US20090221032A1

US20090221032A1 - Entropic bristle domain sequences and their use in recombinant protein production

Info

Publication number: US20090221032A1
Application number: US12/358,058
Authority: US
Inventors: A. Keith Dunker; Vladimir N. Uversky; Marc S. Cortese; James Mueller
Original assignee: Molecular Kinetics Inc
Current assignee: Molecular Kinetics Inc
Priority date: 2005-07-11
Filing date: 2009-01-22
Publication date: 2009-09-03
Also published as: US20070105195A1; US7494788B2

Abstract

Compositions and methods for recombinant protein production and, more particularly, fusion polypeptides, polynucleotides encoding fusion polypeptides, expression vectors, kits, and related methods for recombinant protein production, are provided.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 11/485,613, filed Jul. 11, 2006, now U.S. Pat. No. 7,494,788, which application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application No. 60/698,456, filed Jul. 11, 2005, where these applications are incorporated herein by reference in their entireties.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 670098_—402Cl_SEQUENCE_LISTING.txt. The text file is 151 KB, was created on Jan. 22, 2009, and is being submitted electronically via EFS-Web.

FIELD OF THE INVENTION

The present invention relates generally to compositions and methods for recombinant protein production and, more particularly, to fusion polypeptides, polynucleotides encoding fusion polypeptides, expression vectors, kits, and related methods for recombinant protein production.

DETAILED OF THE RELATED ART

A large percentage of the proteins identified via the different genome sequencing effort have been difficult to express and/or purify as recombinant proteins using standard methods. For example, a trial study using Methanobacterium thermoautotrophicum as a model system identified a number of problems associated with high throughput structure determination (Christendat et al. (2000) Prog. Biophys. Mol. Biol. 73(5): 339-345; Christendat et al. (2000) Nat Struct Biol 7(10): 903-909). The complete list of genome-encoded proteins was filtered to remove proteins with predicted transmembrane regions or homologues to known structures. When these filtered proteins were taken through the cloning, expression, and structural determination steps of a high throughput process, only about 50% of the selected proteins could be purified in a state suitable for structural studies, with roughly 45% of large expressed proteins and 30% of small expressed proteins failing due to insolubility. The study concluded that considerable effort must be invested in improving the attrition rate due to proteins with poor expression levels and unfavorable biophysical properties. (Christendat et al. (2000) Prog. Biophys. Mol. Biol. 73(5): 339-345; Christendat et al. (2000) Nat Struct Biol 7(10): 903-909).
Similar results have been observed for other prokaryotic proteomes. One study reported the successful cloning and attempted expression of 1376 (73%) of the predicted 1877 genes of the Thermotoga maritima proteome. However, crystallization conditions were able to be determined for only 432 proteins (23%). A significant component of the decrease between the cloned and crystallized success levels was due to poor protein solubility and stability (Kuhn et al. (2002) Proteins 49(1): 142-5).
Similarly low success rates have been reported for eukaryotic proteomes. A study of a sample set of human proteins, for example, reported that the failure rate using high-throughput methods for three classes of proteins based on cellular location was 50% for soluble proteins, 70% for extracellular proteins, and more than 80% for membrane proteins (Braun et al. (2002) Proc Natl Acad Sci USA 99(5): 2654-9).
Interactions between individual recombinant proteins are responsible for a significant number of the previously mentioned failures. In a high-throughput structural determination study, Christendat and colleagues found that 24 of 32 proteins that were classified by nuclear magnetic resonance as aggregated displayed circular dichroism spectra consistent with stable folded proteins, suggesting that these proteins were folded properly but aggregated due to surface interactions (Christendat et al. (2000) Prog. Biophys. Mol. Biol. 73(5): 339-345). One possible explanation for this is that these proteins function in vivo as part of multimeric units but when they are recombinantly expressed, dimerization domains are exposed that mediate protein-protein interactions.
Prior methods used to increase recombinant protein stability include production in E. coli strains that are deficient in proteases (Gottesman and Zipser (1978) J Bacteriol 133(2): 844-51) and production of fusions of bacterial protein fragments to a recombinant polypeptide/protein of interest (Itakura et al., Science, 1977. 198:1056-63; Shen, Proc Natl Acad Sci USA, 1984. 81:4627-31), has also been attempted to stabilize foreign proteins in E. coli. In addition, fusing a leader sequence to a recombinant protein may cause a gene product to accumulate in the periplasm or be excreted, which may result in increased recovery of properly folded soluble protein (Nilsson et al., EMBO J, 1985. 4:1075-80; Abrahmsen et al., Nucleic Acids Res, 1986. 14:7487-500). These strategies have advantages for some proteins but they generally do not succeed when used, for example, with membrane proteins or proteins capable of strong protein-protein interactions.
Fusion polypeptides have also been used as an approach for improving the solubility and folding of recombinant polypeptides/proteins produced in E. coli (Zhan et al., Gene, 2001. 281:1-9). Some commonly used fusion partners which have been linked to heterologous protein sequences of interest include calmodulin-binding peptide (CBP) (Vaillancourt et al., Biotechniques, 1997. 22:451-3), glutathione-S-transferase (GST) (Smith, Methods Enzymol, 2000. 326:254-70), thioredoxin (TRX) (Martin Hammarström et al., Protein Science, 2002. 11:313-321), and maltose-binding protein (MBP) (Sachdev et al., Methods Enzymol, 2000. 326:312-21). Glutathione-S-transferase and maltose-binding protein have been found to increase the recombinant protein purification success rate when fused to a heterologous sequence in a controlled trial of 32 human test proteins (Braun et al., Proc Natl Acad Sci USA, 2002. 99:2654-9). Further, maltose-binding protein domain fusions have been shown to increase the solubility of recombinant proteins (Kapust et al., Protein Sci, 1999. 8:1668-74; Braun et al., Proc Natl Acad Sci USA, 2002. 99:2654-9; Martin Hammarström et al., Protein Science, 2002. 11:313-321). Maltose-binding protein may further benefit recombinant protein solubility and folding in that it may have chaperone-like properties that assist in folding of the fusion partner (Richarme et al., J Biol Chem, 1997. 272:15607-12; Bach et al., J Mol Biol, 2001. 312:79-93. However, these fusion approaches used to date have not been amendable to all classes of proteins, and have thus met with only limited success.
Entropic bristles have been used in a variety of polymers to reduce aggregation of small particles such as latex particles in paints and to stabilize a wide variety of other colloidal products (Hoh, Proteins, 1998. 32:223-228). Entropic bristles generally comprise amino acid residues that do not have a tendency to form secondary structure and in the process of random motion about their attachment points sweep out a significant region in space and entropically exclude other molecules by their random motion (Hoh, Proteins, 1998. 32:223-228). Entropic bristles are singular elements, comprising highly flexible, non-aggregating polymer chains, of which entropic brushes are assembled. In polymer chemistry, entropic bristles have been affixed to the surfaces of particles (e.g. latex beads), thereby forming entropic brushes which, in turn, prevent particle aggregation (Stabilization by attached polymer: steric stabilization, in Polymeric stabilization of colloidal dispersions, D. H. Napper, Editor. 1983, Academic Press: London. p. 18-30). EBDs can exclude large molecules but do not exclude small molecules such as water, salts, metal ions, or cofactors (Hoh, Proteins, 1998. 32:223-228).
EBDs can also function as steric stabilizers and operate through steric hindrance stabilization (Stabilization by attached polymer: steric stabilization, in Polymeric stabilization of colloidal dispersions, D. H. Napper, Editor. 1983, Academic Press: London. p. 18-30). Naper described characteristics that contribute to steric stabilization functions, including (1) they have an amphipathic sequence; (2) they are attached to the colloidal particle by one end rather than being totally adsorbed; (3) they are soluble in the medium used; (4) they are mutually repulsive; (5) they are thermodynamically stable; and (6) they exhibit stabilizing ability in proportion to their length. Steric stabilizers intended to function in aqueous media extend from the surface of colloidal molecules thus transforming their surfaces from hydrophobic to hydrophilic. The fact that sterically stabilized particles are thermodynamically stable leads them to spontaneously re-disperse when dried residue is reintroduced to solvent. Entropic bristles can adopt random-walk configurations in solution (Milner, Science, 1991. 251:905-914). These chains extend from an attachment point because of their affinity for the solvent. This affinity is due in part to the highly charged nature of the entropic bristle sequence.
While certain prior approaches have met with some success, there remains a need for new compositions and methods for improving the properties and characteristics of recombinant proteins, e.g., improving solubility, stability, yield and/or folding of recombinant proteins. The present invention addresses these needs and offers other related advantages by employing entropic bristle domain sequences as fusion partners in recombinant protein production, as described herein.

