily self-administer the composition.

Extended release formulations useful in the present invention may be oral formulations comprising a matrix and a coating composition. Suitable matrix materials may include waxes (e.g., camauba, bees wax, paraffin wax, ceresine, shellac wax, fatty acids, and fatty alcohols), oils, hardened oils or fats (e.g., hardened rapeseed oil, castor oil, beef tallow, palm oil, and soya bean oil), and polymers (e.g., hydroxypropyl cellulose, polyvinylpyrrolidone, hydroxypropyl methyl cellulose, and polyethylene glycol). Other suitable matrix tabletting materials are microcrystalline cellulose, powdered cellulose, hydroxypropyl cellulose, ethyl cellulose, with other carriers, and fillers. Tablets may also contain granulates, coated powders, or pellets. Tablets may also be multi-layered. Multi-layered tablets are especially preferred when the active ingredients have markedly different pharmacokinetic profiles. Optionally, the finished tablet may be coated or uncoated.

The coating composition may comprise an insoluble matrix polymer and/or a water soluble material. Water soluble materials can be polymers such as polyethylene glycol, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, polyvinylpyrrolidone, polyvinyl alcohol, or monomeric materials such as sugars (e.g., lactose, sucrose, fructose, mannitol and the like), salts (e.g., sodium chloride, potassium chloride and the like), organic acids (e.g., fumaric acid, succinic acid, lactic acid, and tartaric acid), and mixtures thereof. Optionally, an enteric polymer may be incorporated into the coating composition. Suitable enteric polymers include hydroxypropyl methyl cellulose, acetate succinate, hydroxypropyl methyl cellulose, phthalate, polyvinyl acetate phthalate, cellulose acetate phthalate, cellulose acetate trimellitate, shellac, zein, and polymethacrylates containing carboxyl groups. The coating composition may be plasticised by adding suitable plasticisers such as, for example, diethyl phthalate, citrate esters, polyethylene glycol, glycerol, acetylated glycerides, acetylated citrate esters, dibutylsebacate, and castor oil. The coating composition may also include a filler, which can be an insoluble material such as silicon dioxide, titanium dioxide, talc, kaolin, alumina, starch, powdered cellulose, MCC, or polacrilin potassium. The coating composition may be applied as a solution or latex in organic solvents or aqueous solvents or mixtures thereof. Solvents such as water, lower alcohol, lower chlorinated hydrocarbons, ketones, or mixtures thereof may be used.

The compositions of the invention may be formulated using a variety of excipients. Suitable excipients include microcrystalline cellulose (e.g. Avicel PH102, Avicel PH101), polymethacrylate, poly(ethyl acrylate, methyl methacrylate, trimethylammonioethyl methacrylate chloride) (such as Eudragit RS-30D), hydroxypropyl methylcellulose (Methocel K100M, Premium CR Methocel K100M, Methocel E5, Opadry®), magnesium stearate, talc, triethyl citrate, aqueous ethylcellulose dispersion (Surelease®), and protamine sulfate. The slow release agent may also comprise a carrier, which can comprise, for example, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents. Pharmaceutically acceptable salts can also be used in these slow release agents, for example, mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates, as well as the salts of organic acids such as acetates, proprionates, malonates, or benzoates. The composition may also contain liquids, such as water, saline, glycerol, and ethanol, as well as substances such as wetting agents, emulsifying agents, or pH buffering agents. Liposomes may also be used as a carrier.

In another embodiment, the compositions of the present invention are encapsulated in liposomes, which have demonstrated utility in delivering beneficial active agents in a controlled manner over prolonged periods of time. Liposomes are closed bilayer membranes containing an entrapped aqueous volume. Liposomes may also be unilamellar vesicles possessing a single membrane bilayer or multilamellar vesicles with multiple membrane bilayers, each separated from the next by an aqueous layer. The structure of the resulting membrane bilayer is such that the hydrophobic (non-polar) tails of the lipid are oriented toward the center of the bilayer while the hydrophilic (polar) heads orient towards the aqueous phase. In one embodiment, the liposome may be coated with a flexible water soluble polymer that avoids uptake by the organs of the mononuclear phagocyte system, primarily the liver and spleen. Suitable hydrophilic polymers for surrounding the liposomes include, without limitation, PEG, polyvinylpyrrolidone, polyvinylmethylether, polymethyloxazoline, polyethyloxazoline, polyhydroxypropyloxazoline, polyhydroxypropylmethacrylamide, polymethacrylamide, polydimethylacrylamide, polyhydroxypropylmethacrylate, polyhydroxethylacrylate, hydroxymethylcellulose hydroxyethylcellulose, polyethyleneglycol, polyaspartamide and hydrophilic peptide sequences as described in U.S. Pat. Nos. 6,316,024; 6,126,966; 6,056,973; 6,043,094, the contents of which are incorporated by reference in their entirety.

Liposomes may be comprised of any lipid or lipid combination known in the art. For example, the vesicle-forming lipids may be naturally-occurring or synthetic lipids, including phospholipids, such as phosphatidylcholine, phosphatidylethanolamine, phosphatidic acid, phosphatidylserine, phasphatidylglycerol, phosphatidylinositol, and sphingomyelin as disclosed in U.S. Pat. Nos. 6,056,973 and 5,874,104. The vesicle-forming lipids may also be glycolipids, cerebrosides, or cationic lipids, such as 1,2-dioleyloxy-3-(trimethylamino) propane (DOTAP); N-[1-(2,3,-ditetradecyloxy)propyl]-N,N-dimethyl-N-hydroxyethylammonium bromide (DMRIE); N-[1-[(2,3,-dioleyloxy)propyl]-N,N-dimethyl-N-hydroxy ethylammonium bromide (DORIE); N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA); 3 [N—(N′,N′-dimethylaminoethane) carbamoly] cholesterol (DC-Chol); or dimethyldioctadecylammonium (DDAB) also as disclosed in U.S. Pat. No. 6,056,973. Cholesterol may also be present in the proper range to impart stability to the vesicle as disclosed in U.S. Pat. Nos. 5,916,588 and 5,874,104.

Additional liposomal technologies are described in U.S. Pat. Nos. 6,759,057; 6,406,713; 6,352,716; 6,316,024; 6,294,191; 6,126,966; 6,056,973; 6,043,094; 5,965,156; 5,916,588; 5,874,104; 5,215,680; and 4,684,479, the contents of which are incorporated herein by reference. These describe liposomes and lipid-coated microbubbles, and methods for their manufacture. Thus, one skilled in the art, considering both the disclosure of this invention and the disclosures of these other patents could produce a liposome for the extended release of the polypeptides of the present invention.

For liquid formulations, a desired property is that the formulation be supplied in a form that can pass through a 25, 28, 30, 31, 32 gauge needle for intravenous, intramuscular, intraarticular, or subcutaneous administration.

Administration via transdermal formulations can be performed using methods also known in the art, including those described generally in, e.g., U.S. Pat. Nos. 5,186,938 and 6,183,770, 4,861,800, 6,743,211, 6,945,952, 4,284,444, and WO 89/09051, incorporated herein by reference in their entireties. A transdermal patch is a particularly useful embodiment with polypeptides having absorption problems. Patches can be made to control the release of skin-permeable active ingredients over a 12 hour, 24 hour, 3 day, and 7 day period. In one example, a 2-fold daily excess of a polypeptide of the present invention is placed in a non-volatile fluid. The compositions of the invention are provided in the form of a viscous, non-volatile liquid. The penetration through skin of specific formulations may be measures by standard methods in the art (for example, Franz et al., J. Invest. Derm. 64:194-195 (1975)). Examples of suitable patches are passive transfer skin patches, iontophoretic skin patches, or patches with microneedles such as Nicoderm.

In other embodiments, the composition may be delivered via intranasal, buccal, or sublingual routes to the brain to enable transfer of the active agents through the olfactory passages into the CNS and reducing the systemic administration. Devices commonly used for this route of administration are included in U.S. Pat. No. 6,715,485. Compositions delivered via this route may enable increased CNS dosing or reduced total body burden reducing systemic toxicity risks associated with certain drugs. Preparation of a pharmaceutical composition for delivery in a subdermally implantable device can be performed using methods known in the art, such as those described in, e.g., U.S. Pat. Nos. 3,992,518; 5,660,848; and 5,756,115.

Osmotic pumps may be used as slow release agents in the form of tablets, pills, capsules or implantable devices. Osmotic pumps are well known in the art and readily available to one of ordinary skill in the art from companies experienced in providing osmotic pumps for extended release drug delivery. Examples are ALZA's DUROS™; ALZA's OROS™; Osmotica Pharmaceutical's Osmodex™ system; Shire Laboratories' EnSoTrol™ system; and Alzet™. Patents that describe osmotic pump technology are U.S. Pat. Nos. 6,890,918; 6,838,093; 6,814,979; 6,713,086; 6,534,090; 6,514,532; 6,361,796; 6,352,721; 6,294,201; 6,284,276; 6,110,498; 5,573,776; 4,200,0984; and 4,088,864, the contents of which are incorporated herein by reference. One skilled in the art, considering both the disclosure of this invention and the disclosures of these other patents could produce an osmotic pump for the extended release of the polypeptides of the present invention.

Syringe pumps may also be used as slow release agents. Such devices are described in U.S. Pat. Nos. 4,976,696; 4,933,185; 5,017,378; 6,309,370; 6,254,573; 4,435,173; 4,398,908; 6,572,585; 5,298,022; 5,176,502; 5,492,534; 5,318,540; and 4,988,337, the contents of which are incorporated herein by reference. One skilled in the art, considering both the disclosure of this invention and the disclosures of these other patents could produce a syringe pump for the extended release of the compositions of the present invention.

IX) Pharmaceutical Kits

In another aspect, the invention provides a kit to facilitate the use of the GPXTEN polypeptides. The kit comprises the pharmaceutical composition provided herein, a label identifying the pharmaceutical composition, and an instruction for storage, reconstitution and/or administration of the pharmaceutical compositions to a subject In some embodiment, the kit comprises, preferably: (a) an amount of a GPXTEN fusion protein composition sufficient to treat a disease, condition or disorder upon administration to a subject in need thereof; and (b) an amount of a pharmaceutically acceptable carrier; together in a formulation ready for injection or for reconstitution with sterile water, buffer, or dextrose; together with a label identifying the GPXTEN drug and storage and handling conditions, and a sheet of the approved indications for the drug, instructions for the reconstitution and/or administration of the GPXTEN drug for the use for the prevention and/or treatment of a approved indication, appropriate dosage and safety information, and information identifying the lot and expiration of the drug. In another embodiment of the foregoing, the kit can comprise a second container that can carry a suitable diluent for the GPXTEN composition, which will provide the user with the appropriate concentration of GPXTEN to be delivered to the subject.

EXAMPLES

Example 1: Construction of XTEN_AD36 Motif Segments

The following example describes the construction of a collection of codon-optimized genes encoding motif sequences of 36 amino acids. As a first step, a stuffer vector pCW0359 was constructed based on a pET vector and that includes a T7 promoter. pCW0359 encodes a cellulose binding domain (CBD) and a TEV protease recognition site followed by a stuffer sequence that is flanked by BsaI, BbsI, and KpnI sites. The BsaI and BbsI sites were inserted such that they generate compatible overhangs after digestion. The stuffer sequence is followed by a truncated version of the GFP gene and a His tag. The stuffer sequence contains stop codons and thus E. coli cells carrying the stuffer plasmid pCW0359 form non-fluorescent colonies. The stuffer vector pCW0359 was digested with BsaI and KpnI to remove the stuffer segment and the resulting vector fragment was isolated by agarose gel purification. The sequences were designated XTEN_AD36, reflecting the AD family of motifs. Its segments have the amino acid sequence [X]3 where X is a 12 mer peptide with the sequences: GESPGGSSGSES (SEQ ID NO: 263), GSEGSSGPGESS (SEQ ID NO: 264), GSSESGSSEGGP (SEQ ID NO: 265), or GSGGEPSESGSS (SEQ ID NO: 266). The insert was obtained by annealing the following pairs of phosphorylated synthetic oligonucleotide pairs:


AD1for:
(SEQ ID NO: 267)
AGGTGAATCTCCDGGTGGYTCYAGCGGTTCYGARTC
AD1rev:
(SEQ ID NO: 268)
ACCTGAYTCRGAACCGCTRGARCCACCHGGAGATTC
AD2for:
(SEQ ID NO: 269)
AGGTAGCGAAGGTTCTTCYGGTCCDGGYGARTCYTC
AD2rev:
(SEQ ID NO: 270)
ACCTGARGAYTCRCCHGGACCRGAAGAACCTTCGCT
AD3for:
(SEQ ID NO: 271)
AGGTTCYTCYGAAAGCGGTTCTTCYGARGGYGGTCC
AD3rev:
(SEQ ID NO: 272)
ACCTGGACCRCCYTCRGAAGAACCGCTTTCRGARGA
AD4for:
(SEQ ID NO: 273)
AGGTTCYGGTGGYGAACCDTCYGARTCTGGTAGCTC

We also annealed the phosphorylated oligonucleotide 3KpnIstopperFor: AGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 274) and the non-phosphorylated oligonucleotide pr_3 KpnIstopperRev: CCTCGAGTGAAGACGA (SEQ ID NO: 275). The annealed oligonucleotide pairs were ligated, which resulted in a mixture of products with varying length that represents the varying number of 12 mer repeats ligated to one BbsI/KpnI segment. The products corresponding to the length of 36 amino acids were isolated from the mixture by preparative agarose gel electrophoresis and ligated into the BsaI/KpnI digested stuffer vector pCW0359. Most of the clones in the resulting library designated LCW0401 showed green fluorescence after induction, which shows that the sequence of XTEN_AD36 had been ligated in frame with the GFP gene and that most sequences of XTEN_AD36 had good expression levels.

We screened 96 isolates from library LCW0401 for high level of fluorescence by stamping them onto agar plate containing IPTG. The same isolates were evaluated by PCR and 48 isolates were identified that contained segments with 36 amino acids as well as strong fluorescence. These isolates were sequenced and 39 clones were identified that contained correct XTEN_AD36 segments. The file names of the nucleotide and amino acid constructs for these segments are listed in Table 10.


TABLE 10
DNA and Amino Acid Sequences for 36-mer motifs
Amino acid
SEQ ID
SEQ ID
File name
sequence
NO:
Nucleotide sequence
NO:
LCW0401_001_GFP-
GSGGEPSESGSSGE
276
GGTTCTGGTGGCGAACCGTCCGAGTCTGGTAGCTCAGG
277
N_A01.ab1
SPGGSSGSESGESP
TGAATCTCCGGGTGGCTCTAGCGGTTCCGAGTCAGGTG
GGSSGSES
AATCTCCTGGTGGTTCCAGCGGTTCCGAGTCA
LCW0401_002_GFP-
GSEGSSGPGESSGE
278
GGTAGCGAAGGTTCTTCTGGTCCTGGCGAGTCTTCAGG
279
N_B01.ab1
SPGGSSGSESGSSE
TGAATCTCCTGGTGGTTCCAGCGGTTCTGAATCAGGTT
SGSSEGGP
CCTCCGAAAGCGGTTCTTCCGAGGGCGGTCCA
LCW0401_003_GFP-
GSSESGSSEGGPGS
280
GGTTCCTCTGAAAGCGGTTCTTCCGAAGGTGGTCCAGG
281
N_C01.ab1
SESGSSEGGPGESP
TTCCTCTGAAAGCGGTTCTTCTGAGGGTGGTCCAGGTG
GGSSGSES
AATCTCCGGGTGGCTCCAGCGGTTCCGAGTCA
LCW0401_004_GFP-
GSGGEPSESGSSGS
282
GGTTCCGGTGGCGAACCGTCTGAATCTGGTAGCTCAGG
283
N_D01.ab1
SESGSSEGGPGSGG
TTCTTCTGAAAGCGGTTCTTCCGAGGGTGGTCCAGGTT
EPSESGSS
CTGGTGGTGAACCTTCCGAGTCTGGTAGCTCA
LCW0401_007_GFP-
GSSESGSSEGGPGS
284
GGTTCTTCCGAAAGCGGTTCTTCTGAGGGTGGTCCAGG
285
N_F01.ab1
EGSSGPGESSGSEG
TAGCGAAGGTTCTTCCGGTCCAGGTGAGTCTTCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCTGGTGAATCTTCA
LCW0401_008_GFP-
GSSESGSSEGGPGE
286
GGTTCCTCTGAAAGCGGTTCTTCCGAGGGTGGTCCAGG
287
N_G01.ab1
SPGGSSGSESGSEG
TGAATCTCCAGGTGGTTCCAGCGGTTCTGAGTCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCAGGTGAATCCTCA
LCW0401_012_GFP-
GSGGEPSESGSSGS
288
GGTTCTGGTGGTGAACCGTCTGAGTCTGGTAGCTCAGG
289
N_H01.ab1
GGEPSESGSSGSEG
TTCCGGTGGCGAACCATCCGAATCTGGTAGCTCAGGTA
SSGPGESS
GCGAAGGTTCTTCCGGTCCAGGTGAGTCTTCA
LCW0401_015_GFP-
GSSESGSSEGGPGS
290
GGTTCTTCCGAAAGCGGTTCTTCCGAAGGCGGTCCAGG
291
N_A02.ab1
EGSSGPGESSGESP
TAGCGAAGGTTCTTCTGGTCCAGGCGAATCTTCAGGTG
GGSSGSES
AATCTCCTGGTGGCTCCAGCGGTTCTGAGTCA
LCW0401_016_GFP-
GSSESGSSEGGPGS
292
GGTTCCTCCGAAAGCGGTTCTTCTGAGGGCGGTCCAGG
293
N_B02.ab1
SESGSSEGGPGSSE
TTCCTCCGAAAGCGGTTCTTCCGAGGGCGGTCCAGGTT
SGSSEGGP
CTTCTGAAAGCGGTTCTTCCGAGGGCGGTCCA
LCW0401_020_GFP-
GSGGEPSESGSSGS
294
GGTTCCGGTGGCGAACCGTCCGAATCTGGTAGCTCAGG
295
N_E02.ab1
EGSSGPGESSGSSE
TAGCGAAGGTTCTTCTGGTCCAGGCGAATCTTCAGGTT
SGSSEGGP
CCTCTGAAAGCGGTTCTTCTGAGGGCGGTCCA
LCW0401_022_GFP-
GSGGEPSESGSSGS
296
GGTTCTGGTGGTGAACCGTCCGAATCTGGTAGCTCAGG
297
N_F02.ab1
SESGSSEGGPGSGG
TTCTTCCGAAAGCGGTTCTTCTGAAGGTGGTCCAGGTT
EPSESGSS
CCGGTGGCGAACCTTCTGAATCTGGTAGCTCA
LCW0401_024_GFP-
GSGGEPSESGSSGS
298
GGTTCTGGTGGCGAACCGTCCGAATCTGGTAGCTCAGG
299
N_G02.ab1
SESGSSEGGPGESP
TTCCTCCGAAAGCGGTTCTTCTGAAGGTGGTCCAGGTG
GGSSGSES
AATCTCCAGGTGGTTCTAGCGGTTCTGAATCA
LCW0401_026_GFP-
GSGGEPSESGSSGE
300
GGTTCTGGTGGCGAACCGTCTGAGTCTGGTAGCTCAGG
301
N_H02.ab1
SPGGSSGSESGSEG
TGAATCTCCTGGTGGCTCCAGCGGTTCTGAATCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCTGGTGAATCTTCA
LCW0401_027_GFP-
GSGGEPSESGSSGE
302
GGTTCCGGTGGCGAACCTTCCGAATCTGGTAGCTCAGG
303
N_A03.ab1
SPGGSSGSESGSGG
TGAATCTCCGGGTGGTTCTAGCGGTTCTGAGTCAGGTT
EPSESGSS
CTGGTGGTGAACCTTCCGAGTCTGGTAGCTCA
LCW0401_028_GFP-
GSSESGSSEGGPGS
304
GGTTCCTCTGAAAGCGGTTCTTCTGAGGGCGGTCCAGG
305
N_B03.ab1
SESGSSEGGPGSSE
TTCTTCCGAAAGCGGTTCTTCCGAGGGCGGTCCAGGTT
SGSSEGGP
CTTCCGAAAGCGGTTCTTCTGAAGGCGGTCCA
LCW0401_030_GFP-
GESPGGSSGSESGS
306
GGTGAATCTCCGGGTGGCTCCAGCGGTTCTGAGTCAGG
307
N_C03.ab1
EGSSGPGESSGSEG
TAGCGAAGGTTCTTCCGGTCCGGGTGAGTCCTCAGGTA
SSGPGESS
GCGAAGGTTCTTCCGGTCCTGGTGAGTCTTCA
LCW0401_031_GFP-
GSGGEPSESGSSGS
308
GGTTCTGGTGGCGAACCTTCCGAATCTGGTAGCTCAGG
309
N_D03.ab1
GGEPSESGSSGSSE
TTCCGGTGGTGAACCTTCTGAATCTGGTAGCTCAGGTT
SGSSEGGP
CTTCTGAAAGCGGTTCTTCCGAGGGCGGTCCA
LCW0401_033_GFP-
GSGGEPSESGSSGS
310
GGTTCCGGTGGTGAACCTTCTGAATCTGGTAGCTCAGG
311
N_E03.ab1
GGEPSESGSSGSGG
TTCCGGTGGCGAACCATCCGAGTCTGGTAGCTCAGGTT
EPSESGSS
CCGGTGGTGAACCATCCGAGTCTGGTAGCTCA
LCW0401_037_GFP-
GSGGEPSESGSSGS
312
GGTTCCGGTGGCGAACCTTCTGAATCTGGTAGCTCAGG
313
N_F03.ab1
SESGSSEGGPGSEG
TTCCTCCGAAAGCGGTTCTTCTGAGGGCGGTCCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCGGGCGAGTCTTCA
LCW0401_038_GFP-
GSGGEPSESGSSGS
314
GGTTCCGGTGGTGAACCGTCCGAGTCTGGTAGCTCAGG
315
N_G03.ab1
EGSSGPGESSGSGG
TAGCGAAGGTTCTTCTGGTCCGGGTGAGTCTTCAGGTT
EPSESGSS
CTGGTGGCGAACCGTCCGAATCTGGTAGCTCA
LCW0401_039_GFP-
GSGGEPSESGSSGE
316
GGTTCTGGTGGCGAACCGTCCGAATCTGGTAGCTCAGG
317
N_H03.ab1
SPGGSSGSESGSGG
TGAATCTCCTGGTGGTTCCAGCGGTTCCGAGTCAGGTT
EPSESGSS
CTGGTGGCGAACCTTCCGAATCTGGTAGCTCA
LCW0401_040_GFP-
GSSESGSSEGGPGS
318
GGTTCTTCCGAAAGCGGTTCTTCCGAGGGCGGTCCAGG
319
N_A04.ab1
GGEPSESGSSGSSE
TTCCGGTGGTGAACCATCTGAATCTGGTAGCTCAGGTT
SGSSEGGP
CTTCTGAAAGCGGTTCTTCTGAAGGTGGTCCA
LCW0401_042_GFP-
GSEGSSGPGESSGE
320
GGTAGCGAAGGTTCTTCCGGTCCTGGTGAGTCTTCAGG
321
N_C04.ab1
SPGGSSGSESGSEG
TGAATCTCCAGGTGGCTCTAGCGGTTCCGAGTCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCTGGCGAGTCCTCA
LCW0401_046_GFP-
GSSESGSSEGGPGS
322
GGTTCCTCTGAAAGCGGTTCTTCCGAAGGCGGTCCAGG
323
N_D04.ab1
SESGSSEGGPGSSE
TTCTTCCGAAAGCGGTTCTTCTGAGGGCGGTCCAGGTT
SGSSEGGP
CCTCCGAAAGCGGTTCTTCTGAGGGTGGTCCA
LCW0401_047_GFP-
GSGGEPSESGSSGE
324
GGTTCTGGTGGCGAACCTTCCGAGTCTGGTAGCTCAGG
325
N_E04.ab1
SPGGSSGSESGESP
TGAATCTCCGGGTGGTTCTAGCGGTTCCGAGTCAGGTG
GGSSGSES
AATCTCCGGGTGGTTCCAGCGGTTCTGAGTCA
LCW0401_051_GFP-
GSGGEPSESGSSGS
326
GGTTCTGGTGGCGAACCATCTGAGTCTGGTAGCTCAGG
327
N_F04.ab1
EGSSGPGESSGESP
TAGCGAAGGTTCTTCCGGTCCAGGCGAGTCTTCAGGTG
GGSSGSES
AATCTCCTGGTGGCTCCAGCGGTTCTGAGTCA
LCW0401_053_GFP-
GESPGGSSGSESGE
328
GGTGAATCTCCTGGTGGTTCCAGCGGTTCCGAGTCAGG
329
N_H04.ab1
SPGGSSGSESGESP
TGAATCTCCAGGTGGCTCTAGCGGTTCCGAGTCAGGTG
GGSSGSES
AATCTCCTGGTGGTTCTAGCGGTTCTGAATCA
LCW0401_054_GFP-
GSEGSSGPGESSGS
330
GGTAGCGAAGGTTCTTCCGGTCCAGGTGAATCTTCAGG
331
N_A05.ab1
EGSSGPGESSGSGG
TAGCGAAGGTTCTTCTGGTCCTGGTGAATCCTCAGGTT
EPSESGSS
CCGGTGGCGAACCATCTGAATCTGGTAGCTCA
LCW0401_059_GFP-
GSGGEPSESGSSGS
332
GGTTCTGGTGGCGAACCATCCGAATCTGGTAGCTCAGG
333
N_D05.ab1
EGSSGPGESSGESP
TAGCGAAGGTTCTTCTGGTCCTGGCGAATCTTCAGGTG
GGSSGSES
AATCTCCAGGTGGCTCTAGCGGTTCCGAATCA
LCW0401_060_GFP-
GSGGEPSESGSSGS
334
GGTTCCGGTGGTGAACCGTCCGAATCTGGTAGCTCAGG
335
N_E05.ab1
SESGSSEGGPGSGG
TTCCTCTGAAAGCGGTTCTTCCGAGGGTGGTCCAGGTT
EPSESGSS
CCGGTGGTGAACCTTCTGAGTCTGGTAGCTCA
LCW0401_061_GFP-
GSSESGSSEGGPGS
336
GGTTCCTCTGAAAGCGGTTCTTCTGAGGGCGGTCCAGG
337
N_F05.ab1
GGEPSESGSSGSEG
TTCTGGTGGCGAACCATCTGAATCTGGTAGCTCAGGTA
SSGPGESS
GCGAAGGTTCTTCCGGTCCGGGTGAATCTTCA
LCW0401_063_GFP-
GSGGEPSESGSSGS
338
GGTTCTGGTGGTGAACCGTCCGAATCTGGTAGCTCAGG
339
N_H05.ab1
EGSSGPGESSGSEG
TAGCGAAGGTTCTTCTGGTCCTGGCGAGTCTTCAGGTA
SSGPGESS
GCGAAGGTTCTTCTGGTCCTGGTGAATCTTCA
LCW0401_066_GFP-
GSGGEPSESGSSGS
340
GGTTCTGGTGGCGAACCATCCGAGTCTGGTAGCTCAGG
341
N_B06.ab1
SESGSSEGGPGSGG
TTCTTCCGAAAGCGGTTCTTCCGAAGGCGGTCCAGGTT
EPSESGSS
CTGGTGGTGAACCGTCCGAATCTGGTAGCTCA
LCW0401_067_GFP-
GSGGEPSESGSSGE
342
GGTTCCGGTGGCGAACCTTCCGAATCTGGTAGCTCAGG
343
N_C06.ab1
SPGGSSGSESGESP
TGAATCTCCGGGTGGTTCTAGCGGTTCCGAATCAGGTG
GGSSGSES
AATCTCCAGGTGGTTCTAGCGGTTCCGAATCA
LCW0401_069_GFP-
GSGGEPSESGSSGS
344
GGTTCCGGTGGTGAACCATCTGAGTCTGGTAGCTCAGG
345
N_D06.ab1
GGEPSESGSSGESP
TTCCGGTGGCGAACCGTCCGAGTCTGGTAGCTCAGGTG
GGSSGSES
AATCTCCGGGTGGTTCCAGCGGTTCCGAATCA
LCW0401_070_GFP-
GSEGSSGPGESSGS
346
GGTAGCGAAGGTTCTTCTGGTCCGGGCGAATCCTCAGG
347
N_E06.ab1
SESGSSEGGPGSEG
TTCCTCCGAAAGCGGTTCTTCCGAAGGTGGTCCAGGTA
SSGPGESS
GCGAAGGTTCTTCCGGTCCTGGTGAATCTTCA
LCW0401_078_GFP-
GSSESGSSEGGPGE
348
GGTTCCTCTGAAAGCGGTTCTTCTGAAGGCGGTCCAGG
349
N_F06.ab1
SPGGSSGSESGESP
TGAATCTCCGGGTGGCTCCAGCGGTTCTGAATCAGGTG
GGSSGSES
AATCTCCTGGTGGCTCCAGCGGTTCCGAGTCA
LCW0401_079_GFP-
GSEGSSGPGESSGS
350
GGTAGCGAAGGTTCTTCTGGTCCAGGCGAGTCTTCAGG
351
N_G06.ab1
EGSSGPGESSGSGG
TAGCGAAGGTTCTTCCGGTCCTGGCGAGTCTTCAGGTT
EPSESGSS
CCGGTGGCGAACCGTCCGAATCTGGTAGCTCA

Example 2: Construction of XTEN_AE36 Segments

A codon library encoding XTEN sequences of 36 amino acid length was constructed. The XTEN sequence was designated XTEN_AE36. Its segments have the amino acid sequence [X]3 where X is a 12 mer peptide with the sequence: GSPAGSPTSTEE (SEQ ID NO: 352), GSEPATSGSE TP (SEQ ID NO: 353), GTSESA TPESGP (SEQ ID NO: 354), or GTSTEPSEGSAP (SEQ ID NO: 355). The insert was obtained by annealing the following pairs of phosphorylated synthetic oligonucleotide pairs:


AE1for:
(SEQ ID NO: 356)
AGGTAGCCCDGCWGGYTCTCCDACYTCYACYGARGA
AE1rev:
(SEQ ID NO: 357)
ACCTTCYTCRGTRGARGTHGGAGARCCWGCHGGGCT
AE2for:
(SEQ ID NO: 358)
AGGTAGCGAACCKGCWACYTCYGGYTCTGARACYCC
AE2rev:
(SEQ ID NO: 359)
ACCTGGRGTYTCAGARCCRGARGTWGCMGGTTCGCT
AE3for:
(SEQ ID NO: 360)
AGGTACYTCTGAAAGCGCWACYCCKGARTCYGGYCC
AE3rev:
(SEQ ID NO: 361)
ACCTGGRCCRGAYTCMGGRGTWGCGCTTTCAGARGT
AE4for:
(SEQ ID NO: 362)
AGGTACYTCTACYGAACCKTCYGARGGYAGCGCWCC
AE4rev:
(SEQ ID NO: 363)
ACCTGGWGCGCTRCCYTCRGAMGGTTCRGTAGARGT

We also annealed the phosphorylated oligonucleotide 3KpnIstopperFor: AGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 364) and the non-phosphorylated oligonucleotide pr_3 KpnIstopperRev: CCTCGAGTGAAGACGA (SEQ ID NO: 365). The annealed oligonucleotide pairs were ligated, which resulted in a mixture of products with varying length that represents the varying number of 12 mer repeats ligated to one BbsI/KpnI segment. The products corresponding to the length of 36 amino acids were isolated from the mixture by preparative agarose gel electrophoresis and ligated into the BsaI/KpnI digested stuffer vector pCW0359. Most of the clones in the resulting library designated LCW0402 showed green fluorescence after induction which shows that the sequence of XTEN_AE36 had been ligated in frame with the GFP gene and most sequences of XTEN_AE36 show good expression.

We screened 96 isolates from library LCW0402 for high level of fluorescence by stamping them onto agar plate containing IPTG. The same isolates were evaluated by PCR and 48 isolates were identified that contained segments with 36 amino acids as well as strong fluorescence. These isolates were sequenced and 37 clones were identified that contained correct XTEN_AE36 segments. The file names of the nucleotide and amino acid constructs for these segments are listed in Table 11.


TABLE 11
DNA and Amino Acid Sequences for 36-mer motifs
File
Amino acid
SEQ ID
SEQ ID
name
sequence
NO:
Nucleotide sequence
NO:
LCW0402_002_GFP-
GSPAGSPTSTEE
366
GGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAAGGT
367
N_A07.ab1
GTSESATPESGP
ACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCAGGTACC
GTSTEPSEGSAP
TCTACCGAACCGTCTGAGGGCAGCGCACCA
LCW0402_003_GFP-
GTSTEPSEGSAP
368
GGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGT
369
N_B07.ab1
GTSTEPSEGSAP
ACCTCTACTGAACCTTCCGAGGGCAGCGCTCCAGGTACC
GTSTEPSEGSAP
TCTACCGAACCTTCTGAAGGTAGCGCACCA
LCW0402_004_GFP-
GTSTEPSEGSAP
370
GGTACCTCTACCGAACCGTCTGAAGGTAGCGCACCAGGT
371
N_C07.ab1
GTSESATPESGP
ACCTCTGAAAGCGCAACTCCTGAGTCCGGTCCAGGTACT
GTSESATPESGP
TCTGAAAGCGCAACCCCGGAGTCTGGCCCA
LCW0402_005_GFP-
GTSTEPSEGSAP
372
GGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCAGGT
373
N_D07.ab1
GTSESATPESGP
ACTTCTGAAAGCGCAACCCCGGAATCCGGCCCAGGTACC
GTSESATPESGP
TCTGAAAGCGCAACCCCGGAGTCCGGCCCA
LCW0402_006_GFP-
GSEPATSGSETP
374
GGTAGCGAACCGGCAACCTCCGGCTCTGAAACCCCAGGT
375
N_E07.ab1
GTSESATPESGP
ACCTCTGAAAGCGCTACTCCTGAATCCGGCCCAGGTAGC
GSPAGSPTSTEE
CCGGCAGGTTCTCCGACTTCCACTGAGGAA
LCW0402_008_GFP-
GTSESATPESGP
376
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCAGGT
377
N_F07.ab1
GSEPATSGSETP
AGCGAACCGGCTACTTCTGGCTCTGAGACTCCAGGTACT
GTSTEPSEGSAP
TCTACCGAACCGTCCGAAGGTAGCGCACCA
LCW0402_009_GFP-
GSPAGSPTSTEE
378
GGTAGCCCGGCTGGCTCTCCAACCTCCACTGAGGAAGGT
379
N_G07.ab1
GSPAGSPTSTEE
AGCCCGGCTGGCTCTCCAACCTCCACTGAAGAAGGTAGC
GSEPATSGSETP
GAACCGGCTACCTCCGGCTCTGAAACTCCA
LCW0402_011_GFP-
GSPAGSPTSTEE
380
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAAGGT
381
N_A08.ab1
GTSESATPESGP
ACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCAGGTACC
GTSTEPSEGSAP
TCTACTGAACCGTCCGAAGGTAGCGCTCCA
LCW0402_012_GFP-
GSPAGSPTSTEE
382
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAAGGT
383
N_B08.ab1
GSPAGSPTSTEE
AGCCCGGCTGGTTCTCCGACTTCTACTGAGGAAGGTACT
GTSTEPSEGSAP
TCTACCGAACCTTCCGAAGGTAGCGCTCCA
LCW0402_013_GFP-
GTSESATPESGP
384
GGTACTTCTGAAAGCGCTACTCCGGAGTCCGGTCCAGGT
385
N_C08.ab1
GTSTEPSEGSAP
ACCTCTACCGAACCGTCCGAAGGCAGCGCTCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCTTCTGAGGGTAGCGCTCCA
LCW0402_014_GFP-
GTSTEPSEGSAP
386
GGTACCTCTACCGAACCTTCCGAAGGTAGCGCTCCAGGT
387
N_D08.ab1
GSPAGSPTSTEE
AGCCCGGCAGGTTCTCCTACTTCCACTGAGGAAGGTACT
GTSTEPSEGSAP
TCTACCGAACCTTCTGAGGGTAGCGCACCA
LCW0402_015_GFP-
GSEPATSGSETP
388
GGTAGCGAACCGGCTACTTCCGGCTCTGAGACTCCAGGT
389
N_E08.ab1
GSPAGSPTSTEE
AGCCCTGCTGGCTCTCCGACCTCTACCGAAGAAGGTACC
GTSESATPESGP
TCTGAAAGCGCTACCCCTGAGTCTGGCCCA
LCW0402_016_GFP-
GTSTEPSEGSAP
390
GGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCAGGT
391
N_F08.ab1
GTSESATPESGP
ACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCAGGTACT
GTSESATPESGP
TCTGAAAGCGCTACTCCTGAATCCGGTCCA
LCW0402_020_GFP-
GTSTEPSEGSAP
392
GGTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGT
393
N_G08.ab1
GSEPATSGSETP
AGCGAACCGGCTACTTCCGGTTCTGAAACCCCAGGTAGC
GSPAGSPTSTEE
CCAGCAGGTTCTCCAACTTCTACTGAAGAA
LCW0402_023_GFP-
GSPAGSPTSTEE
394
GGTAGCCCTGCTGGCTCTCCAACCTCCACCGAAGAAGGT
395
N_A09.ab1
GTSESATPESGP
ACCTCTGAAAGCGCAACCCCTGAATCCGGCCCAGGTAGC
GSEPATSGSETP
GAACCGGCAACCTCCGGTTCTGAAACCCCA
LCW0402_024_GFP-
GTSESATPESGP
396
GGTACTTCTGAAAGCGCTACTCCTGAGTCCGGCCCAGGT
397
N_B09.ab1
GSPAGSPTSTEE
AGCCCGGCTGGCTCTCCGACTTCCACCGAGGAAGGTAGC
GSPAGSPTSTEE
CCGGCTGGCTCTCCAACTTCTACTGAAGAA
LCW0402_025_GFP-
GTSTEPSEGSAP
398
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCAGGT
399
N_C09.ab1
GTSESATPESGP
ACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCGTCCGAAGGTAGCGCACCA
LCW0402_026_GFP-
GSPAGSPTSTEE
400
GGTAGCCCGGCAGGCTCTCCGACTTCCACCGAGGAAGGT
401
N_D09.ab1
GTSTEPSEGSAP
ACCTCTACTGAACCTTCTGAGGGTAGCGCTCCAGGTAGC
GSEPATSGSETP
GAACCGGCAACCTCTGGCTCTGAAACCCCA
LCW0402_027_GFP-
GSPAGSPTSTEE
402
GGTAGCCCAGCAGGCTCTCCGACTTCCACTGAGGAAGGT
403
N_E09.ab1
GTSTEPSEGSAP
ACTTCTACTGAACCTTCCGAAGGCAGCGCACCAGGTACC
GTSTEPSEGSAP
TCTACTGAACCTTCTGAGGGCAGCGCTCCA
LCW0402_032_GFP-
GSEPATSGSETP
404
GGTAGCGAACCTGCTACCTCCGGTTCTGAAACCCCAGGT
405
N_H09.ab1
GTSESATPESGP
ACCTCTGAAAGCGCAACTCCGGAGTCTGGTCCAGGTAGC
GSPAGSPTSTEE
CCTGCAGGTTCTCCTACCTCCACTGAGGAA
LCW0402_034_GFP-
GTSESATPESGP
406
GGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCAGGT
407
N_A10.ab1
GTSTEPSEGSAP
ACCTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCGTCCGAAGGTAGCGCACCA
LCW0402_036_GFP-
GSPAGSPTSTEE
408
GGTAGCCCGGCTGGTTCTCCGACTTCCACCGAGGAAGGT
409
N_C10.ab1
GTSTEPSEGSAP
ACCTCTACTGAACCTTCTGAGGGTAGCGCTCCAGGTACC
GTSTEPSEGSAP
TCTACTGAACCTTCCGAAGGCAGCGCTCCA
LCW0402_039_GFP-
GTSTEPSEGSAP
410
GGTACTTCTACCGAACCGTCCGAGGGCAGCGCTCCAGGT
411
N_E10.ab1
GTSTEPSEGSAP
ACTTCTACTGAACCTTCTGAAGGCAGCGCTCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCTTCCGAAGGTAGCGCACCA
LCW0402_040_GFP-
GSEPATSGSETP
412
GGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCAGGT
413
N_F10.ab1
GTSESATPESGP
ACCTCTGAAAGCGCTACTCCTGAATCTGGCCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCGTCCGAGGGCAGCGCACCA
LCW0402_041_GFP-
GTSTEPSEGSAP
414
GGTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGT
415
N_G10.ab1
GSPAGSPTSTEE
AGCCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACT
GTSTEPSEGSAP
TCTACCGAACCGTCCGAGGGTAGCGCACCA
LCW0402_050_GFP-
GSEPATSGSETP
416
GGTAGCGAACCGGCAACCTCCGGCTCTGAAACTCCAGGT
417
N_A11.ab1
GTSESATPESGP
ACTTCTGAAAGCGCTACTCCGGAATCCGGCCCAGGTAGC
GSEPATSGSETP
GAACCGGCTACTTCCGGCTCTGAAACCCCA
LCW0402_051_GFP-
GSEPATSGSETP
418
GGTAGCGAACCGGCAACTTCCGGCTCTGAAACCCCAGGT
419
N_B11.ab1
GTSESATPESGP
ACTTCTGAAAGCGCTACTCCTGAGTCTGGCCCAGGTAGC
GSEPATSGSETP
GAACCTGCTACCTCTGGCTCTGAAACCCCA
LCW0402_059_GFP-
GSEPATSGSETP
420
GGTAGCGAACCGGCAACCTCTGGCTCTGAAACTCCAGGT
421
N_E11.ab1
GSEPATSGSETP
AGCGAACCTGCAACCTCCGGCTCTGAAACCCCAGGTACT
GTSTEPSEGSAP
TCTACTGAACCTTCTGAGGGCAGCGCACCA
LCW0402_060_GFP-
GTSESATPESGP
422
GGTACTTCTGAAAGCGCTACCCCGGAATCTGGCCCAGGT
423
N_F11.ab1
GSEPATSGSETP
AGCGAACCGGCTACTTCTGGTTCTGAAACCCCAGGTAGC
GSEPATSGSETP
GAACCGGCTACCTCCGGTTCTGAAACTCCA
LCW0402_061_GFP-
GTSTEPSEGSAP
424
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCAGGT
425
N_G11.ab1
GTSTEPSEGSAP
ACCTCTACCGAACCGTCCGAGGGCAGCGCACCAGGTACT
GTSESATPESGP
TCTGAAAGCGCAACCCCTGAATCCGGTCCA
LCW0402_065_GFP-
GSEPATSGSETP
426
GGTAGCGAACCGGCAACCTCTGGCTCTGAAACCCCAGGT
427
N_A12.ab1
GTSESATPESGP
ACCTCTGAAAGCGCTACTCCGGAATCTGGTCCAGGTACT
GTSESATPESGP
TCTGAAAGCGCTACTCCGGAATCCGGTCCA
LCW0402_066_GFP-
GSEPATSGSETP
428
GGTAGCGAACCTGCTACCTCCGGCTCTGAAACTCCAGGT
429
N_B12.ab1
GSEPATSGSETP
AGCGAACCGGCTACTTCCGGTTCTGAAACTCCAGGTACC
GTSTEPSEGSAP
TCTACCGAACCTTCCGAAGGCAGCGCACCA
LCW0402_067_GFP-
GSEPATSGSETP
430
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACTCCAGGT
431
N_C12.ab1
GTSTEPSEGSAP
ACTTCTACCGAACCGTCCGAGGGTAGCGCTCCAGGTAGC
GSEPATSGSETP
GAACCTGCTACTTCTGGTTCTGAAACTCCA
LCW0402_069_GFP-
GTSTEPSEGSAP
432
GGTACCTCTACCGAACCGTCCGAGGGTAGCGCACCAGGT
433
N_D12.ab1
GTSTEPSEGSAP
ACCTCTACTGAACCGTCTGAGGGTAGCGCTCCAGGTAGC
GSEPATSGSETP
GAACCGGCAACCTCCGGTTCTGAAACTCCA
LCW0402_073_GFP-
GTSTEPSEGSAP
434
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCTCCAGGT
435
N_F12.ab1
GSEPATSGSETP
AGCGAACCTGCTACTTCTGGTTCTGAAACCCCAGGTAGC
GSPAGSPTSTEE
CCGGCTGGCTCTCCGACCTCCACCGAGGAA
LCW0402_074_GFP-
GSEPATSGSETP
436
GGTAGCGAACCGGCTACTTCCGGCTCTGAGACTCCAGGT
437
N_G12.ab1
GSPAGSPTSTEE
AGCCCAGCTGGTTCTCCAACCTCTACTGAGGAAGGTACT
GTSESATPESGP
TCTGAAAGCGCTACCCCTGAATCTGGTCCA
LCW0402_075_GFP-
GTSESATPESGP
438
GGTACCTCTGAAAGCGCAACTCCTGAGTCTGGCCCAGGT
439
N_H12.ab1
GSEPATSGSETP
AGCGAACCTGCTACCTCCGGCTCTGAGACTCCAGGTACC
GTSESATPESGP
TCTGAAAGCGCAACCCCGGAATCTGGTCCA

Example 3: Construction of XTEN_AF36 Segments

A codon library encoding sequences of 36 amino acid length was constructed. The sequences were designated XTEN_AF36. Its segments have the amino acid sequence [X]3 where X is a 12 mer peptide with the sequence: GSTSESPSGTAP (SEQ ID NO: 440), GTSTPESGSASP (SEQ ID NO: 441), GTSPSGESSTAP (SEQ ID NO: 442), or GSTSSTAESPGP (SEQ ID NO: 443). The insert was obtained by annealing the following pairs of phosphorylated synthetic oligonucleotide pairs:


AF1for:
(SEQ ID NO: 444)
AGGTTCTACYAGCGAATCYCCKTCTGGYACYGCWCC
AF1rev:
(SEQ ID NO: 445)
ACCTGGWGCRGTRCCAGAMGGRGATTCGCTRGTAGA
AF2for:
(SEQ ID NO: 446)
AGGTACYTCTACYCCKGAAAGCGGYTCYGCWTCTCC
AF2rev:
(SEQ ID NO: 447)
ACCTGGAGAWGCRGARCCGCTTTCMGGRGTAGARGT
AF3for:
(SEQ ID NO: 448)
AGGTACYTCYCCKAGCGGYGAATCTTCTACYGCWCC
AF3rev:
(SEQ ID NO: 449)
ACCTGGWGCRGTAGAAGATTCRCCGCTMGGRGARGT
AF4for:
(SEQ ID NO: 450)
AGGTTCYACYAGCTCTACYGCWGAATCTCCKGGYCC
AF4rev:
(SEQ ID NO: 451)
ACCTGGRCCMGGAGATTCWGCRGTAGAGCTRGTRGA

We also annealed the phosphorylated oligonucleotide 3KpnIstopperFor: AGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 452) and the non-phosphorylated oligonucleotide pr_3 KpnIstopperRev: CCTCGAGTGAAGACGA (SEQ ID NO: 453). The annealed oligonucleotide pairs were ligated, which resulted in a mixture of products with varying length that represents the varying number of 12 mer repeats ligated to one BbsI/KpnI segment The products corresponding to the length of 36 amino acids were isolated from the mixture by preparative agarose gel electrophoresis and ligated into the BsaI/KpnI digested stuffer vector pCW0359. Most of the clones in the resulting library designated LCW0403 showed green fluorescence after induction which shows that the sequence of XTEN_AF36 had been ligated in frame with the GFP gene and most sequences of XTEN_AF36 show good expression.

We screened 96 isolates from library LCW0403 for high level of fluorescence by stamping them onto agar plate containing IPTG. The same isolates were evaluated by PCR and 48 isolates were identified that contained segments with 36 amino acids as well as strong fluorescence. These isolates were sequenced and 44 clones were identified that contained correct XTEN_AF36 segments. The file names of the nucleotide and amino acid constructs for these segments are listed in Table 12.


TABLE 12
DNA and Amino Acid Sequences for 36-mer motifs
File
Amino acid
SEQ ID
SEQ ID
name
sequence
NO:
Nucleotide sequence
NO:
LCW0403_004_GFP-
GTSTPESGSASPG
454
GGTACTTCTACTCCGGAAAGCGGTTCCGCATCTCC
455
N_A01.ab1
TSPSGESSTAPGT
AGGTACTTCTCCTAGCGGTGAATCTTCTACTGCTC
SPSGESSTAP
CAGGTACCTCTCCTAGCGGCGAATCTTCTACTGCT
CCA
LCW0403_005_GFP-
GTSPSGESSTAPG
456
GGTACTTCTCCGAGCGGTGAATCTTCTACCGCACC
457
N_B01.ab1
STSSTAESPGPGT
AGGTTCTACTAGCTCTACCGCTGAATCTCCGGGCC
SPSGESSTAP
CAGGTACTTCTCCGAGCGGTGAATCTTCTACTGCT
CCA
LCW0403_006_GFP-
GSTSSTAESPGPG
458
GGTTCCACCAGCTCTACTGCTGAATCTCCTGGTCC
459
N_C01.ab1
TSPSGESSTAPGT
AGGTACCTCTCCTAGCGGTGAATCTTCTACTGCTC
STPESGSASP
CAGGTACTTCTACTCCTGAAAGCGGCTCTGCTTCT
CCA
LCW0403_007_GFP-
GSTSSTAESPGPG
460
GGTTCTACCAGCTCTACTGCAGAATCTCCTGGCCC
461
N_D01.ab1
STSSTAESPGPGT
AGGTTCCACCAGCTCTACCGCAGAATCTCCGGGTC
SPSGESSTAP
CAGGTACTTCCCCTAGCGGTGAATCTTCTACCGCA
CCA
LCW0403_008_GFP-
GSTSSTAESPGPG
462
GGTTCTACTAGCTCTACTGCTGAATCTCCTGGCCC
463
N_E01.ab1
TSPSGESSTAPGT
AGGTACTTCTCCTAGCGGTGAATCTTCTACCGCTC
STPESGSASP
CAGGTACCTCTACTCCGGAAAGCGGTTCTGCATCT
CCA
LCW0403_010_GFP-
GSTSSTAESPGPG
464
GGTTCTACCAGCTCTACCGCAGAATCTCCTGGTCC
465
N_F01.ab1
TSTPESGSASPGS
AGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTC
TSESPSGTAP
CAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCA
CCA
LCW0403_011_GFP-
GSTSSTAESPGPG
466
GGTTCTACTAGCTCTACTGCAGAATCTCCTGGCCC
467
N_G01.ab1
TSTPESGSASPGT
AGGTACCTCTACTCCGGAAAGCGGCTCTGCATCTC
STPESGSASP
CAGGTACTTCTACCCCTGAAAGCGGTTCTGCATCT
CCA
LCW0403_012_GFP-
GSTSESPSGTAPG
468
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCC
469
N_H01.ab1
TSPSGESSTAPGS
AGGTACCTCTCCTAGCGGCGAATCTTCTACCGCTC
TSESPSGTAP
CAGGTTCTACTAGCGAATCTCCTTCTGGCACTGCA
CCA
LCW0403_013_GFP-
GSTSSTAESPGPG
470
GGTTCCACCAGCTCTACTGCAGAATCTCCGGGCCC
471
N_A02.ab1
STSSTAESPGPGT
AGGTTCTACTAGCTCTACTGCAGAATCTCCGGGTC
SPSGESSTAP
CAGGTACTTCTCCTAGCGGCGAATCTTCTACCGCT
CCA
LCW0403_014_GFP-
GSTSSTAESPGPG
472
GGTTCCACTAGCTCTACTGCAGAATCTCCTGGCCC
473
N_B02.ab1
TSTPESGSASPGS
AGGTACCTCTACCCCTGAAAGCGGCTCTGCATCTC
TSESPSGTAP
CAGGTTCTACCAGCGAATCCCCGTCTGGCACCGCA
CCA
LCW0403_015_GFP-
GSTSSTAESPGPG
474
GGTTCTACTAGCTCTACTGCTGAATCTCCGGGTCC
475
N_C02.ab1
STSSTAESPGPGT
AGGTTCTACCAGCTCTACTGCTGAATCTCCTGGTC
SPSGESSTAP
CAGGTACCTCCCCGAGCGGTGAATCTTCTACTGCA
CCA
LCW0403_017_GFP-
GSTSSTAESPGPG
476
GGTTCTACCAGCTCTACCGCTGAATCTCCTGGCCC
477
N_D02.ab1
STSESPSGTAPGS
AGGTTCTACCAGCGAATCCCCGTCTGGCACCGCAC
TSSTAESPGP
CAGGTTCTACTAGCTCTACCGCTGAATCTCCGGGT
CCA
LCW0403_018_GFP-
GSTSSTAESPGPG
478
GGTTCTACCAGCTCTACCGCAGAATCTCCTGGCCC
479
N_E02.ab1
STSSTAESPGPGS
AGGTTCCACTAGCTCTACCGCTGAATCTCCTGGTC
TSSTAESPGP
CAGGTTCTACTAGCTCTACCGCTGAATCTCCTGGT
CCA
LCW0403_019_GFP-
GSTSESPSGTAPG
480
GGTTCTACTAGCGAATCCCCTTCTGGTACTGCTCC
481
N_F02.ab1
STSSTAESPGPGS
AGGTTCCACTAGCTCTACCGCTGAATCTCCTGGCC
TSSTAESPGP
CAGGTTCCACTAGCTCTACTGCAGAATCTCCTGGT
CCA
LCW0403_023_GFP-
GSTSESPSGTAPG
482
GGTTCTACTAGCGAATCTCCTTCTGGTACCGCTCC
483
N_H02.ab1
STSESPSGTAPGS
AGGTTCTACCAGCGAATCCCCGTCTGGTACTGCTC
TSESPSGTAP
CAGGTTCTACCAGCGAATCTCCTTCTGGTACTGCA
CCA
LCW0403_024_GFP-
GSTSSTAESPGPG
484
GGTTCCACCAGCTCTACTGCTGAATCTCCTGGCCC
485
N_A03.ab1
STSSTAESPGPGS
AGGTTCTACCAGCTCTACTGCTGAATCTCCGGGCC
TSSTAESPGP
CAGGTTCCACCAGCTCTACCGCTGAATCTCCGGGT
CCA
LCW0403_025_GFP-
GSTSSTAESPGPG
486
GGTTCCACTAGCTCTACCGCAGAATCTCCTGGTCC
487
N_B03.ab1
STSSTAESPGPGT
AGGTTCTACTAGCTCTACTGCTGAATCTCCGGGTC
SPSGESSTAP
CAGGTACCTCCCCTAGCGGCGAATCTTCTACCGCT
CCA
LCW0403_028_GFP-
GSSPSASTGTGPG
488
GGTTCTAGCCCTTCTGCTTCCACCGGTACCGGCCC
489
N_D03.ab1
SSTPSGATGSPGS
AGGTAGCTCTACTCCGTCTGGTGCAACTGGCTCTC
STPSGATGSP
CAGGTAGCTCTACTCCGTCTGGTGCAACCGGCTCC
CCA
LCW0403_029_GFP-
GTSPSGESSTAPG
490
GGTACTTCCCCTAGCGGTGAATCTTCTACTGCTCC
491
N_E03.ab1
TSTPESGSASPGS
AGGTACCTCTACTCCGGAAAGCGGCTCCGCATCTC
TSSTAESPGP
CAGGTTCTACTAGCTCTACTGCTGAATCTCCTGGT
CCA
LCW0403_030_GFP-
GSTSSTAESPGPG
492
GGTTCTACTAGCTCTACCGCTGAATCTCCGGGTCC
493
N_F03.ab1
STSSTAESPGPGT
AGGTTCTACCAGCTCTACTGCAGAATCTCCTGGCC
STPESGSASP
CAGGTACTTCTACTCCGGAAAGCGGTTCCGCTTCT
CCA
LCW0403_031_GFP-
GTSPSGESSTAPG
494
GGTACTTCTCCTAGCGGTGAATCTTCTACCGCTCC
495
N_G03.ab1
STSSTAESPGPGT
AGGTTCTACCAGCTCTACTGCTGAATCTCCTGGCC
STPESGSASP
CAGGTACTTCTACCCCGGAAAGCGGCTCCGCTTCT
CCA
LCW0403_033_GFP-
GSTSESPSGTAPG
496
GGTTCTACTAGCGAATCCCCTTCTGGTACTGCACC
497
N_H03.ab1
STSSTAESPGPGS
AGGTTCTACCAGCTCTACTGCTGAATCTCCGGGCC
TSSTAESPGP
CAGGTTCCACCAGCTCTACCGCAGAATCTCCTGGT
CCA
LCW0403_035_GFP-
GSTSSTAESPGPG
498
GGTTCCACCAGCTCTACCGCTGAATCTCCGGGCCC
499
N_A04.ab1
STSESPSGTAPGS
AGGTTCTACCAGCGAATCCCCTTCTGGCACTGCAC
TSSTAESPGP
CAGGTTCTACTAGCTCTACCGCAGAATCTCCGGGC
CCA
LCW0403_036_GFP-
GSTSSTAESPGPG
500
GGTTCTACCAGCTCTACTGCTGAATCTCCGGGTCC
501
N_B04.ab1
TSPSGESSTAPGT
AGGTACTTCCCCGAGCGGTGAATCTTCTACTGCAC
STPESGSASP
CAGGTACTTCTACTCCGGAAAGCGGTTCCGCTTCT
CCA
LCW0403_039_GFP-
GSTSESPSGTAPG
502
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCC
503
N_C04.ab1
STSESPSGTAPGT
AGGTTCTACTAGCGAATCCCCGTCTGGTACCGCAC
SPSGESSTAP
CAGGTACTTCTCCTAGCGGCGAATCTTCTACCGCA
CCA
LCW0403_041_GFP-
GSTSESPSGTAPG
504
GGTTCTACCAGCGAATCCCCTTCTGGTACTGCTCC
505
N_D04.ab1
STSESPSGTAPGT
AGGTTCTACCAGCGAATCCCCTTCTGGCACCGCAC
STPESGSASP
CAGGTACTTCTACCCCTGAAAGCGGCTCCGCTTCT
CCA
LCW0403_044_GFP-
GTSTPESGSASPG
506
GGTACCTCTACTCCTGAAAGCGGTTCTGCATCTCC
507
N_E04.ab1
STSSTAESPGPGS
AGGTTCCACTAGCTCTACCGCAGAATCTCCGGGCC
TSSTAESPGP
CAGGTTCTACTAGCTCTACTGCTGAATCTCCTGGC
CCA
LCW0403_046_GFP-
GSTSESPSGTAPG
508
GGTTCTACCAGCGAATCCCCTTCTGGCACTGCACC
509
N_F04.ab1
STSESPSGTAPGT
AGGTTCTACTAGCGAATCCCCTTCTGGTACCGCAC
SPSGESSTAP
CAGGTACTTCTCCGAGCGGCGAATCTTCTACTGCT
CCA
LCW0403_047_GFP-
GSTSSTAESPGPG
510
GGTTCTACTAGCTCTACCGCTGAATCTCCTGGCCC
511
N_G04.ab1
STSSTAESPGPGS
AGGTTCCACTAGCTCTACCGCAGAATCTCCGGGCC
TSESPSGTAP
CAGGTTCTACTAGCGAATCCCCTTCTGGTACCGCT
CCA
LCW0403_049_GFP-
GSTSSTAESPGPG
512
GGTTCCACCAGCTCTACTGCAGAATCTCCTGGCCC
513
N_H04.ab1
STSSTAESPGPGT
AGGTTCTACTAGCTCTACCGCAGAATCTCCTGGTC
STPESGSASP
CAGGTACCTCTACTCCTGAAAGCGGTTCCGCATCT
CCA
LCW0403_051_GFP-
GSTSSTAESPGPG
514
GGTTCTACTAGCTCTACTGCTGAATCTCCGGGCCC
515
N_A05.ab1
STSSTAESPGPGS
AGGTTCTACTAGCTCTACCGCTGAATCTCCGGGTC
TSESPSGTAP
CAGGTTCTACTAGCGAATCTCCTTCTGGTACCGCT
CCA
LCW0403_053_GFP-
GTSPSGESSTAPG
516
GGTACCTCCCCGAGCGGTGAATCTTCTACTGCACC
517
N_B05.ab1
STSESPSGTAPGS
AGGTTCTACTAGCGAATCCCCTTCTGGTACTGCTC
TSSTAESPGP
CAGGTTCCACCAGCTCTACTGCAGAATCTCCGGGT
CCA
LCW0403_054_GFP-
GSTSESPSGTAPG
518
GGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCC
519
N_C05.ab1
TSPSGESSTAPGS
AGGTACTTCCCCTAGCGGTGAATCTTCTACTGCTC
TSSTAESPGP
CAGGTTCTACCAGCTCTACCGCAGAATCTCCGGGT
CCA
LCW0403_057_GFP-
GSTSSTAESPGPG
520
GGTTCTACCAGCTCTACCGCTGAATCTCCTGGCCC
521
N_D05.ab1
STSESPSGTAPGT
AGGTTCTACTAGCGAATCTCCGTCTGGCACCGCAC
SPSGESSTAP
CAGGTACTTCCCCTAGCGGTGAATCTTCTACTGCA
CCA
LCW0403_058_GFP-
GSTSESPSGTAPG
522
GGTTCTACTAGCGAATCTCCTTCTGGCACTGCACC
523
N_E05.ab1
STSESPSGTAPGT
AGGTTCTACCAGCGAATCTCCGTCTGGCACTGCAC
STPESGSASP
CAGGTACCTCTACCCCTGAAAGCGGTTCCGCTTCT
CCA
LCW0403_060_GFP-
GTSTPESGSASPG
524
GGTACCTCTACTCCGGAAAGCGGTTCCGCATCTCC
525
N_F05.ab1
STSESPSGTAPGS
AGGTTCTACCAGCGAATCCCCGTCTGGCACCGCAC
TSSTAESPGP
CAGGTTCTACTAGCTCTACTGCTGAATCTCCGGGC
CCA
LCW0403_063_GFP-
GSTSSTAESPGPG
526
GGTTCTACTAGCTCTACTGCAGAATCTCCGGGCCC
527
N_G05.ab1
TSPSGESSTAPGT
AGGTACCTCTCCTAGCGGTGAATCTTCTACCGCTC
SPSGESSTAP
CAGGTACTTCTCCGAGCGGTGAATCTTCTACCGCT
CCA
LCW0403_064_GFP-
GTSPSGESSTAPG
528
GGTACCTCCCCTAGCGGCGAATCTTCTACTGCTCC
529
N_H05.ab1
TSPSGESSTAPGT
AGGTACCTCTCCTAGCGGCGAATCTTCTACCGCTC
SPSGESSTAP
CAGGTACCTCCCCTAGCGGTGAATCTTCTACCGCA
CCA
LCW0403_065_GFP-
GSTSSTAESPGPG
530
GGTTCCACTAGCTCTACTGCTGAATCTCCTGGCCC
531
N_A06.ab1
TSTPESGSASPGS
AGGTACTTCTACTCCGGAAAGCGGTTCCGCTTCTC
TSESPSGTAP
CAGGTTCTACTAGCGAATCTCCGTCTGGCACCGCA
CCA
LCW0403_066_GFP-
GSTSESPSGTAPG
532
GGTTCTACTAGCGAATCTCCGTCTGGCACTGCTCC
533
N_B06.ab1
TSPSGESSTAPGT
AGGTACTTCTCCTAGCGGTGAATCTTCTACCGCTC
SPSGESSTAP
CAGGTACTTCCCCTAGCGGCGAATCTTCTACCGCT
CCA
LCW0403_067_GFP-
GSTSESPSGTAPG
534
GGTTCTACTAGCGAATCTCCTTCTGGTACCGCTCC
535
N_C06.ab1
TSTPESGSASPGS
AGGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTC
TSSTAESPGP
CAGGTTCCACTAGCTCTACCGCTGAATCTCCGGGT
CCA
LCW0403_068_GFP-
GSTSSTAESPGPG
536
GGTTCCACTAGCTCTACTGCTGAATCTCCTGGCCC
537
N_D06.ab1
STSSTAESPGPGS
AGGTTCTACCAGCTCTACCGCTGAATCTCCTGGCC
TSESPSGTAP
CAGGTTCTACCAGCGAATCTCCGTCTGGCACCGCA
CCA
LCW0403_069_GFP-
GSTSESPSGTAPG
538
GGTTCTACTAGCGAATCCCCGTCTGGTACCGCACC
539
N_E06.ab1
TSTPESGSASPGT
AGGTACTTCTACCCCGGAAAGCGGCTCTGCTTCTC
STPESGSASP
CAGGTACTTCTACCCCGGAAAGCGGCTCCGCATCT
CCA
LCW0403_070_GFP-
GSTSESPSGTAPG
540
GGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCC
541
N_F06.ab1
TSTPESGSASPGT
AGGTACTTCTACTCCTGAAAGCGGTTCCGCTTCTC
STPESGSASP
CAGGTACCTCTACTCCGGAAAGCGGTTCTGCATCT
CCA

Example 4: Construction of XTEN_AG36 Segments

A codon library encoding sequences of 36 amino acid length was constructed. The sequences were designated XTEN_AG36. Its segments have the amino acid sequence [X]3 where X is a 12 mer peptide with the sequence: GTPGSGTASSSP (SEQ ID NO: 542), GSSTPSGATGSP (SEQ ID NO: 543), GSSPSASTGTGP (SEQ ID NO: 544), or GASPGTSSTGSP (SEQ ID NO: 545). The insert was obtained by annealing the following pairs of phosphorylated synthetic oligonucleotide pairs:


AG1for:
(SEQ ID NO: 546)
AGGTACYCCKGGYAGCGGTACYGCWTCTTCYTCTCC
AG1rev:
(SEQ ID NO: 547)
ACCTGGAGARGAAGAWGCRGTACCGCTRCCMGGRGT
AG2for:
(SEQ ID NO: 548)
AGGTAGCTCTACYCCKTCTGGTGCWACYGGYTCYCC
AG2rev:
(SEQ ID NO: 549)
ACCTGGRGARCCRGTWGCACCAGAMGGRGTAGAGCT
AG3for:
(SEQ ID NO: 550)
AGGTTCTAGCCCKTCTGCWTCYACYGGTACYGGYCC
AG3rev:
(SEQ ID NO: 551)
ACCTGGRCCRGTACCRGTRGAWGCAGAMGGGCTAGA
AG4for:
(SEQ ID NO: 552)
AGGTGCWTCYCCKGGYACYAGCTCTACYGGTTCTCC
AG4rev:
(SEQ ID NO: 553)
ACCTGGAGAACCRGTAGAGCTRGTRCCMGGRGAWGC

We also annealed the phosphorylated oligonucleotide 3KpnIstopperFor: AGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 554) and the non-phosphorylated oligonucleotide pr_3 KpnIstopperRev: CCTCGAGTGAAGACGA (SEQ ID NO: 555). The annealed oligonucleotide pairs were ligated, which resulted in a mixture of products with varying length that represents the varying number of 12 mer repeats ligated to one BbsI/KpnI segment. The products corresponding to the length of 36 amino acids were isolated from the mixture by preparative agarose gel electrophoresis and ligated into the BsaI/KpnI digested stuffer vector pCW0359. Most of the clones in the resulting library designated LCW0404 showed green fluorescence after induction which shows that the sequence of XTEN_AG36 had been ligated in frame with the GFP gene and most sequences of XTEN_AG36 show good expression.

We screened 96 isolates from library LCW0404 for high level of fluorescence by stamping them onto agar plate containing IPTG. The same isolates were evaluated by PCR and 48 isolates were identified that contained segments with 36 amino acids as well as strong fluorescence. These isolates were sequenced and 44 clones were identified that contained correct XTEN_AG36 segments. The file names of the nucleotide and amino acid constructs for these segments are listed in Table 13.


TABLE 13
DNA and Amino Acid Sequences for 36-mer motifs
File
Amino acid
SEQ ID
SEQ ID
name
sequence
NO:
Nucleotide sequence
NO:
LCW0404_001_GFP-
GASPGTSSTGSP
556
GGTGCATCCCCGGGCACTAGCTCTACCGGTTCTCCAGGTAC
557
N_A07.ab1
GTPGSGTASSSP
TCCTGGTAGCGGTACTGCTTCTTCTTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCTTCTGGTGCTACTGGTTCTCCA
LCW0404_003_GFP-
GSSTPSGATGSP
558
GGTAGCTCTACCCCTTCTGGTGCTACCGGCTCTCCAGGTTC
559
N_B07.ab1
GSSPSASTGTGP
TAGCCCGTCTGCTTCTACCGGTACCGGTCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCTTCTGGTGCTACTGGTTCTCCA
LCW0404_006_GFP-
GASPGTSSTGSP
560
GGTGCATCTCCGGGTACTAGCTCTACCGGTTCTCCAGGTTC
561
N_C07.ab1
GSSPSASTGTGP
TAGCCCTTCTGCTTCCACTGGTACCGGCCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCGTCTGGTGCTACTGGTTCCCCA
LCW0404_007_GFP-
GTPGSGTASSSP
562
GGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCAGGTAG
563
N_D07.ab1
GSSTPSGATGSP
CTCTACCCCTTCTGGTGCAACTGGTTCCCCAGGTGCATCCCC
GASPGTSSTGSP
TGGTACTAGCTCTACCGGTTCTCCA
LCW0404_009_GFP-
GTPGSGTASSSP
564
GGTACCCCTGGCAGCGGTACTGCTTCTTCTTCTCCAGGTGC
565
N_E07.ab1
GASPGTSSTGSP
TTCCCCTGGTACCAGCTCTACCGGTTCTCCAGGTTCTAGAC
GSRPSASTGTGP
CTTCTGCATCCACCGGTACTGGTCCA
LCW0404_011_GFP-
GASPGTSSTGSP
566
GGTGCATCTCCTGGTACCAGCTCTACCGGTTCTCCAGGTAG
567
N_F07.ab1
GSSTPSGATGSP
CTCTACTCCTTCTGGTGCTACTGGCTCTCCAGGTGCTTCCCC
GASPGTSSTGSP
GGGTACCAGCTCTACCGGTTCTCCA
LCW0404_012_GFP-
GTPGSGTASSSP
568
GGTACCCCGGGCAGCGGTACCGCATCTTCCTCTCCAGGTAG
569
N_G07.ab1
GSSTPSGATGSP
CTCTACCCCGTCTGGTGCTACCGGTTCCCCAGGTAGCTCTAC
GSSTPSGATGSP
CCCGTCTGGTGCAACCGGCTCCCCA
LCW0404_014_GFP-
GASPGTSSTGSP
570
GGTGCATCTCCGGGCACTAGCTCTACTGGTTCTCCAGGTGC
571
N_H07.ab1
GASPGTSSTGSP
ATCCCCTGGCACTAGCTCTACTGGTTCTCCAGGTGCTTCTCC
GASPGTSSTGSP
TGGTACCAGCTCTACTGGTTCTCCA
LCW0404_015_GFP-
GSSTPSGATGSP
572
GGTAGCTCTACTCCGTCTGGTGCAACCGGCTCCCCAGGTTC
573
N_A08.ab1
GSSPSASTGTGP
TAGCCCGTCTGCTTCCACTGGTACTGGCCCAGGTGCTTCCCC
GASPGTSSTGSP
GGGCACCAGCTCTACTGGTTCTCCA
LCW0404_016_GFP-
GSSTPSGATGSP
574
GGTAGCTCTACTCCTTCTGGTGCTACCGGTTCCCCAGGTAG
575
N_B08.ab1
GSSTPSGATGSP
CTCTACTCCTTCTGGTGCTACTGGTTCCCCAGGTACTCCGG
GTPGSGTASSSP
GCAGCGGTACTGCTTCTTCCTCTCCA
LCW0404_017_GFP-
GSSTPSGATGSP
576
GGTAGCTCTACTCCGTCTGGTGCAACCGGTTCCCCAGGTAG
577
N_C08.ab1
GSSTPSGATGSP
CTCTACTCCTTCTGGTGCTACTGGCTCCCCAGGTGCATCCCC
GASPGTSSTGSP
TGGCACCAGCTCTACCGGTTCTCCA
LCW0404_018_GFP-
GTPGSGTASSSP
578
GGTACTCCTGGTAGCGGTACCGCATCTTCCTCTCCAGGTTC
579
N_D08.ab1
GSSPSASTGTGP
TAGCCCTTCTGCATCTACCGGTACCGGTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCTTCTGGTGCTACTGGCTCTCCA
LCW0404_023_GFP-
GASPGTSSTGSP
580
GGTGCTTCCCCGGGCACTAGCTCTACCGGTTCTCCAGGTTC
581
N_F08.ab1
GSSPSASTGTGP
TAGCCCTTCTGCATCTACTGGTACTGGCCCAGGTACTCCGG
GTPGSGTASSSP
GCAGCGGTACTGCTTCTTCCTCTCCA
LCW0404_025_GFP-
GSSTPSGATGSP
582
GGTAGCTCTACTCCGTCTGGTGCTACCGGCTCTCCAGGTAG
583
N_G08.ab1
GSSTPSGATGSP
CTCTACCCCTTCTGGTGCAACCGGCTCCCCAGGTGCTTCTCC
GASPGTSSTGSP
GGGTACCAGCTCTACTGGTTCTCCA
LCW0404_029_GFP-
GTPGSGTASSSP
584
GGTACCCCTGGCAGCGGTACCGCTTCTTCCTCTCCAGGTAG
585
N_A09.ab1
GSSTPSGATGSP
CTCTACCCCGTCTGGTGCTACTGGCTCTCCAGGTTCTAGCCC
GSSPSASTGTGP
GTCTGCATCTACCGGTACCGGCCCA
LCW0404_030_GFP-
GSSTPSGATGSP
586
GGTAGCTCTACTCCTTCTGGTGCAACCGGCTCCCCAGGTAC
587
N_B09.ab1
GTPGSGTASSSP
CCCGGGCAGCGGTACCGCATCTTCCTCTCCAGGTACTCCGG
GTPGSGTASSSP
GTAGCGGTACTGCTTCTTCTTCTCCA
LCW0404_031_GFP-
GTPGSGTASSSP
588
GGTACCCCGGGTAGCGGTACTGCTTCTTCCTCTCCAGGTAG
589
N_C09.ab1
GSSTPSGATGSP
CTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTCTCC
GASPGTSSTGSP
GGGCACCAGCTCTACCGGTTCTCCA
LCW0404_034_GFP-
GSSTPSGATGSP
590
GGTAGCTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAG
591
N_D09.ab1
GSSTPSGATGSP
CTCTACCCCGTCTGGTGCAACCGGCTCCCCAGGTGCATCCCC
GASPGTSSTGSP
GGGTACTAGCTCTACCGGTTCTCCA
LCW0404_035_GFP-
GASPGTSSTGSP
592
GGTGCTTCTCCGGGCACCAGCTCTACTGGTTCTCCAGGTAC
593
N_E09.ab1
GTPGSGTASSSP
CCCGGGCAGCGGTACCGCATCTTCTTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCTTCTGGTGCAACTGGTTCTCCA
LCW0404_036_GFP-
GSSPSASTGTGP
594
GGTTCTAGCCCGTCTGCTTCCACCGGTACTGGCCCAGGTAG
595
N_F09.ab1
GSSTPSGATGSP
CTCTACCCCGTCTGGTGCAACTGGTTCCCCAGGTACCCCTGG
GTPGSGTASSSP
TAGCGGTACCGCTTCTTCTTCTCCA
LCW0404_037_GFP-
GASPGTSSTGSP
596
GGTGCTTCTCCGGGCACCAGCTCTACTGGTTCTCCAGGTTC
597
N_G09.ab1
GSSPSASTGTGP
TAGCCCTTCTGCATCCACCGGTACCGGTCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCTTCTGGTGCAACCGGCTCTCCA
LCW0404_040_GFP-
GASPGTSSTGSP
598
GGTGCATCCCCGGGCACCAGCTCTACCGGTTCTCCAGGTAG
599
N_H09.ab1
GSSTPSGATGSP
CTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTAC
GSSTPSGATGSP
CCCGTCTGGTGCTACTGGCTCTCCA
LCW0404_041_GFP-
GTPGSGTASSSP
600
GGTACCCCTGGTAGCGGTACTGCTTCTTCCTCTCCAGGTAG
601
N_A10.ab1
GSSTPSGATGSP
CTCTACTCCGTCTGGTGCTACCGGTTCTCCAGGTACCCCGG
GTPGSGTASSSP
GTAGCGGTACCGCATCTTCTTCTCCA
LCW0404_043_GFP-
GSSPSASTGTGP
602
GGTTCTAGCCCTTCTGCTTCCACCGGTACTGGCCCAGGTAG
603
N_C10.ab1
GSSTPSGATGSP
CTCTACCCCTTCTGGTGCTACCGGCTCCCCAGGTAGCTCTAC
GSSTPSGATGSP
TCCTTCTGGTGCAACTGGCTCTCCA
LCW0404_045_GFP-
GASPGTSSTGSP
604
GGTGCTTCTCCTGGCACCAGCTCTACTGGTTCTCCAGGTTC
605
N_D10.ab1
GSSPSASTGTGP
TAGCCCTTCTGCTTCTACCGGTACTGGTCCAGGTTCTAGCC
GSSPSASTGTGP
CTTCTGCATCCACTGGTACTGGTCCA
LCW0404_047_GFP-
GTPGSGTASSSP
606
GGTACTCCTGGCAGCGGTACCGCTTCTTCTTCTCCAGGTGC
607
N_F10.ab1
GASPGTSSTGSP
TTCTCCTGGTACTAGCTCTACTGGTTCTCCAGGTGCTTCTC
GASPGTSSTGSP
CGGGCACTAGCTCTACTGGTTCTCCA
LCW0404_048_GFP-
GSSTPSGATGSP
608
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCAGGTGC
609
N_G10.ab1
GASPGTSSTGSP
TTCTCCTGGTACTAGCTCTACCGGTTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCGTCTGGTGCTACTGGCTCTCCA
LCW0404_049_GFP-
GSSTPSGATGSP
610
GGTAGCTCTACCCCGTCTGGTGCTACTGGTTCTCCAGGTAC
611
N_H10.ab1
GTPGSGTASSSP
TCCGGGCAGCGGTACTGCTTCTTCCTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCTTCTGGTGCTACTGGCTCTCCA
LCW0404_050_GFP-
GASPGTSSTGSP
612
GGTGCATCTCCTGGTACCAGCTCTACTGGTTCTCCAGGTTC
613
N_A11.ab1
GSSPSASTGTGP
TAGCCCTTCTGCTTCTACCGGTACCGGTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCTTCTGGTGCTACCGGTTCTCCA
LCW0404_051_GFP-
GSSTPSGATGSP
614
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCAGGTAG
615
N_B11.ab1
GSSTPSGATGSP
CTCTACTCCTTCTGGTGCTACTGGTTCCCCAGGTAGCTCTA
GSSTPSGATGSP
CCCCGTCTGGTGCAACTGGCTCTCCA
LCW0404_052_GFP-
GASPGTSSTGSP
616
GGTGCATCCCCGGGTACCAGCTCTACCGGTTCTCCAGGTAC
617
N_C11.ab1
GTPGSGTASSSP
TCCTGGCAGCGGTACTGCATCTTCCTCTCCAGGTGCTTCTCC
GASPGTSSTGSP
GGGCACCAGCTCTACTGGTTCTCCA
LCW0404_053_GFP-
GSSTPSGATGSP
618
GGTAGCTCTACTCCTTCTGGTGCAACTGGTTCTCCAGGTTC
619
N_D11.ab1
GSSPSASTGTGP
TAGCCCGTCTGCATCCACTGGTACCGGTCCAGGTGCTTCCCC
GASPGTSSTGSP
TGGCACCAGCTCTACCGGTTCTCCA
LCW0404_057_GFP-
GASPGTSSTGSP
620
GGTGCATCTCCTGGTACTAGCTCTACTGGTTCTCCAGGTAG
621
N_E11.ab1
GSSTPSGATGSP
CTCTACTCCGTCTGGTGCAACCGGCTCTCCAGGTTCTAGCCC
GSSPSASTGTGP
TTCTGCATCTACCGGTACTGGTCCA
LCW0404_060_GFP-
GTPGSGTASSSP
622
GGTACTCCTGGCAGCGGTACCGCATCTTCCTCTCCAGGTAG
623
N_F11.ab1
GSSTPSGATGSP
CTCTACTCCGTCTGGTGCAACTGGTTCCCCAGGTGCTTCTCC
GASPGTSSTGSP
GGGTACCAGCTCTACCGGTTCTCCA
LCW0404_062_GFP-
GSSTPSGATGSP
624
GGTAGCTCTACCCCGTCTGGTGCAACCGGCTCCCCAGGTAC
625
N_G11.ab1
GTPGSGTASSSP
TCCTGGTAGCGGTACCGCTTCTTCTTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCGTCTGGTGCTACCGGCTCCCCA
LCW0404_066_GFP-
GSSPSASTGTGP
626
GGTTCTAGCCCTTCTGCATCCACCGGTACCGGCCCAGGTTC
627
N_H11.ab1
GSSPSASTGTGP
TAGCCCGTCTGCTTCTACCGGTACTGGTCCAGGTGCTTCTC
GASPGTSSTGSP
CGGGTACTAGCTCTACTGGTTCTCCA
LCW0404_067_GFP-
GTPGSGTASSSP
628
GGTACCCCGGGTAGCGGTACCGCTTCTTCTTCTCCAGGTAG
629
N_A12.ab1
GSSTPSGATGSP
CTCTACTCCGTCTGGTGCTACCGGCTCTCCAGGTTCTAACCC
GSNPSASTGTGP
TTCTGCATCCACCGGTACCGGCCCA
LCW0404_068_GFP-
GSSPSASTGTGP
630
GGTTCTAGCCCTTCTGCATCTACTGGTACTGGCCCAGGTAG
631
N_B12.ab1
GSSTPSGATGSP
CTCTACTCCTTCTGGTGCTACCGGCTCTCCAGGTGCTTCTCC
GASPGTSSTGSP
GGGTACTAGCTCTACCGGTTCTCCA
LCW0404_069_GFP-
GSSTPSGATGSP
632
GGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGC
633
N_C12.ab1
GASPGTSSTGSP
ATCCCCGGGTACCAGCTCTACCGGTTCTCCAGGTACTCCGG
GTPGSGTASSSP
GTAGCGGTACCGCTTCTTCCTCTCCA
LCW0404_070_GFP-
GSSTPSGATGSP
634
GGTAGCTCTACTCCGTCTGGTGCAACCGGTTCCCCAGGTAG
635
N_D12.ab1
GSSTPSGATGSP
CTCTACCCCTTCTGGTGCAACCGGCTCCCCAGGTAGCTCTAC
GSSTPSGATGSP
CCCTTCTGGTGCAACTGGCTCTCCA
LCW0404_073_GFP-
GASPGTSSTGSP
636
GGTGCTTCTCCTGGCACTAGCTCTACCGGTTCTCCAGGTAC
637
N_E12.ab1
GTPGSGTASSSP
CCCTGGTAGCGGTACCGCATCTTCCTCTCCAGGTAGCTCTA
GSSTPSGATGSP
CTCCTTCTGGTGCTACTGGTTCCCCA
LCW0404_075_GFP-
GSSTPSGATGSP
638
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCCCCAGGTTC
639
N_F12.ab1
GSSPSASTGTGP
TAGCCCTTCTGCATCCACCGGTACCGGTCCAGGTTCTAGCC
GSSPSASTGTGP
CGTCTGCATCTACTGGTACTGGTCCA
LCW0404_080_GFP-
GASPGTSSTGSP
640
GGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCAGGTTC
641
N_G12.ab1
GSSPSASTGTGP
TAGCCCGTCTGCTTCTACTGGTACTGGTCCAGGTTCTAGCC
GSSPSASTGTGP
CTTCTGCTTCCACTGGTACTGGTCCA
LCW0404_081_GFP-
GASPGTSSTGSP
642
GGTGCTTCCCCGGGTACCAGCTCTACCGGTTCTCCAGGTTC
643
N_H12.ab1
GSSPSASTGTGP
TAGCCCTTCTGCTTCTACCGGTACCGGTCCAGGTACCCCTG
GTPGSGTASSSP
GCAGCGGTACCGCATCTTCCTCTCCA

Example 5: Construction of XTEN_AE864

XTEN_AE864 was constructed from serial dimerization of XTEN_AE36 to AE72, 144, 288, 576 and 864. A collection of XTEN_AE72 segments was constructed from 37 different segments of XTEN_AE36. Cultures of E. coli harboring all 37 different 36-amino acid segments were mixed and plasmid was isolated. This plasmid pool was digested with BsaI/NcoI to generate the small fragment as the insert. The same plasmid pool was digested with BbsI/NcoI to generate the large fragment as the vector. The insert and vector fragments were ligated resulting in a doubling of the length and the ligation mixture was transformed into BL21Gold(DE3) cells to obtain colonies of XTEN_AE72.

This library of XTEN_AE72 segments was designated LCW0406. All clones from LCW0406 were combined and dimerized again using the same process as described above yielding library LCW0410 of XTEN_AE144. All clones from LCW0410 were combined and dimerized again using the same process as described above yielding library LCW0414 of XTEN_AE288. Two isolates LCW0414.001 and LCW0414.002 were randomly picked from the library and sequenced to verify the identities. All clones from LCW0414 were combined and dimerized again using the same process as described above yielding library LCW0418 of XTEN_AE576. We screened 96 isolates from library LCW0418 for high level of GFP fluorescence. 8 isolates with right sizes of inserts by PCR and strong fluorescence were sequenced and 2 isolates (LCW0418.018 and LCW0418.052) were chosen for future use based on sequencing and expression data.

The specific clone pCW0432 of XTEN_AE864 was constructed by combining LCW0418.018 of XTEN_AE576 and LCW0414.002 of XTEN_AE288 using the same dimerization process as described above.

Example 6: Construction of XTEN_AM144

A collection of XTEN_AM144 segments was constructed starting from 37 different segments of XTEN_AE36, 44 segments of XTEN_AF36, and 44 segments of XTEN_AG36.

Cultures of E. coli harboring all 125 different 36-amino acid segments were mixed and plasmid was isolated. This plasmid pool was digested with BsaI/NcoI to generate the small fragment as the insert. The same plasmid pool was digested with BbsI/NcoI to generate the large fragment as the vector. The insert and vector fragments were ligated resulting in a doubling of the length and the ligation mixture was transformed into BL21Gold(DE3) cells to obtain colonies of XTEN_AM72.

This library of XTEN_AM72 segments was designated LCW0461. All clones from LCW0461 were combined and dimerized again using the same process as described above yielding library LCW0462. 1512 Isolates from library LCW0462 were screened for protein expression. Individual colonies were transferred into 96 well plates and cultured overnight as starter cultures. These starter cultures were diluted into fresh autoinduction medium and cultured for 20-30 h. Expression was measured using a fluorescence plate reader with excitation at 395 nm and emission at 510 nm. 192 isolates showed high level expression and were submitted to DNA sequencing. Most clones in library LCW0462 showed good expression and similar physicochemical properties suggesting that most combinations of XTEN_AM36 segments yield useful XTEN sequences. 30 isolates from LCW0462 were chosen as a preferred collection of XTEN_AM144 segments for the construction of multifunctional proteins that contain multiple XTEN segments. The file names of the nucleotide and amino acid constructs for these segments are listed in Table 14.


TABLE 14
DNA and amino acid sequences for AM144 segments
SEQ ID
SEQ ID
Clone
Sequence Trimmed
NO:
Protein Sequence
NO:
LCW462_r1
GGTACCCCGGGCAGCGGTACCGCATCTTCCTCTCCA
644
GTPGSGTASSSPGSSTPSGA
645
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCA
TGSPGSSTPSGATGSPGSPA
GGTAGCTCTACCCCGTCTGGTGCAACCGGCTCCCCA
GSPTSTEEGTSESATPESGP
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAA
GTSTEPSEGSAPGSSPSAST
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCA
GTGPGSSPSASTGTGPGAS
GGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCA
PGTSSTGSPGTSTEPSEGSA
GGTTCTAGCCCTTCTGCATCCACCGGTACCGGCCCA
PGTSTEPSEGSAPGSEPATS
GGTTCTAGCCCGTCTGCTTCTACCGGTACTGGTCCA
GSETP
GGTGCTTCTCCGGGTACTAGCTCTACTGGTTCTCCA
GGTACCTCTACCGAACCGTCCGAGGGTAGCGCACCA
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCCA
LCW462_r5
GGTTCTACCAGCGAATCCCCTTCTGGCACTGCACCA
646
GSTSESPSGTAPGSTSESPS
647
GGTTCTACTAGCGAATCCCCTTCTGGTACCGCACCA
GTAPGTSPSGESSTAPGTST
GGTACTTCTCCGAGCGGCGAATCTTCTACTGCTCCA
EPSEGSAPGTSTEPSEGSAP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GTSESATPESGPGASPGTSS
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
TGSPGSSTPSGATGSPGASP
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GTSSTGSPGSTSESPSGTAP
GGTGCATCTCCTGGTACCAGCTCTACCGGTTCTCCA
GSTSESPSGTAPGTSTPESG
GGTAGCTCTACTCCTTCTGGTGCTACTGGCTCTCCA
SASP
GGTGCTTCCCCGGGTACCAGCTCTACCGGTTCTCCA
GGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCA
GGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCA
GGTACCTCTACCCCTGAAAGCGGTTCCGCTTCTCCA
LCW462_r9
GGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCA
648
GTSTEPSEGSAPGTSESATP
649
GGTACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCA
ESGPGTSESATPESGPGTST
GGTACTTCTGAAAGCGCTACTCCTGAATCCGGTCCA
EPSEGSAPGTSESATPESGP
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCA
GTSTEPSEGSAPGTSTEPSE
GGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCA
GSAPGSEPATSGSETPGSPA
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
GSPTSTEEGASPGTSSTGSP
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCTCCA
GSSPSASTGTGPGSSPSAST
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACCCCA
GTGP
GGTAGCCCGGCTGGCTCTCCGACCTCCACCGAGGAA
GGTGCTTCTCCTGGCACCAGCTCTACTGGTTCTCCA
GGTTCTAGCCCTTCTGCTTCTACCGGTACTGGTCCA
GGTTCTAGCCCTTCTGCATCCACTGGTACTGGTCCA
LCW462_r10
GGTAGCGAACCGGCAACCTCTGGCTCTGAAACCCCA
650
GSEPATSGSETPGTSESATP
651
GGTACCTCTGAAAGCGCTACTCCGGAATCTGGTCCA
ESGPGTSESATPESGPGSTS
GGTACTTCTGAAAGCGCTACTCCGGAATCCGGTCCA
ESPSGTAPGSTSESPSGTAP
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCA
GTSPSGESSTAPGASPGTSS
GGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCA
TGSPGSSPSASTGTGPGSST
GGTACTTCTCCTAGCGGCGAATCTTCTACCGCACCA
PSGATGSPGSSTPSGATGSP
GGTGCATCTCCGGGTACTAGCTCTACCGGTTCTCCA
GSSTPSGATGSPGASPGTSS
GGTTCTAGCCCTTCTGCTTCCACTGGTACCGGCCCA
TGSP
GGTAGCTCTACCCCGTCTGGTGCTACTGGTTCCCCA
GGTAGCTCTACTCCGTCTGGTGCAACCGGTTCCCCA
GGTAGCTCTACTCCTTCTGGTGCTACTGGCTCCCCA
GGTGCATCCCCTGGCACCAGCTCTACCGGTTCTCCA
LCW462_r15
GGTGCTTCTCCGGGCACCAGCTCTACTGGTTCTCCA
652
GASPGTSSTGSPGSSPSAST
653
GGTTCTAGCCCTTCTGCATCCACCGGTACCGGTCCA
GTGPGSSTPSGATGSPGTSE
GGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCA
SATPESGPGSEPATSGSETP
GGTACTTCTGAAAGCGCTACCCCGGAATCTGGCCCA
GSEPATSGSETPGTSESATP
GGTAGCGAACCGGCTACTTCTGGTTCTGAAACCCCA
ESGPGTSTEPSEGSAPGTST
GGTAGCGAACCGGCTACCTCCGGTTCTGAAACTCCA
EPSEGSAPGTSTEPSEGSAP
GGTACTTCTGAAAGCGCTACTCCGGAGTCCGGTCCA
GTSTEPSEGSAPGSEPATSG
GGTACCTCTACCGAACCGTCCGAAGGCAGCGCTCCA
SETP
GGTACTTCTACTGAACCTTCTGAGGGTAGCGCTCCA
GGTACCTCTACCGAACCGTCCGAGGGTAGCGCACCA
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCCA
LCW462_r16
GGTACCTCTACCGAACCTTCCGAAGGTAGCGCTCCA
654
GTSTEPSEGSAPGSPAGSPT
655
GGTAGCCCGGCAGGTTCTCCTACTTCCACTGAGGAA
STEEGTSTEPSEGSAPGTSE
GGTACTTCTACCGAACCTTCTGAGGGTAGCGCACCA
SATPESGPGSEPATSGSETP
GGTACCTCTGAAAGCGCAACTCCTGAGTCTGGCCCA
GTSESATPESGPGSPAGSPT
GGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCA
STEEGTSESATPESGPGTST
GGTACCTCTGAAAGCGCAACCCCGGAATCTGGTCCA
EPSEGSAPGSEPATSGSETP
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAA
GTSTEPSEGSAPGSEPATSG
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCA
SETP
GGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCA
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACTCCA
GGTACTTCTACCGAACCGTCCGAGGGTAGCGCTCCA
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACTCCA
LCW462_r20
GGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCA
656
GTSTEPSEGSAPGTSTEPSE
657
GGTACCTCTACTGAACCTTCCGAGGGCAGCGCTCCA
GSAPGTSTEPSEGSAPGTST
GGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCA
EPSEGSAPGTSTEPSEGSAP
GGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCA
GTSTEPSEGSAPGTSTEPSE
GGTACCTCTACTGAACCTTCCGAGGGCAGCGCTCCA
GSAPGTSESATPESGPGTSE
GGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCA
SATPESGPGTSTEPSEGSAP
GGTACTTCTACCGAACCTTCCGAGGGCAGCGCACCA
GSEPATSGSETPGSPAGSPT
GGTACTTCTGAAAGCGCTACCCCTGAGTCCGGCCCA
STEE
GGTACTTCTGAAAGCGCTACTCCTGAATCCGGTCCA
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCTCCA
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACCCCA
GGTAGCCCGGCTGGCTCTCCGACCTCCACCGAGGAA
LCW462_r23
GGTACTTCTACCGAACCGTCCGAGGGCAGCGCTCCA
658
GTSTEPSEGSAPGTSTEPSE
659
GGTACTTCTACTGAACCTTCTGAAGGCAGCGCTCCA
GSAPGTSTEPSEGSAPGSTS
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCACCA
ESPSGTAPGSTSESPSGTAP
GGTTCTACCAGCGAATCCCCTTCTGGTACTGCTCCA
GTSTPESGSASPGSEPATSG
GGTTCTACCAGCGAATCCCCTTCTGGCACCGCACCA
SETPGTSESATPESGPGTST
GGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTCCA
EPSEGSAPGTSTEPSEGSAP
GGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCA
GTSESATPESGPGTSESATP
GGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCA
ESGP
GGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
GGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCA
GGTACTTCTGAAAGCGCAACCCCGGAATCCGGCCCA
GGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
LCW462_r24
GGTAGCTCTACCCCTTCTGGTGCTACCGGCTCTCCA
660
GSSTPSGATGSPGSSPSAST
661
GGTTCTAGCCCGTCTGCTTCTACCGGTACCGGTCCA
GTGPGSSTPSGATGSPGSP
GGTAGCTCTACCCCTTCTGGTGCTACTGGTTCTCCA
AGSPTSTEEGSPAGSPTSTE
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAA
EGTSTEPSEGSAPGASPGTS
GGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAA
STGSPGSSPSASTGTGPGTP
GGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCA
GSGTASSSPGSTSSTAESPG
GGTGCTTCCCCGGGCACTAGCTCTACCGGTTCTCCA
PGTSPSGESSTAPGTSTPES
GGTTCTAGCCCTTCTGCATCTACTGGTACTGGCCCA
GSASP
GGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCA
GGTTCTACTAGCTCTACTGCTGAATCTCCTGGCCCA
GGTACTTCTCCTAGCGGTGAATCTTCTACCGCTCCA
GGTACCTCTACTCCGGAAAGCGGTTCTGCATCTCCA
LCW462_r27
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCA
662
GTSTEPSEGSAPGTSESATP
663
GGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCA
ESGPGTSTEPSEGSAPGTST
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
EPSEGSAPGTSESATPESGP
GGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCA
GTSESATPESGPGTPGSGT
GGTACTTCTGAAAGCGCAACCCCGGAATCCGGCCCA
ASSSPGASPGTSSTGSPGAS
GGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
PGTSSTGSPGSPAGSPTSTE
GGTACTCCTGGCAGCGGTACCGCTTCTTCTTCTCCA
EGSPAGSPTSTEEGTSTEPS
GGTGCTTCTCCTGGTACTAGCTCTACTGGTTCTCCA
EGSAP
GGTGCTTCTCCGGGCACTAGCTCTACTGGTTCTCCA
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAA
GGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAA
GGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCA
LCW462_r28
GGTAGCCCAGCAGGCTCTCCGACTTCCACTGAGGAA
664
GSPAGSPTSTEEGTSTEPSE
665
GGTACTTCTACTGAACCTTCCGAAGGCAGCGCACCA
GSAPGTSTEPSEGSAPGTST
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCA
EPSEGSAPGTSESATPESGP
GGTACCTCTACCGAACCGTCTGAAGGTAGCGCACCA
GTSESATPESGPGTPGSGT
GGTACCTCTGAAAGCGCAACTCCTGAGTCCGGTCCA
ASSSPGSSTPSGATGSPGAS
GGTACTTCTGAAAGCGCAACCCCGGAGTCTGGCCCA
PGTSSTGSPGTSTEPSEGSA
GGTACCCCGGGTAGCGGTACTGCTTCTTCCTCTCCA
PGTSESATPESGPGTSTEPS
GGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCA
EGSAP
GGTGCTTCTCCGGGCACCAGCTCTACCGGTTCTCCA
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCA
GGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCA
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
LCW462_r38
GGTAGCGAACCGGCAACCTCCGGCTCTGAAACTCCA
666
GSEPATSGSETPGTSESATP
667
GGTACTTCTGAAAGCGCTACTCCGGAATCCGGCCCA
ESGPGSEPATSGSETPGSST
GGTAGCGAACCGGCTACTTCCGGCTCTGAAACCCCA
PSGATGSPGTPGSGTASSSP
GGTAGCTCTACCCCGTCTGGTGCAACCGGCTCCCCA
GSSTPSGATGSPGASPGTSS
GGTACTCCTGGTAGCGGTACCGCTTCTTCTTCTCCA
TGSPGSSTPSGATGSPGASP
GGTAGCTCTACTCCGTCTGGTGCTACCGGCTCCCCA
GTSSTGSPGSEPATSGSETP
GGTGCATCTCCTGGTACCAGCTCTACCGGTTCTCCA
GTSTEPSEGSAPGSEPATSG
GGTAGCTCTACTCCTTCTGGTGCTACTGGCTCTCCA
SETP
GGTGCTTCCCCGGGTACCAGCTCTACCGGTTCTCCA
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACTCCA
GGTACTTCTACCGAACCGTCCGAGGGTAGCGCTCCA
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACTCCA
LCW462_r39
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
668
GTSTEPSEGSAPGTSTEPSE
669
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
GSAPGTSESATPESGPGSPA
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GSPTSTEEGSPAGSPTSTEE
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAA
GTSTEPSEGSAPGSPAGSPT
GGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAA
STEEGTSTEPSEGSAPGTST
GGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCA
EPSEGSAPGASPGTSSTGSP
GGTAGCCCGGCTGGTTCTCCGACTTCCACCGAGGAA
GSSPSASTGTGPGSSPSAST
GGTACCTCTACTGAACCTTCTGAGGGTAGCGCTCCA
GTGP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCA
GGTTCTAGCCCGTCTGCTTCTACTGGTACTGGTCCA
GGTTCTAGCCCTTCTGCTTCCACTGGTACTGGTCCA
LCW462_r41
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCA
670
GSSTPSGATGSPGASPGTSS
671
GGTGCTTCTCCTGGTACTAGCTCTACCGGTTCTCCA
TGSPGSSTPSGATGSPGSPA
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCA
GSPTSTEEGTSESATPESGP
GGTAGCCCTGCTGGCTCTCCAACCTCCACCGAAGAA
GSEPATSGSETPGASPGTSS
GGTACCTCTGAAAGCGCAACCCCTGAATCCGGCCCA
TGSPGSSTPSGATGSPGSSP
GGTAGCGAACCGGCAACCTCCGGTTCTGAAACCCCA
SASTGTGPGSTSESPSGTAP
GGTGCATCTCCTGGTACTAGCTCTACTGGTTCTCCA
GSTSESPSGTAPGTSTPESG
GGTAGCTCTACTCCGTCTGGTGCAACCGGCTCTCCA
SASP
GGTTCTAGCCCTTCTGCATCTACCGGTACTGGTCCA
GGTTCTACCAGCGAATCCCCTTCTGGTACTGCTCCA
GGTTCTACCAGCGAATCCCCTTCTGGCACCGCACCA
GGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTCCA
LCW462_r42
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCA
672
GSTSESPSGTAPGSTSESPS
673
GGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCA
GTAPGTSPSGESSTAPGTSE
GGTACTTCTCCTAGCGGCGAATCTTCTACCGCACCA
SATPESGPGTSTEPSEGSAP
GGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCA
GTSTEPSEGSAPGTSTEPSE
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GSAPGTSESATPESGPGTST
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
EPSEGSAPGSSTPSGATGSP
GGTACCTCTACTGAACCTTCTGAGGGCAGCGCTCCA
GASPGTSSTGSPGSSTPSGA
GGTACTTCTGAAAGCGCTACCCCGGAGTCCGGTCCA
TGSP
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCA
GGTGCTTCTCCTGGTACTAGCTCTACCGGTTCTCCA
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCA
LCW462_r43
GGTTCTACTAGCTCTACTGCAGAATCTCCGGGCCCA
674
GSTSSTAESPGPGTSPSGES
675
GGTACCTCTCCTAGCGGTGAATCTTCTACCGCTCCA
STAPGTSPSGESSTAPGSTS
GGTACTTCTCCGAGCGGTGAATCTTCTACCGCTCCA
STAESPGPGSTSSTAESPGP
GGTTCTACTAGCTCTACCGCTGAATCTCCGGGTCCA
GTSTPESGSASPGTSPSGES
GGTTCTACCAGCTCTACTGCAGAATCTCCTGGCCCA
STAPGSTSSTAESPGPGTST
GGTACTTCTACTCCGGAAAGCGGTTCCGCTTCTCCA
PESGSASPGSTSSTAESPGP
GGTACTTCTCCTAGCGGTGAATCTTCTACCGCTCCA
GSTSESPSGTAPGTSPSGES
GGTTCTACCAGCTCTACTGCTGAATCTCCTGGCCCA
STAP
GGTACTTCTACCCCGGAAAGCGGCTCCGCTTCTCCA
GGTTCTACCAGCTCTACCGCTGAATCTCCTGGCCCA
GGTTCTACTAGCGAATCTCCGTCTGGCACCGCACCA
GGTACTTCCCCTAGCGGTGAATCTTCTACTGCACCA
LCW462_r45
GGTACCTCTACTCCGGAAAGCGGTTCCGCATCTCCA
676
GTSTPESGSASPGSTSESPS
677
GGTTCTACCAGCGAATCCCCGTCTGGCACCGCACCA
GTAPGSTSSTAESPGPGTST
GGTTCTACTAGCTCTACTGCTGAATCTCCGGGCCCA
EPSEGSAPGTSTEPSEGSAP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GTSESATPESGPGTSESATP
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
ESGPGTSTEPSEGSAPGTST
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
EPSEGSAPGTSESATPESGP
GGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCA
GTSTEPSEGSAPGTSTEPSE
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GSAP
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
GGTACTTCTGAAAGCGCTACTCCGGAGTCCGGTCCA
GGTACCTCTACCGAACCGTCCGAAGGCAGCGCTCCA
GGTACTTCTACTGAACCTTCTGAGGGTAGCGCTCCC
LCW462_r47
GGTACCTCTACCGAACCGTCCGAGGGTAGCGCACCA
678
GTSTEPSEGSAPGTSTEPSE
679
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GSAPGSEPATSGSETPGTST
GGTAGCGAACCGGCAACCTCCGGTTCTGAAACTCCA
EPSEGSAPGTSESATPESGP
GGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCA
GTSESATPESGPGASPGTSS
GGTACTTCTGAAAGCGCAACCCCGGAATCCGGCCCA
TGSPGSSPSASTGTGPGSST
GGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
PSGATGSPGSSTPSGATGSP
GGTGCATCTCCGGGTACTAGCTCTACCGGTTCTCCA
GSSTPSGATGSPGASPGTSS
GGTTCTAGCCCTTCTGCTTCCACTGGTACCGGCCCA
TGSP
GGTAGCTCTACCCCGTCTGGTGCTACTGGTTCCCCA
GGTAGCTCTACTCCGTCTGGTGCAACCGGTTCCCCA
GGTAGCTCTACTCCTTCTGGTGCTACTGGCTCCCCA
GGTGCATCCCCTGGCACCAGCTCTACCGGTTCTCCA
LCW462_r54
GGTAGCGAACCGGCAACCTCTGGCTCTGAAACTCCA
680
GSEPATSGSETPGSEPATSG
681
GGTAGCGAACCTGCAACCTCCGGCTCTGAAACCCCA
SETPGTSTEPSEGSAPGSEP
GGTACTTCTACTGAACCTTCTGAGGGCAGCGCACCA
ATSGSETPGTSESATPESGP
GGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCA
GTSTEPSEGSAPGSSTPSGA
GGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCA
TGSPGSSTPSGATGSPGASP
GGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
GTSSTGSPGSSTPSGATGSP
GGTAGCTCTACTCCGTCTGGTGCTACCGGCTCTCCA
GASPGTSSTGSPGSSTPSGA
GGTAGCTCTACCCCTTCTGGTGCAACCGGCTCCCCA
TGSP
GGTGCTTCTCCGGGTACCAGCTCTACTGGTTCTCCA
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCA
GGTGCTTCTCCTGGTACTAGCTCTACCGGTTCTCCA
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCA
LCW462_r55
GGTACTTCTACCGAACCGTCCGAGGGCAGCGCTCCA
682
GTSTEPSEGSAPGTSTEPSE
683
GGTACTTCTACTGAACCTTCTGAAGGCAGCGCTCCA
GSAPGTSTEPSEGSAPGTSE
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCACCA
SATPESGPGTSTEPSEGSAP
GGTACTTCTGAAAGCGCTACTCCGGAGTCCGGTCCA
GTSTEPSEGSAPGSTSESPS
GGTACCTCTACCGAACCGTCCGAAGGCAGCGCTCCA
GTAPGTSPSGESSTAPGTSP
GGTACTTCTACTGAACCTTCTGAGGGTAGCGCTCCA
SGESSTAPGSPAGSPTSTEE
GGTTCTACTAGCGAATCTCCGTCTGGCACTGCTCCA
GTSESATPESGPGTSTEPSE
GGTACTTCTCCTAGCGGTGAATCTTCTACCGCTCCA
GSAP
GGTACTTCCCCTAGCGGCGAATCTTCTACCGCTCCA
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAA
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCA
GGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCA
LCW462_r57
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCTCCA
684
GTSTEPSEGSAPGSEPATSG
685
GGTAGCGAACCTGCTACTTCTGGTTCTGAAACCCCA
SETPGSPAGSPTSTEEGSPA
GGTAGCCCGGCTGGCTCTCCGACCTCCACCGAGGAA
GSPTSTEEGTSESATPESGP
GGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAA
GTSTEPSEGSAPGTSTEPSE
GGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
GSAPGTSTEPSEGSAPGTSE
GGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCA
SATPESGPGSSTPSGATGSP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GSSPSASTGTGPGASPGTSS
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
TGSP
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GGTAGCTCTACTCCGTCTGGTGCAACCGGCTCCCCA
GGTTCTAGCCCGTCTGCTTCCACTGGTACTGGCCCA
GGTGCTTCCCCGGGCACCAGCTCTACTGGTTCTCCA
LCW462_r61
GGTAGCGAACCGGCTACTTCCGGCTCTGAGACTCCA
686
GSEPATSGSETPGSPAGSPT
687
GGTAGCCCTGCTGGCTCTCCGACCTCTACCGAAGAA
STEEGTSESATPESGPGTST
GGTACCTCTGAAAGCGCTACCCCTGAGTCTGGCCCA
EPSEGSAPGTSTEPSEGSAP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GTSESATPESGPGTSTPESG
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
SASPGSTSESPSGTAPGSTS
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
STAESPGPGTSESATPESGP
GGTACCTCTACTCCGGAAAGCGGTTCCGCATCTCCA
GTSTEPSEGSAPGTSTEPSE
GGTTCTACCAGCGAATCCCCGTCTGGCACCGCACCA
GSAP
GGTTCTACTAGCTCTACTGCTGAATCTCCGGGCCCA
GGTACTTCTGAAAGCGCTACTCCGGAGTCCGGTCCA
GGTACCTCTACCGAACCGTCCGAAGGCAGCGCTCCA
GGTACTTCTACTGAACCTTCTGAGGGTAGCGCTCCA
LCW462_r64
GGTACTTCTACCGAACCGTCCGAGGGCAGCGCTCCA
688
GTSTEPSEGSAPGTSTEPSE
689
GGTACTTCTACTGAACCTTCTGAAGGCAGCGCTCCA
GSAPGTSTEPSEGSAPGTST
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCACCA
EPSEGSAPGTSESATPESGP
GGTACCTCTACCGAACCGTCTGAAGGTAGCGCACCA
GTSESATPESGPGTPGSGT
GGTACCTCTGAAAGCGCAACTCCTGAGTCCGGTCCA
ASSSPGSSTPSGATGSPGAS
GGTACTTCTGAAAGCGCAACCCCGGAGTCTGGCCCA
PGTSSTGSPGSTSSTAESPG
GGTACTCCTGGCAGCGGTACCGCATCTTCCTCTCCA
PGTSPSGESSTAPGTSTPES
GGTAGCTCTACTCCGTCTGGTGCAACTGGTTCCCCA
GSASP
GGTGCTTCTCCGGGTACCAGCTCTACCGGTTCTCCA
GGTTCCACCAGCTCTACTGCTGAATCTCCTGGTCCA
GGTACCTCTCCTAGCGGTGAATCTTCTACTGCTCCA
GGTACTTCTACTCCTGAAAGCGGCTCTGCTTCTCCA
LCW462_r67
GGTAGCCCGGCAGGCTCTCCGACCTCTACTGAGGAA
690
GSPAGSPTSTEEGTSESATP
691
GGTACTTCTGAAAGCGCAACCCCGGAGTCCGGCCCA
ESGPGTSTEPSEGSAPGTSE
GGTACCTCTACCGAACCGTCTGAGGGCAGCGCACCA
SATPESGPGSEPATSGSETP
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GTSTEPSEGSAPGSPAGSPT
GGTAGCGAACCGGCTACTTCTGGCTCTGAGACTCCA
STEEGTSTEPSEGSAPGTST
GGTACTTCTACCGAACCGTCCGAAGGTAGCGCACCA
EPSEGSAPGTSTEPSEGSAP
GGTAGCCCGGCTGGTTCTCCGACTTCCACCGAGGAA
GTSTEPSEGSAPGTSTEPSE
GGTACCTCTACTGAACCTTCTGAGGGTAGCGCTCCA
GSAP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GGTACTTCTACCGAACCGTCCGAGGGCAGCGCTCCA
GGTACTTCTACTGAACCTTCTGAAGGCAGCGCTCCA
GGTACTTCTACTGAACCTTCCGAAGGTAGCGCACCA
LCW462_r69
GGTACTTCTCCGAGCGGTGAATCTTCTACCGCACCA
692
GTSPSGESSTAPGSTSSTAE
693
GGTTCTACTAGCTCTACCGCTGAATCTCCGGGCCCA
SPGPGTSPSGESSTAPGTSE
GGTACTTCTCCGAGCGGTGAATCTTCTACTGCTCCA
SATPESGPGTSTEPSEGSAP
GGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCA
GTSTEPSEGSAPGSSPSAST
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GTGPGSSTPSGATGSPGAS
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
PGTSSTGSPGTSTPESGSAS
GGTTCTAGCCCTTCTGCATCTACTGGTACTGGCCCA
PGTSPSGESSTAPGTSPSGE
GGTAGCTCTACTCCTTCTGGTGCTACCGGCTCTCCA
SSTAP
GGTGCTTCTCCGGGTACTAGCTCTACCGGTTCTCCA
GGTACTTCTACTCCGGAAAGCGGTTCCGCATCTCCA
GGTACTTCTCCTAGCGGTGAATCTTCTACTGCTCCA
GGTACCTCTCCTAGCGGCGAATCTTCTACTGCTCCA
LCW462_r70
GGTACCTCTGAAAGCGCTACTCCGGAGTCTGGCCCA
694
GTSESATPESGPGTSTEPSE
695
GGTACCTCTACTGAACCGTCTGAGGGTAGCGCTCCA
GSAPGTSTEPSEGSAPGSPA
GGTACTTCTACTGAACCGTCCGAAGGTAGCGCACCA
GSPTSTEEGSPAGSPTSTEE
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAA
GTSTEPSEGSAPGSSPSAST
GGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAA
GTGPGSSTPSGATGSPGSST
GGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCA
PSGATGSPGSEPATSGSETP
GGTTCTAGCCCTTCTGCTTCCACCGGTACTGGCCCA
GTSESATPESGPGSEPATSG
GGTAGCTCTACCCCTTCTGGTGCTACCGGCTCCCCA
SETP
GGTAGCTCTACTCCTTCTGGTGCAACTGGCTCTCCA
GGTAGCGAACCGGCAACTTCCGGCTCTGAAACCCCA
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGCCCA
GGTAGCGAACCTGCTACCTCTGGCTCTGAAACCCCA
LCW462_r72
GGTACTTCTACCGAACCGTCCGAAGGCAGCGCTCCA
696
GTSTEPSEGSAPGTSTEPSE
697
GGTACCTCTACTGAACCTTCCGAGGGCAGCGCTCCA
GSAPGTSTEPSEGSAPGSST
GGTACCTCTACCGAACCTTCTGAAGGTAGCGCACCA
PSGATGSPGASPGTSSTGSP
GGTAGCTCTACCCCGTCTGGTGCTACCGGTTCCCCA
GSSTPSGATGSPGTSESATP
GGTGCTTCTCCTGGTACTAGCTCTACCGGTTCTCCA
ESGPGSEPATSGSETPGTST
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCA
EPSEGSAPGSTSESPSGTAP
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GSTSESPSGTAPGTSTPESG
GGTAGCGAACCGGCTACTTCTGGCTCTGAGACTCCA
SASP
GGTACTTCTACCGAACCGTCCGAAGGTAGCGCACCA
GGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCA
GGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCA
GGTACCTCTACCCCTGAAAGCGGTTCCGCTTCTCCA
LCW462_r73
GGTACCTCTACTCCTGAAAGCGGTTCTGCATCTCCA
698
GTSTPESGSASPGSTSSTAE
699
GGTTCCACTAGCTCTACCGCAGAATCTCCGGGCCCA
SPGPGSTSSTAESPGPGSSP
GGTTCTACTAGCTCTACTGCTGAATCTCCTGGCCCA
SASTGTGPGSSTPSGATGSP
GGTTCTAGCCCTTCTGCATCTACTGGTACTGGCCCA
GASPGTSSTGSPGSEPATSG
GGTAGCTCTACTCCTTCTGGTGCTACCGGCTCTCCA
SETPGTSESATPESGPGSPA
GGTGCTTCTCCGGGTACTAGCTCTACCGGTTCTCCA
GSPTSTEEGSTSESPSGTAP
GGTAGCGAACCGGCAACCTCCGGCTCTGAAACCCCA
GSTSESPSGTAPGTSTPESG
GGTACCTCTGAAAGCGCTACTCCTGAATCCGGCCCA
SASP
GGTAGCCCGGCAGGTTCTCCGACTTCCACTGAGGAA
GGTTCTACTAGCGAATCTCCTTCTGGCACTGCACCA
GGTTCTACCAGCGAATCTCCGTCTGGCACTGCACCA
GGTACCTCTACCCCTGAAAGCGGTTCCGCTTCTCCC
LCW462_r78
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAA
700
GSPAGSPTSTEEGTSESATP
701
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCA
ESGPGTSTEPSEGSAPGSTS
GGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCA
ESPSGTAPGSTSESPSGTAP
GGTTCTACCAGCGAATCTCCTTCTGGCACCGCTCCA
GTSPSGESSTAPGTSTEPSE
GGTTCTACTAGCGAATCCCCGTCTGGTACCGCACCA
GSAPGSPAGSPTSTEEGTST
GGTACTTCTCCTAGCGGCGAATCTTCTACCGCACCA
EPSEGSAPGSEPATSGSETP
GGTACCTCTACCGAACCTTCCGAAGGTAGCGCTCCA
GTSESATPESGPGTSTEPSE
GGTAGCCCGGCAGGTTCTCCTACTTCCACTGAGGAA
GSAP
GGTACTTCTACCGAACCTTCTGAGGGTAGCGCACCA
GGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCA
GGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCA
GGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
LCW462_r79
GGTACCTCTACCGAACCTTCCGAAGGTAGCGCTCCA
702
GTSTEPSEGSAPGSPAGSPT
703
GGTAGCCCGGCAGGTTCTCCTACTTCCACTGAGGAA
STEEGTSTEPSEGSAPGTSP
GGTACTTCTACCGAACCTTCTGAGGGTAGCGCACCA
SGESSTAPGTSPSGESSTAP
GGTACCTCCCCTAGCGGCGAATCTTCTACTGCTCCA
GTSPSGESSTAPGSTSESPS
GGTACCTCTCCTAGCGGCGAATCTTCTACCGCTCCA
GTAPGSTSESPSGTAPGTST
GGTACCTCCCCTAGCGGTGAATCTTCTACCGCACCA
PESGSASPGSEPATSGSETP
GGTTCTACCAGCGAATCCCCTTCTGGTACTGCTCCA
GTSESATPESGPGTSTEPSE
GGTTCTACCAGCGAATCCCCTTCTGGCACCGCACCA
GSAP
GGTACTTCTACCCCTGAAAGCGGCTCCGCTTCTCCA
GGTAGCGAACCTGCAACCTCTGGCTCTGAAACCCCA
GGTACCTCTGAAAGCGCTACTCCTGAATCTGGCCCA
GGTACTTCTACTGAACCGTCCGAGGGCAGCGCACCA
LCW462_r87
GGTAGCGAACCGGCAACCTCTGGCTCTGAAACCCCA
704
GSEPATSGSETPGTSESATP
705
GGTACCTCTGAAAGCGCTACTCCGGAATCTGGTCCA
ESGPGTSESATPESGPGTSP
GGTACTTCTGAAAGCGCTACTCCGGAATCCGGTCCA
SGESSTAPGSTSSTAESPGP
GGTACTTCTCCGAGCGGTGAATCTTCTACCGCACCA
GTSPSGESSTAPGSTSESPS
GGTTCTACTAGCTCTACCGCTGAATCTCCGGGCCCA
GTAPGTSPSGESSTAPGSTS
GGTACTTCTCCGAGCGGTGAATCTTCTACTGCTCCA
STAESPGPGSSTPSGATGSP
GGTTCTACTAGCGAATCCCCGTCTGGTACTGCTCCA
GSSTPSGATGSPGSSTPSGA
GGTACTTCCCCTAGCGGTGAATCTTCTACTGCTCCA
NWLS
GGTTCTACCAGCTCTACCGCAGAATCTCCGGGTCCA
GGTAGCTCTACTCCGTCTGGTGCAACCGGTTCCCCA
GGTAGCTCTACCCCTTCTGGTGCAACCGGCTCCCCA
GGTAGCTCTACCCCTTCTGGTGCAAACTGGCTCTCC
LCW462_r88
GGTAGCCCTGCTGGCTCTCCGACTTCTACTGAGGAA
706
GSPAGSPTSTEEGSPAGSPT
707
GGTAGCCCGGCTGGTTCTCCGACTTCTACTGAGGAA
STEEGTSTEPSEGSAPGTST
GGTACTTCTACCGAACCTTCCGAAGGTAGCGCTCCA
EPSEGSAPGTSTEPSEGSAP
GGTACCTCTACTGAACCTTCCGAAGGCAGCGCTCCA
GTSESATPESGPGASPGTSS
GGTACCTCTACCGAACCGTCCGAGGGCAGCGCACCA
TGSPGSSTPSGATGSPGASP
GGTACTTCTGAAAGCGCAACCCCTGAATCCGGTCCA
GTSSTGSPGSSTPSGATGSP
GGTGCATCTCCTGGTACCAGCTCTACCGGTTCTCCA
GTPGSGTASSSPGSSTPSGA
GGTAGCTCTACTCCTTCTGGTGCTACTGGCTCTCCA
TGSP
GGTGCTTCCCCGGGTACCAGCTCTACCGGTTCTCCA
GGTAGCTCTACCCCGTCTGGTGCTACTGGTTCTCCA
GGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCA
GGTAGCTCTACCCCTTCTGGTGCTACTGGCTCTCCA
LCW462_r89
GGTAGCTCTACCCCGTCTGGTGCTACTGGTTCTCCA
708
GSSTPSGATGSPGTPGSGT
709
GGTACTCCGGGCAGCGGTACTGCTTCTTCCTCTCCA
ASSSPGSSTPSGATGSPGSP
GGTAGCTCTACCCCTTCTGGTGCTACTGGCTCTCCA
AGSPTSTEEGTSESATPESG
GGTAGCCCGGCTGGCTCTCCTACCTCTACTGAGGAA
PGTSTEPSEGSAPGTSESAT
GGTACTTCTGAAAGCGCTACTCCTGAGTCTGGTCCA
PESGPGSEPATSGSETPGTS
GGTACCTCTACTGAACCGTCCGAAGGTAGCGCTCCA
ESATPESGPGTSTEPSEGSA
GGTACCTCTGAAAGCGCAACTCCTGAGTCTGGCCCA
PGTSESATPESGPGTSESAT
GGTAGCGAACCTGCTACCTCCGGCTCTGAGACTCCA
PESGP
GGTACCTCTGAAAGCGCAACCCCGGAATCTGGTCCA
GGTACTTCTACTGAACCGTCTGAAGGTAGCGCACCA
GGTACTTCTGAAAGCGCAACCCCGGAATCCGGCCCA
GGTACCTCTGAAAGCGCAACCCCGGAGTCCGGCCCA

Example 7: Construction of XTEN_AM288

The entire library LCW0462 was dimerized as described in Example 6 resulting in a library of XTEN_AM288 clones designated LCW0463. 1512 isolates from library LCW0463 were screened using the protocol described in Example 6. 176 highly expressing clones were sequenced and 40 preferred XTEN_AM288 segments were chosen for the construction of multifunctional proteins that contain multiple XTEN segments with 288 amino acid residues.

Example 8: Construction of XTEN_AM432

We generated a library of XTEN_AM432 segments by recombining segments from library LCW0462 of XTEN_AM144 segments and segments from library LCW0463 of XTEN_AM288 segments. This new library of XTEN_AM432 segment was designated LCW0464. Plasmid was isolated from cultures of E. coli harboring LCW0462 and LCW0463, respectively. 1512 isolates from library LCW0464 were screened using the protocol described in Example 6. 176 highly expressing clones were sequenced and 39 preferred XTEN_AM432 segment were chosen for the construction of longer XTENs and for the construction of multifunctional proteins that contain multiple XTEN segments with 432 amino acid residues.

In parallel we constructed library LMS0100 of XTEN_AM432 segments using preferred segments of XTEN_AM144 and XTEN_AM288. Screening this library yielded 4 isolates that were selected for further construction

Example 9: Construction of XTEN_AM875

The stuffer vector pCW0359 was digested with BsaI and KpnI to remove the stuffer segment and the resulting vector fragment was isolated by agarose gel purification.

We annealed the phosphorylated oligonucleotide BsaI-AscI-KpnIforP: AGGTGCAAGCGCAAGCGGCGCGCCAAGCACGGGAGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 710) and the non-phosphorylated oligonucleotide BsaI-AscI-KpnIrev: CCTCGAGTGAAGACGAACCTCCCGTGCTTGGCGCGCCGCTTGCGCTTGC (SEQ ID NO: 711) for introducing the sequencing island A (SI-A) which encodes amino acids GASASGAPSTG (SEQ ID NO: 712) and has the restriction enzyme AscI recognition nucleotide sequence GGCGCGCC inside. The annealed oligonucleotide pairs were ligated with BsaI and KpnI digested stuffer vector pCW0359 prepared above to yield pCW0466 containing SI-A. We then generated a library of XTEN_AM443 segments by recombining 43 preferred XTEN_AM432 segments from Example 8 and SI-A segments from pCW0466 at C-terminus using the same dimerization process described in Example 5. This new library of XTEN_AM443 segments was designated LCW0479.

We generated a library of XTEN_AM875 segments by recombining segments from library LCW0479 of XTEN_AM443 segments and 43 preferred XTEN_AM432 segments from Example 8 using the same dimerization process described in Example 5. This new library of XTEN_AM875 segment was designated LCW0481.

Example 10: Construction of XTEN_AM1318

We annealed the phosphorylated oligonucleotide BsaI-FseI-KpnIforP: AGGTCCAGAACCAACGGGGCCGGCCCCAAGCGGAGGTTCGTCTTCACTCGAGGGTAC (SEQ ID NO: 713) and the non-phosphorylated oligonucleotide BsaI-FseI-KpnIrev: CCTCGAGTGAAGACGAACCTCCGCTTGGGGCCGGCCCCGTTGGTTCTGG (SEQ ID NO: 714) for introducing the sequencing island B (SI-B) which encodes amino acids GPEPTGPAPSG (SEQ ID NO: 715) and has the restriction enzyme FseI recognition nucleotide sequence GGCCGGCC inside. The annealed oligonucleotide pairs were ligated with BsaI and KpnI digested stuffer vector pCW0359 as used in Example 9 to yield pCW0467 containing SI-B. We then generated a library of XTEN_AM443 segments by recombining 43 preferred XTEN_AM432 segments from Example 8 and SI-B segments from pCW0467 at C-terminus using the same dimerization process described in Example 5. This new library of XTEN_AM443 segments was designated LCW0480.

We generated a library of XTEN_AM1318 segments by recombining segments from library LCW0480 of XTEN_AM443 segments and segments from library LCW0481 of XTEN_AM875 segments using the same dimerization process as in Example 5. This new library of XTEN_AM1318 segment was designated LCW0487.

Example 11: Construction of XTEN_AD864

Using the several consecutive rounds of dimerization, we assembled a collection of XTEN_AD864 sequences starting from segments of XTEN_AD36 listed in Example 1. These sequences were assembled as described in Example 5. Several isolates from XTEN_AD864 were evaluated and found to show good expression and excellent solubility under physiological conditions. One intermediate construct of XTEN_AD576 was sequenced. This clone was evaluated in a PK experiment in cynomolgus monkeys and a half-life of about 20 h was measured.

Example 12: Construction of XTEN_AF864

Using the several consecutive rounds of dimerization, we assembled a collection of XTEN_AF864 sequences starting from segments of XTEN_AF36 listed in Example 3. These sequences were assembled as described in Example 5. Several isolates from XTEN_AF864 were evaluated and found to show good expression and excellent solubility under physiological conditions. One intermediate construct of XTEN_AF540 was sequenced. This clone was evaluated in a PK experiment in cynomolgus monkeys and a half-life of about 20 h was measured. A full length clone of XTEN_AF864 had excellent solubility and showed half-life exceeding 60 h in cynomolgus monkeys. A second set of XTEN_AF sequences was assembled including a sequencing island as described in Example 9.

Example 13: Construction of XTEN_AG864

Using the several consecutive rounds of dimerization, we assembled a collection of XTEN_AG864 sequences starting from segments of XTEN_AD36 listed in Example 1. These sequences were assembled as described in Example 5. Several isolates from XTEN_AG864 were evaluated and found to show good expression and excellent solubility under physiological conditions. A full-length clone of XTEN_AG864 had excellent solubility and showed half-life exceeding 60 h in cynomolgus monkeys.

Example 14: Construction of N-Terminal Extensions of XTEN-Construction and Screening of 12 mer Addition Libraries

This example details a step in the optimization of the N-terminus of the XTEN protein to promote the initiation of translation to allow for expression of XTEN fusions at the N-terminus of fusion proteins without the presence of a helper domain. Historically expression of proteins with XTEN at the N-terminus was poor, yielding values that would essentially undetectable in the GFP fluorescence assay (<25% of the expression with the N-terminal CBD helper domain) To create diversity at the codon level, seven amino acid sequences were selected and prepared with a diversity of codons. Seven pairs of oligonucleotides encoding 12 amino acids with codon diversities were designed, annealed and ligated into the NdeI/BsaI restriction enzyme digested stuffer vector pCW0551 (Stuffer-XTEN_AM875-GFP), and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of seven libraries. The resulting clones have N-terminal XTEN 12 mers fused in-frame to XTEN_AM875-GFP to allow use of GFP fluorescence for screening the expression. Individual colonies from the seven created libraries were picked and grown overnight to saturation in 500 μl of super broth media in a 96 deep well plate. The number of colonies picked ranged from approximately half to a third of the theoretical diversity of the library (see Table 15).


TABLE 15
Theoretical Diversity and Sampling Numbers for 12mer Addition
Libraries. The amino acid residues with randomized codons are
underlined.
Motif
Amino Acid
Theoretical
Number
Library
Family
Sequence
SEQ ID NO:
Diversity
screened
LCW546
AE12
MASPAGSPTSTEE
716
572
2 plates
(168)
LCW547
AE12
MATSESATPESGP
717
1536
5 plates
(420)
LCW548
AF12
MATSPSGESSTAP
718
192
2 plates
(168)
LCW549
AF12
MESTSSTAESPGP
719
384
2 plates
(168)
LCW552
AG12
MASSTPSGATGSP
720
384
2 plates
(168)
LCW553
AG12
MEASPGTSSTGSP
721
384
2 plates
(168)
LCW554
(CBD-like)
MASTPESGSSG
722
32
1 plate (84)

The saturated overnight cultures were used to inoculate fresh 500 μl cultures in auto-induction media in which they were grown overnight at 26° C. These expression cultures were then assayed using a fluorescence plate reader (excitation 395 nm, emission 510 nm) to determine the amount of GFP reporter present (see FIG. 9 for results of expression assays). The results, graphed as box and whisker plots, indicate that while median expression levels were approximately half of the expression levels compared to the “benchmark” CBD N-terminal helper domain, the best clones from the libraries were much closer to the benchmarks, indicating that further optimization around those sequences was warranted. This is in contrast to previous XTEN versions that were <25% of the expression levels of the CBD N-terminal benchmark. The results also show that the libraries starting with amino acids MA had better expression levels than those beginning with ME. This was most apparent when looking at the best clones, which were closer to the benchmarks as they mostly start with MA. Of the 176 clones within 33% of the CBD-AM875 benchmark, 87% begin with MA, where as only 75% of the sequences in the libraries beginning with MA, a clear over representation of the clones beginning with MA at the highest level of expression. 96 of the best clones were sequenced to confirm identity and twelve sequences (see Table 16), 4 from LCW546, 4 from LCW547 and 4 from LCW552 were selected for further optimization.


TABLE 16
Advanced 12mer DNA Nucleotide Sequences
Clone
DNA Nucleotide Sequence
SEQ ID NO:
LCW546_02
ATGGCTAGTCCGGCTGGCTCTCCGACCTCCACTGAGGAAGGTACTTCTACT
723
LCW546_06
ATGGCTAGTCCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTACTTCTACT
724
LCW546_07
ATGGCTAGTCCAGCAGGCTCTCCTACCTCCACCGAGGAAGGTACTTCTACT
725
LCW546_09
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAGGTACTTCTACT
726
LCW547_03
ATGGCTACATCCGAAAGCGCAACCCCTGAGTCCGGTCCAGGTACTTCTACT
727
LCW547_06
ATGGCTACATCCGAAAGCGCAACCCCTGAATCTGGTCCAGGTACTTCTACT
728
LCW547_10
ATGGCTACGTCTGAAAGCGCTACTCCGGAATCTGGTCCAGGTACTTCTACT
729
LCW547_17
ATGGCTACGTCCGAAAGCGCTACCCCTGAATCCGGTCCAGGTACTTCTACT
730
LCW552_03
ATGGCTAGTTCTACCCCGTCTGGTGCAACCGGTTCCCCAGGTACTTCTACT
731
LCW552_05
ATGGCTAGCTCCACTCCGTCTGGTGCTACCGGTTCCCCAGGTACTTCTACT
732
LCW552_10
ATGGCTAGCTCTACTCCGTCTGGTGCTACTGGTTCCCCAGGTACTTCTACT
733
LCW552_11
ATGGCTAGTTCTACCCCTTCTGGTGCTACTGGTTCTCCAGGTACTTCTACT
734

Example 15: Construction of N-Terminal Extensions of XTEN-Construction and Screening of Libraries Optimizing Codons 3 and 4

This example details a step in the optimization of the N-terminus of the XTEN protein to promote the initiation of translation to allow for expression of XTEN fusions at the N-terminus of proteins without the presence of a helper domain. With preferences for the first two codons established (see Example supra), the third and fourth codons were randomized to determine preferences. Three libraries, based upon best clones from LCW546, LCW547 and LCW552, were designed with the third and fourth residues modified such that all combinations of allowable XTEN codons were present at these positions (see FIG. 10). In order to include all the allowable XTEN codons for each library, nine pairs of oligonucleotides encoding 12 amino acids with codon diversities of third and fourth residues were designed, annealed and ligated into the NdeI/BsaI restriction enzyme digested stuffer vector pCW0551 (Stuffer-XTEN_AM875-GFP), and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of three libraries LCW0569-571. With 24 XTEN codons the theoretical diversity of each library is 576 unique clones. A total of 504 individual colonies from the three created libraries were picked and grown overnight to saturation in 500 μl of super broth media in a 96 deep well plate. This provided sufficient coverage to understand relative library performance and sequence preferences. The saturated overnight cultures were used to inoculate new 500 μl cultures in auto-induction media in which were grown overnight at 26° C. These expression cultures were then assayed using a fluorescence plate reader (excitation 395 nm, emission 510 nm) to determine the amount of GFP reporter present. The top 75 clones from the screen were sequenced and retested for GFP reporter expression versus the benchmark samples (see FIG. 11). 52 clones yielded usable sequencing data and were used for subsequent analysis. The results were broken down by library and indicate that LCW546 was the superior library. The results are presented in Table 17. Surprisingly, it was discovered that base-lined fluorescence readings for the best clones were ˜900 AU, whereas the CBD N-terminal benchmark was only ˜600 AU. This indicates that this library had instituted an approximately 33% improvement over the best clones from the previous library which were approximately equal in expression to the CBD N-terminal benchmark (Example 14).


TABLE 17
Third and Fourth Codon Optimization Library Comparison
LCW569
LCW570
LCW571
N
21
15
16
Mean Fluorescence (AU)
628
491
537
SD
173
71
232
CV
28%
15%
43%

Further trends were seen in the data showing preferences for particular codons at the third and fourth position. Within the LCW569 library the glutamate codon GAA at the third position and the threonine codon ACT were associated with higher expression as seen in Table 18.


TABLE 18
Preferred Third and Fourth Codons in LCW569
3 = GAA
Rest
4 = ACT
Rest
N
8
13
4
17
Mean Fluorescence (AU)
749
554
744
601
SD
234
47
197
162
CV
31%
9%
26%
27%

Additionally, the retest of the top 75 clones indicated that several were now superior to the benchmark clones.

Example 16: Construction of N-Terminal Extensions of XTEN-Construction and Screening of Combinatorial 12 mer and 36 mer Libraries

This example details a step in the optimization of the N-terminus of the XTEN protein to promote the initiation of translation to allow for expression of XTEN fusions at the N-terminus of proteins without the presence of a helper domain. With preferences for the first two codons established (see Example supra), the N-terminus was examined in a broader context by combining the 12 selected 12 mer sequences (see Example supra) at the very N-terminus followed by 125 previously constructed 36 mer segments (see example supra) in a combinatorial manner. This created novel 48 mers at the N-terminus of the XTEN protein and enabled the assessment of the impact of longer-range interactions at the N-terminus on expression of the longer sequences (FIG. 12). Similar to the dimerization procedures used to assemble 36 mers (see Example infra), the plasmids containing the 125 selected 36 mer segments were digested with restriction enzymes BbsI/NcoI and the appropriate fragment was gel-purified. The plasmid from clone AC94 (CBD-XTEN_AM875-GFP) was also digested with BsaI/NcoI and the appropriate fragments were gel-purified. These fragments were ligated together and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of the library LCW0579, which also served as the vector for further cloning 12 selected 12 mers at the very N-terminus. The plasmids of LCW0579 were digested with NdeI/EcoRI/BsaI and the appropriate fragments were gel-purified. 12 pairs of oligonucleotides encoding 12 selected 12 mer sequences were designed, annealed and ligated with the NdeI/EcoRI/BsaI digested LCW0579 vector, and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of the library LCW0580. With a theoretical diversity of 1500 unique clones, a total of 1512 individual colonies from the created library were picked and grown overnight to saturation in 500 μl of super broth media in a 96 deep well plate. This provided sufficient coverage to understand relative library performance and sequence preferences. The saturated overnight cultures were used to inoculate new 500 μl cultures in auto-induction media that were grown overnight at 26° C. These expression cultures were then assayed using a fluorescence plate reader (excitation 395 nm, emission 510 nm) to determine the amount of GFP reporter present. The top 90 clones were sequenced and retested for GFP reporter expression. 83 clones yielded usable sequencing data and were used for subsequent analysis. The sequencing data was used to determine the lead 12 mer that was present in each clone and the impact of each 12 mer on expression was assessed. Clones LCW546_06 and LCW546_09 stood out as being the superior N-terminus (see Table 19).


TABLE 19
Relative Performance of Clones Starting with LCW546_06 and
LCW459_09
All
All
LCW546_06
Others
LCW546_09
Others
N
11
72
9
74
Mean
1100
752
988
775
Fluorescence (AU)
SD
275
154
179
202
CV
25%
20%
18%
26%

The sequencing and retest also revealed several instances of independent replicates of the same sequence in the data producing similar results, thus increasing confidence in the assay. Additionally, 10 clones with 6 unique sequences were superior to the benchmark clone. They are presented in Table 20. It was noted that these were the only occurrences of these sequences and in no case did one of these sequences occur and fail to beat the bench-mark clone. These six sequences were advanced for further optimization.


TABLE 20
Combinatorial 12mer and 36mer Clones Superior to Benchmark Clone
Clone
12mer
36mer
Name
First 60 codons
SEQ ID NO:
Name
Name
LCW580_51
ATGGCTAGTCCTGCTGGCTCTCCAACCTCCACTGAGGAAG
735
LCW546_06
LCW0404_040
GTGCATCCCCGGGCACCAGCTCTACCGGTTCTCCAGGTAG
CTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTA
CCCCGTCTGGTGCTACTGGCTCTCCAGGTACTTCTACTGAA
CCGTCTGAAGGCAGCGCA
LCW580_81
ATGGCTAGTCCTGCTGGCTCTCCAACCTCCACTGAGGAAG
736
LCW546_06
LCW0404_040
GTGCATCCCCGGGCACCAGCTCTACCGGTTCTCCAGGTAG
CTCTACCCCGTCTGGTGCTACCGGCTCTCCAGGTAGCTCTA
CCCCGTCTGGTGCTACTGGCTCTCCAGGTACTTCTACTGAA
CCGTCTGAAGGCAGCGCA
LCW580_38
ATGGCTAGTCCTGCTGGCTCTCCAACCTCCACTGAGGAAG
737
LCW546_06
LCW0402_041
GTACTTCTACCGAACCGTCCGAGGGTAGCGCACCAGGTAG
CCCAGCAGGTTCTCCTACCTCCACCGAGGAAGGTACTTCT
ACCGAACCGTCCGAGGGTAGCGCACCAGGTACTTCTACTG
AACCGTCTGAAGGCAGCGCA
LCW580_63
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
738
LCW546_09
LCW0402_020
GTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGTAG
CGAACCGGCTACTTCCGGTTCTGAAACCCCAGGTAGCCCA
GCAGGTTCTCCAACTTCTACTGAAGAAGGTACTTCTACTGA
ACCGTCTGAAGGCAGCGCA
LCW580_06
ATGGCTAGTCCTGCTGGCTCTCCAACCTCCACTGAGGAAG
739
LCW546_06
LCW0404_031
GTACCCCGGGTAGCGGTACTGCTTCTTCCTCTCCAGGTAGC
TCTACCCCTTCTGGTGCAACCGGCTCTCCAGGTGCTTCTCC
GGGCACCAGCTCTACCGGTTCTCCAGGTACTTCTACTGAAC
CGTCTGAAGGCAGCGCA
LCW580_35
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
740
LCW546_09
LCW0402_020
GTACTTCTACTGAACCGTCTGAAGGCAGCGCACCAGGTAG
CGAACCGGCTACTTCCGGTTCTGAAACCCCAGGTAGCCCA
GCAGGTTCTCCAACTTCTACTGAAGAAGGTACTTCTACTGA
ACCGTCTGAAGGCAGCGCA
LCW580_67
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
741
LCW546_09
LCW0403_064
GTACCTCCCCTAGCGGCGAATCTTCTACTGCTCCAGGTACC
TCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTACCTCCCC
TAGCGGTGAATCTTCTACCGCACCAGGTACTTCTACTGAAC
CGTCTGAAGGCAGCGCA
LCW580_13
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
742
LCW546_09
LCW0403_060
GTACCTCTACTCCGGAAAGCGGTTCCGCATCTCCAGGTTCT
ACCAGCGAATCCCCGTCTGGCACCGCACCAGGTTCTACTA
GCTCTACTGCTGAATCTCCGGGCCCAGGTACTTCTACTGAA
CCGTCTGAAGGCAGCGCA
LCW580_88
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
743
LCW546_09
LCW0403_064
GTACCTCCCCTAGCGGCGAATCTTCTACTGCTCCAGGTACC
TCTCCTAGCGGCGAATCTTCTACCGCTCCAGGTACCTCCCC
TAGCGGTGAATCTTCTACCGCACCAGGTACTTCTACTGAAC
CGTCTGAAGGCAGCGCA
LCW580_11
ATGGCTAGTCCTGCTGGCTCTCCGACCTCTACTGAGGAAG
744
LCW546_09
LCW0403_060
GTACCTCTACTCCGGAAAGCGGTTCCGCATCTCCAGGTTCT
ACCAGCGAATCCCCGTCTGGCACCGCACCAGGTTCTACTA
GCTCTACTGCTGAATCTCCGGGCCCAGGTACTTCTACTGAA
CCGTCTGAAGGCAGCGCA

Example 17: Construction of N-Terminal Extensions of XTEN-Construction and Screening of Combinatorial 12 mer and 36 mer Libraries for XTEN-AM875 and XTEN-AE864

This example details a step in the optimization of the N-terminus of the XTEN protein to promote the initiation of translation to allow for expression of XTEN fusions at the N-terminus of proteins without the presence of a helper domain. With preferences for the first four codons (see Examples supra, and for the best pairing of N-terminal 12 mers and 36 mers (see Example supra) established, a combinatorial approach was undertaken to examine the union of these preferences. This created novel 48 mers at the N-terminus of the XTEN protein and enabled the testing of the confluence of previous conclusions. Additionally, the ability of these leader sequences to be a universal solution for all XTEN proteins was assessed by placing the new 48 mers in front of both XTEN-AE864 and XTEN-AM875. Instead of using all 125 clones of 36 mer segment, the plasmids from 6 selected clones of 36 mer segment with best GFP expression in the combinatorial library were digested with NdeI/EcoRI/BsaI and the appropriate fragments were gel-purified. The plasmids from clones AC94 (CBD-XTEN_AM875-GFP) and AC104 (CBD-XTEN_AE864-GFP) were digested with digested with NdeI/EcoRI/BsaI and the appropriate fragments were gel-purified. These fragments were ligated together and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of the libraries LCW0585 (-XTEN_AM875-GFP) and LCW0586 (-XTEN_AE864-GFP), which could also serve as the vectors for further cloning 8 selected 12 mers at the very N-terminus. The plasmids of LCW0585 and LCW0586 were digested with NdeI/EcoRI/BsaI and the appropriate fragments were gel-purified. 8 pairs of oligonucleotides encoding 8 selected 12 mer sequences with best GFP expression in the previous (Generation 2) screening were designed, annealed and ligated with the NdeI/EcoRI/BsaI digested LCW0585 and LCW0586 vectors, and transformed into E. coli BL21Gold(DE3) competent cells to obtain colonies of the final libraries LCW0587 (XTEN_AM923-GFP) and LCW0588 (XTEN_AE912-GFP). With a theoretical diversity of 48 unique clones, a total of 252 individual colonies from the created libraries were picked and grown overnight to saturation in 500 μl of super broth media in a 96 deep well plate. This provided sufficient coverage to understand relative library performance and sequence preferences. The saturated overnight cultures were used to inoculate new 500 μl cultures in auto-induction media in which were grown overnight at 26° C. These expression cultures were then assayed using a fluorescence plate reader (excitation 395 nm, emission 510 nm) to determine the amount of GFP reporter present. The top 36 clones were sequenced and retested for GFP reporter expression. 36 clones yielded usable sequencing data and these 36 were used for the subsequent analysis. The sequencing data determined the 12 mer, the third codon, the fourth codon and the 36 mer present in the clone and revealed that many of the clones were independent replicates of the same sequence. Additionally, the retest results for these clones are close in value, indicating the screening process was robust. Preferences for certain combinations at the N-terminus were seen and were consistently yielding higher fluorescence values approximately 50% greater than the benchmark controls (see Tables 21 and 22). These date support the conclusion that the inclusion of the sequences encoding the optimized N-terminal XTEN into the fusion protein genes conferred a marked enhancement on the expression of the fusion proteins.


TABLE 21
Preferred N-terminal Combinations for XTEN-AM875
Number of
Clone Name
Replicates
12mer
36mer
Mean
SD
CV
CBD-AM875
NA
NA
NA
1715
418
16%
LCW587_08
7
LCW546_06_3 = GAA
LCW404_40
2333
572
18%
LCW587_17
5
LCW546_09_3 = GAA
LCW403_64
2172
293
10%


TABLE 22
Preferred N-terminal Combinations for XTEN-AE864
Number of
Clone Name
Replicates
12mer
36mer
Mean
SD
CV
AC82
NA
NA
NA
1979
679
24%
LCW588_14
8
LCW546_06_opt3 
LCW404_31
2801
240
 6%
LCW588_27
2
LCW546_06_opt34
LCW404_40
2839
556
15%

Notably, the preferred combination of the N-terminal for the XTEN-AM875 and the preferred combination for the XTEN-AE864 are not the same (Tables 21 and 22), indicating more complex interactions further than 150 bases from the initiation site influence expression levels. The sequences for the preferred nucleotide sequences are listed in Table 23 and the preferred clones were analyzed by SDS-PAGE to independently confirm expression (see FIG. 13). The complete sequences of XTEN_AM923 and XTEN_AE912 were selected for further analysis.


TABLE 23
Preferred DNA Nucleotide Sequences for first 48 Amino Acid Residues of
N-terminal XTEN-AM875 and XTEN-AE864
Clone
XTEN
Name
Modified
Nucleotide Sequence
SEQ ID NO:
LCW587_08
AM875
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTGCATCC
745
CCGGGCACCAGCTCTACCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTG
CTACCGGCTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCC
AGGTACTTCTACTGAACCGTCTGAAGGCAGCGCA
LCW587_17
AM875
ATGGCTGAACCTGCTGGCTCTCCGACCTCTACTGAGGAAGGTACCTCCCCTAGCG
746
GCGAATCTTCTACTGCTCCAGGTACCTCTCCTAGCGGCGAATCTTCTACCGCTCCA
GGTACCTCCCCTAGCGGTGAATCTTCTACCGCACCAGGTACTTCTACTGAACCGTC
TGAAGGCAGCGCA
LCW588_14
AE864
ATGGCTGAACCTGCTGGCTCTCCAACCTCCACTGAGGAAGGTACCCCGGGTAGCG
747
GTACTGCTTCTTCCTCTCCAGGTAGCTCTACCCCTTCTGGTGCAACCGGCTCTCCA
GGTGCTTCTCCGGGCACCAGCTCTACCGGTTCTCCAGGTAGCCCGGCTGGCTCTCC
TACCTCTACTGAG
LCW588_27
AE864
ATGGCTGAAACTGCTGGCTCTCCAACCTCCACTGAGGAAGGTGCATCCCCGGGCA
748
CCAGCTCTACCGGTTCTCCAGGTAGCTCTACCCCGTCTGGTGCTACCGGCTCTCCA
GGTAGCTCTACCCCGTCTGGTGCTACTGGCTCTCCAGGTAGCCCGGCTGGCTCTCC
TACCTCTACTGAG

Example 18: Methods of Producing and Evaluating GPXTEN; XTEN-Ex4 as Example

A general schema for producing and evaluating GPXTEN compositions is presented in FIG. 6, and forms the basis for the general description of this Example. Using the disclosed methods and those known to one of ordinary skill in the art, together with guidance provided in the illustrative examples, a skilled artesian can create and evaluate a range of GPXTEN fusion proteins comprising, XTENs, GP and variants of GP known in the art. The Example is, therefore, to be construed as merely illustrative, and not limitative of the methods in any way whatsoever; numerous variations will be apparent to the ordinarily skilled artisan. In this Example, a GPXTEN of exendin-4 (“Ex4”) linked to an XTEN of the AE family of motifs would be created.

The general schema for producing polynucleotides encoding XTEN is presented in FIGS. 4 and 5. FIG. 5 is a schematic flowchart of representative steps in the assembly of a XTEN polynucleotide construct in one of the embodiments of the invention. Individual oligonucleotides 501 are annealed into sequence motifs 502 such as a 12 amino acid motif (“12-mer”), which is subsequently ligated with an oligo containing BbsI, and KpnI restriction sites 503. The motif libraries can be limited to specific sequence XTEN families; e.g., AD, AE, AF, AG, AM, or AQ sequences of Table 1. In this case, the motifs of the AE family would be used as the motif library, which are annealed to the 12-mer to create a “building block” length; e.g., a segment that encodes 36 amino acids. The gene encoding the XTEN sequence can be assembled by ligation and multimerization of the “building blocks” until the desired length of the XTEN gene 504 is achieved. As illustrated in FIG. 5, the XTEN length in this case is 48 amino acid residues, but longer lengths can be achieved by this process. For example, multimerization can be performed by ligation, overlap extension, PCR assembly or similar cloning techniques known in the art. The XTEN gene can be cloned into a stuffer vector. In the example illustrated in FIG. 5, the vector can encode a Flag sequence 506 followed by a stuffer sequence that is flanked by BsaI, BbsI, and KpnI sites 507 and a GP gene (e.g., exendin-4) 508, resulting in the gene encoding the GPXTEN 500, which, in this case encodes the fusion protein in the configuration, N- to C-terminus, XTEN-Ex4.

DNA sequences encoding Ex4 (or another candidate GP) can be conveniently obtained by standard procedures known in the art from a cDNA library prepared from an appropriate cellular source, from a genomic library, or may be created synthetically (e.g., automated nucleic acid synthesis) using DNA sequences obtained from publicly available databases, patents, or literature references. A gene or polynucleotide encoding the Ex4 portion of the protein can be then be cloned into a construct, such as those described herein, which can be a plasmid or other vector under control of appropriate transcription and translation sequences for high level protein expression in a biological system. A second gene or polynucleotide coding for the XTEN portion (in the case of FIG. 5 illustrated as an AE with 48 amino acid residues) can be genetically fused to the nucleotides encoding the N-terminus (or its complement) of the Ex4 gene by cloning it into the construct adjacent and in frame with the gene coding for the Ex4, through a ligation or multimerization step. Additional nucleotides encoding longer length XTEN can be ligated to the XTEN-Ex4 gene to achieve the desired length of the XTEN component. In addition, polynucleotides encoding XTEN can be ligated adjacent and in frame to the nucleotides encoding the C-terminus (or its complement) of the Ex4 sequence, resulting in a gene that encodes a GPXTEN with XTEN linked to both the N- and C-terminus of the exendin-4 glucose regulating peptide, including the optimized N-terminal sequence (NTS), as illustrated in FIG. 8. In this manner, a chimeric DNA molecule coding for (or complementary to) the XTEN-Ex4 GPXTEN fusion protein would be generated within the construct. The construct can be designed in different configurations to encode the various permutations of the fusion partners as a monomeric polypeptide. For example, the gene can be created to encode the fusion protein in the order (N- to C-terminus): Ex4-XTEN; XTEN-Ex4; Ex4-XTEN-Ex4; XTEN-Ex4-XTEN; as well as multimers of the foregoing. Optionally, this chimeric DNA molecule may be transferred or cloned into another construct that is a more appropriate expression vector. At this point, a host cell capable of expressing the chimeric DNA molecule would be transformed with the chimeric DNA molecule. The vectors containing the DNA segments of interest can be transferred into an appropriate host cell by well-known methods, depending on the type of cellular host, as described supra.

Host cells containing the XTEN-Ex4 expression vector would be cultured in conventional nutrient media modified as appropriate for activating the promoter. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan. After expression of the fusion protein, cells would be harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for purification of the fusion protein, as described below. For GPXTEN compositions secreted by the host cells, supernatant from centrifugation would be separated and retained for further purification.

Gene expression would be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, gene expression would be measured by immunological of fluorescent methods, such as immunohistochemical staining of cells to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal Conveniently, the antibodies may be prepared against the Ex4 sequence polypeptide using a synthetic peptide based on the sequences provided herein or against exogenous sequence fused to Ex4 and encoding a specific antibody epitope. Examples of selectable markers are well known to one of skill in the art and include reporters such as enhanced green fluorescent protein (EGFP), beta-galactosidase (β-gal) or chloramphenicol acetyltransferase (CAT).

The XTEN-Ex4 polypeptide product would be purified via methods known in the art. Procedures such as gel filtration, affinity purification, salt fractionation, ion exchange chromatography, size exclusion chromatography, hydroxyapatite adsorption chromatography, hydrophobic interaction chromatography or gel electrophoresis are all techniques that may be used in the purification. Specific methods of purification are described in Robert K. Scopes, Protein Purification: Principles and Practice, Charles R. Castor, ed., Springer-Verlag 1994, and Sambrook, et al., supra. Multi-step purification separations are also described in Baron, et al., Crit. Rev. Biotechnol. 10:179-90 (1990) and Below, et al., J. Chromatogr. A. 679:67-83 (1994).

As illustrated in FIG. 6, the isolated XTEN-Ex4 fusion proteins would then be characterized for their chemical and activity properties. Isolated fusion protein would be characterized, e.g., for sequence, purity, apparent molecular weight, solubility and stability using standard methods known in the art. The fusion protein meeting expected standards would then be evaluated for activity, which can be measured in vitro or in vivo, using one or more assays disclosed herein; e.g., the assays of the Examples or Table 35.

In addition, the XTEN-Ex4 fusion protein would be administered to one or more animal species to determine standard pharmacokinetic parameters, as described in Example 25.

By the iterative process of producing, expressing, and recovering XTEN-Ex4 constructs, followed by their characterization using methods disclosed herein or others known in the art, the GPXTEN compositions comprising Ex4 and an XTEN can be produced and evaluated by one of ordinary skill in the art to confirm the expected properties such as enhanced solubility, enhanced stability, improved pharmacokinetics and reduced immunogenicity, leading to an overall enhanced therapeutic activity compared to the corresponding unfused Ex4. For those fusion proteins not possessing the desired properties, a different sequence can be constructed, expressed, isolated and evaluated by these methods in order to obtain a composition with such properties.

Example 19: Construction of Exendin-4_XTEN Genes and Vectors

A cellulose binding domain (CBD) was assembled with an exendin-4 encoding sequence and genetically fused to an encoding sequence for the N-terminus of XTEN. The CBD is immediately followed by a tobacco etch virus (TEV) protease cleavage site (ENLYFQ (SEQ ID NO: 749)) for processing the native N-terminus of exendin-4. The CBD-Exendin-4 fragment was assembled by amplifying the CBD gene using a 3′ oligonucleotide that fuses the exendin-4 sequence preceded by the TEV cleavage site resulting in an in frame fusion of the exendin-4 to the C-terminus of the CBD gene. The full-length CBD-exendin-4 was then amplified by polymerase chain reaction (PCR), which introduced NdeI and BbsI restriction sites that are compatible with the NdeI and BsaI sites that flank the stuffer in the XTEN destination vector (FIG. 7A). The prXTEN plasmid is a pET30 derivative from Novagen in which a Stuffer-XTEN sequence has been inserted under control of the T7 promoter, where Stuffer can be a sequence encoding either green fluorescent protein (GFP) or CBD, depending on the specific plasmid used. The XTEN can be any length from 36 to 864 amino acids or greater again depending on the specific plasmid used. Constructs were generated by replacing the stuffer sequence in prXTEN with the CBD-exendin-4-encoding fragment (FIG. 7B). The prXTEN features a T7 promoter upstream of the stuffer sequence, and an XTEN sequence fused in-frame downstream of the stuffer sequence. The XTEN sequence employed in this specific example encodes AE864 with 864 amino acids. The stuffer fragment was removed by restriction digest using NdeI and BsaI endonucleases. Restriction digested CBD-exendin-4 fragments were ligated into the cleaved pXTEN vector using T4 DNA ligase and electroporated into BL21(DE3) Gold (Stratagene). Transformants were screened by DNA miniprep and the desired construct was confirmed by DNA sequencing. The final vector yields the CBD_exendin-4_XTEN gene under the control of a T7 promoter.

Example 20: Construction of Glucagon-XTEN Genes and Vectors

A cellulose binding domain (CBD) was assembled with a glucagon encoding sequence and genetically fused to an encoding sequence for the XTEN. The CBD is immediately followed by a tobacco etch virus (TEV) protease cleavage site (ENLYFQ (SEQ ID NO: 750)) for processing the native N-terminus of glucagon. The CBD-Glucagon fragment was assembled by amplifying the CBD gene using a 3′ oligonucleotide that fuses the glucagon sequence preceded by the TEV cleavage site resulting in an in frame fusion of the Glucagon to the C-terminus of the CBD gene. The full-length CBD-Glucagon was then amplified by polymerase chain reaction (PCR), which introduced NdeI and BbsI restriction sites that are compatible with the NdeI and BsaI sites that flank the stuffer in the XTEN destination vector (pXTEN; FIG. 9A). The pXTEN plasmid is a pET30 derivative from Novagen in which a Stuffer-XTEN sequence has been inserted under control of the T7 promoter, where Stuffer can be a sequence encoding either green fluorescent protein (GFP) or CBD, depending on the specific plasmid used. The XTEN can be any length from 36 to 875 amino acids or greater again depending on the specific plasmid used. Constructs were generated by replacing the stuffer sequence in prXTEN with the CBD-glucagon-encoding fragment. The pXTEN features a T7 promoter upstream of the stuffer sequence, and an XTEN sequence fused in-frame downstream of the stuffer sequence. The XTEN sequences employed in this specific example belong to the Y family of XTEN and encode lengths that include 36, 72, 144, 288, and 576 amino acids. The stuffer fragment was removed by restriction digest using NdeI and BsaI endonucleases. Restriction digested CBD-Glucagon fragments were ligated into the cleaved prXTEN vector using T4 DNA ligase and electroporated into BL21(DE3) Gold (Stratagene). Transformants were screened by DNA miniprep and the desired construct was confirmed by DNA sequencing. The final vector yields the CBD_glucagon_XTEN gene under the control of a T7 promoter. The resulting DNA sequences can encode glucagon linked to XTEN lengths of 36, 72, 144, 288, and 576 amino acids, respectively.

Example 21: Purification and Characterization of Gcg-XTEN

The GPXTEN of glucagon linked to XTEN was produced recombinantly in E. coli and purified to homogeneity using three column steps. The final construct comprised the gene encoding the cellulosome anchoring protein cohesion region cellulose binding domain (CBD) from C. thermocellum (accession #ABN54273), a tobacco etch virus (TEV) protease recognition site (ENLYFQ (SEQ ID NO: 750)), the glucagon sequence, and the appropriate XTEN sequence under control of a T7 promoter. Briefly, protein expression was induced by addition of 1 mM IPTG to a log phase culture of BL21-Gold (DE3) E. coli carrying the expression plasmid. TEV protease was added to heat-treated cell lysate containing Gcg-XTEN to remove the CBD sequence and generate the native N-terminus of glucagon. The cleaved protein was then purified over DE52, MacroCap Q, and Butyl Sepharose FF columns. The final material was formulated in 20 mM Tris pH 7.5, 135 mM NaCl and sterile filtered using a 0.22 micron filter. Expression was determined to be approximately 7 mg protein per gram wet cell weight (˜100 mg/L at final OD ˜4) and overall purification yield was approximately 60%.

Size exclusion chromatography (SEC) was performed using a TSK-Gel, G3000 SWXL, 7.8×300 mm HPLC column (Tosoh Bioscience) connected to an HPLC system equipped with an autosampler and UV/VIS detector (Shimadzu). The system was equilibrated in phosphate buffered saline (PBS) at a flow rate of 0.7 mL/min at ambient temperature. For column calibration, a gel filtration standard (BioRad, cat#151-1901) was used. For sample analysis, 20 μl of 1 mg/ml Gcg-XTEN was injected and absorbance was monitored for 20 min using OD214 nm.

Reverse phase C18 chromatography (RPC18) was performed using a Phenomenex Gemini 5 μm C18—110 A, 4.6×100 mm column (Phenomenex) connected to an HPLC system equipped with an autosampler and UV/VIS detector (Shimadzu) Buffer A was 0.1% TFA in water and Buffer B was 0.1% TFA in 100% acetonitrile. The system was run with a combined flowrate of 1 ml/min. The column was equilibrated in 5% Buffer B at 35° C. The chromatographic separation of Gcg-XTEN was achieved by a linear gradient from 5% to 95% B over 15 minutes. For sample analysis, 10 μl of 1 mg/ml Gcg-XTEN was injected and absorbance was monitored using OD214 nm. Sample analyses were performed by Millipore's GPCRProfiler® service using a transfected GcgR cell line (Cat# HTS112C). Calcium flux was monitored in real-time by FLIPR analysis after addition of serial dilutions of Gcg-XTEN or synthetic glucagon. The results of the characterization and stability assays are shown in FIG. 19. The data show that Gcg-XTEN is a homogeneous, well-defined chemical entity. In addition, the solubility and stability of the final protein are significantly improved over unmodified glucagon (data not shown).

Example 22: Analytical Size Exclusion Chromatography of XTEN Fusion Proteins with Diverse Payloads

Size exclusion chromatography analysis was performed on fusion proteins containing various therapeutic proteins and unstructured recombinant proteins of increasing length. An exemplary assay used a TSKGel-G4000 SWXL (7.8 mm×30 cm) column in which 40 μg of purified glucagon fusion protein at a concentration of 1 mg/ml was separated at a flow rate of 0.6 ml/min in 20 mM phosphate pH 6.8, 114 mM NaCl. Chromatogram profiles were monitored using OD214 nm and OD280 nm. Column calibration for all assays were performed using a size exclusion calibration standard from BioRad; the markers include thyroglobulin (670 kDa), bovine gamma-globulin (158 kDa), chicken ovalbumin (44 kDa), equine myoglobuin (17 kDa) and vitamin B12 (1.35 kDa). Representative chromatographic profiles of Glucagon-Y288, Glucagon-Y144, Glucagon-Y72, Glucagon-Y36 are shown as an overlay in FIG. 16. The data show that the apparent molecular weight of each compound is proportional to the length of the attached XTEN sequence. However, the data also show that the apparent molecular weight of each construct is significantly larger than that expected for a globular protein (as shown by comparison to the standard proteins run in the same assay and by comparison to molecular weight standards shown in the SDS gel of FIG. 15). Based on the SEC analyses for all constructs evaluated, including GPXTEN compositions, the Apparent Molecular Weights, the Apparent Molecular Weight Factor (expressed as the ratio of Apparent Molecular Weight to the calculated molecular weight) and the hydrodynamic radius (RH in nm) are shown in Table 24. The results indicate that incorporation of different XTENs of 576 amino acids or greater confers an apparent molecular weight for the fusion protein of approximately 339 kDa to 760, and that XTEN of 864 amino acids or greater confers an apparent molecular weight greater than approximately 800 kDA. The results of proportional increases in apparent molecular weight to actual molecular weight were consistent for fusion proteins created with XTEN from several different motif families; i.e., AD, AE, AF, AG, and AM, with increases of at least four-fold and ratios as high as about 17-fold. Additionally, the incorporation of XTEN fusion partners with 576 amino acids or more into fusion proteins with the various payloads (and 288 residues in the case of glucagon fused to Y288) resulted with a hydrodynamic radius of 7 nm or greater; well beyond the glomerular pore size of approximately 3-5 nm. Accordingly, it is concluded that fusion proteins comprising growth and XTEN would have reduced renal clearance, contributing to increased terminal half-life and improving the therapeutic or biologic effect relative to a corresponding un-fused biologic payload protein.


TABLE 24
SEC analysis of various polypeptides
Appar-
Apparent
XTEN or
Thera-
Actual
ent
Molecular
Construct
fusion
peutic
MW
MW
Weight
RH
Name
partner
Protein
(kDa)
(kDa)
Factor
(nm)
AC14
Y288
Glucagon
28.7
370
12.9
7.0
AC28
Y144
Glucagon
16.1
117
7.3
5.0
AC34
Y72
Glucagon
9.9
58.6
5.9
3.8
AC33
Y36
Glucagon
6.8
29.4
4.3
2.6
AC89
AF120
Glucagon
14.1
76.4
5.4
4.3
AC88
AF108
Glucagon
13.1
61.2
4.7
3.9
AC73
AF144
Glucagon
16.3
95.2
5.8
4.7
AC53
AG576
GFP
74.9
339
4.5
7.0
AC39
AD576
GFP
76.4
546
7.1
7.7
AC41
AE576
GFP
80.4
760
9.5
8.3
AC52
AF576
GFP
78.3
526
6.7
7.6
AC85
AE864
Exendin-4
83.6
938
11.2
8.9
AC114
AM875
Exendin-4
82.4
1344
16.3
9.4
AC143
AM875
hGH
100.6
846
8.4
8.7
AC227
AM875
IL-1ra
95.4
1103
11.6
9.2
AC228
AM1296
IL-1ra
134.8
2286
17.0
10.5

Example 23: Pharmacokinetics of Extended Polypeptides Fused to GFP in Cynomolgus Monkeys

The pharmacokinetics of GFP-L288, GFP-L576, GFP-XTEN_AF576, GFP-XTEN_Y576 and XTEN_AD836-GFP were tested in cynomolgus monkeys to determine the effect of composition and length of the unstructured polypeptides on PK parameters. Blood samples were analyzed at various times after injection and the concentration of GFP in plasma was measured by ELISA using a polyclonal antibody against GFP for capture and a biotinylated preparation of the same polyclonal antibody for detection. Results are summarized in FIG. 26. They show a surprising increase of half-life with increasing length of the XTEN sequence. For example, a half-life of 10 h was determined for GFP-XTEN_L288 (with 288 amino acid residues in the XTEN). Doubling the length of the unstructured polypeptide fusion partner to 576 amino acids increased the half-life to 20-22 h for multiple fusion protein constructs; i.e., GFP-XTEN_L576, GFP-XTEN_AF576, GFP-XTEN_Y576. A further increase of the unstructured polypeptide fusion partner length to 836 residues resulted in a half-life of 72-75 h for XTEN_AD836-GFP. Thus, increasing the polymer length by 288 residues from 288 to 576 residues increased in vivo half-life by about 10 h. However, increasing the polypeptide length by 260 residues from 576 residues to 836 residues increased half-life by more than 50 h. These results show that there is a surprising threshold of unstructured polypeptide length that results in a greater than proportional gain in in vivo half-life. Thus, fusion proteins comprising extended, unstructured polypeptides are expected to have the property of enhanced pharmacokinetics compared to polypeptides of shorter lengths.

Example 24: Serum Stability of XTEN

A fusion protein containing XTEN_AE864 fused to the N-terminus of GFP was incubated in monkey plasma and rat kidney lysate for up to 7 days at 37° C. Samples were withdrawn at time 0, Day 1 and Day 7 and analyzed by SDS PAGE followed by detection using Western analysis and detection with antibodies against GFP as shown in FIG. 14. The sequence of XTEN_AE864 showed negligible signs of degradation over 7 days in plasma. However, XTEN_AE864 was rapidly degraded in rat kidney lysate over 3 days. The in vivo stability of the fusion protein was tested in plasma samples wherein the GFP-AE864 was immunoprecipitated and analyzed by SDS PAGE as described above. Samples that were withdrawn up to 7 days after injection showed very few signs of degradation. The results demonstrate the resistance of GPXTEN to degradation due to serum proteases; a factor in the enhancement of pharmacokinetic properties of the GPXTEN fusion proteins.

Example 25: PK Analysis of Fusion Proteins Comprising Exendin-4 and XTEN

The GPXTEN fusion protein Ex4_AE864 was evaluated in cynomolgus monkeys in order to determine in vivo pharmacokinetic parameters of the fusion proteins after a single subcutaneous dose.

Methods:

The GPXTEN fusion protein was formulated in 20 mM Tris, pH 7.5, 135 mM NaCl at two different concentrations; 8 mg/mL and 40 mg/mL. Three groups of four monkeys (2 males and 2 females, 2-6 kg) each were dosed at 1 mg/kg (Group 1, 0.125 mL/kg), 1 mg/kg (Group 2, 0.025 mL/kg), or 5 mg/kg (Group 3, 0.125 mL/kg) via bolus injection between the skin and underlying layers of tissue in the scapular region on the back of each animal Serial blood samples (1 ml±0.5 ml) were drawn over fourteen days from the femoral vein or artery of previously acclimated animals through a syringe with no aesthesia utilizing chair restraint. If necessary, chair restraint was utilized for a maximum of 30 minutes. All animals were fasted overnight prior to dosing and through the first 4 hours of blood sample collection (food was returned within 30 minutes following collection of the last blood sample at the 4 hour collection interval, where applicable). Each blood sample was collected into heparin plasma separator and kept on ice (2° C. to 8° C.) for approximately 5 minutes pending centrifugation. The blood samples were centrifuged (8,000×g for 5 min) and the plasma was transferred into a polypropylene tube. Plasma samples were snap frozen, and stored at approximately −70° C. until assayed. Analysis was performed using a sandwich ELISA format.

Results:

The pharmacokinetic parameters were calculated for the monkeys and the results are tabulated in Table 25. The pharmacokinetic parameters were analyzed using both a naïve pooling of all animals and using a standard two-stage analysis. The results show a difference in absorption of the fusion protein, based on dose volume administered in Group 1 versus Group 2, as evidenced by the Tmax, Cmax, AUC and volume of distribution (Vz) values. However, the calculated half-life values are comparable across the three Groups, and greatly exceed the reported terminal half-life of exenatide of 2.4 h.