SUMMARY OF THE INVENTION

According to a general aspect of the present invention, there are provided isolated fusion polypeptides comprising at least one entropic bristle domain (EBD) sequence and at least one heterologous polypeptide sequence of interest. By providing an EBD sequence which effectively sweeps out the three-dimensional space surrounding a newly synthesized heterologous polypeptide, the fusion polypeptides of the invention offer a number of advantages over prior fusion polypeptides and methods relating thereto.
In one embodiment, a fusion polypeptide comprising an EBD sequence and a heterologous polypeptide sequence exhibits improved solubility relative to the corresponding heterologous polypeptide in the absence of the EBD sequence. In a related embodiment, the fusion polypeptide has at least 5% increased solubility relative to the heterologous polypeptide sequence, at least 25% increased solubility relative to the heterologous polypeptide sequence, or at least 50% increased solubility relative to the heterologous polypeptide sequence.
In another embodiment, a fusion polypeptide of the invention exhibits reduced aggregation relative to the level of aggregation of the heterologous polypeptide sequence in the absence of the EBD sequence. For example, a fusion polypeptide of the invention generally exhibits at least 10% reduced aggregation relative to the heterologous polypeptide sequence or at least 25% reduced aggregation relative to the heterologous polypeptide sequence.
In another embodiment, a fusion polypeptide of the invention exhibits improved self-folding relative to the heterologous polypeptide sequence in the absence of the EBD sequence.
In another embodiment of the present invention, an EBD sequence employed in a fusion polypeptide comprises an amino acid sequence that maintains a substantially random coil conformation.
In another embodiment, the EBD sequence of a fusion polypeptide of the invention comprises an amino acid sequence that is substantially mutually repulsive.
In another embodiment, the EBD sequence of a fusion polypeptide of the invention comprises an amino acid sequence that remains in substantially constant motion.
In a more particular embodiment, an EBD sequence of a fusion polypeptide of the invention is derived from a mammalian neurofilament protein. In a related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a mammalian neurofilament NF-H protein. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a human neurofilament NF-H protein having the sequence set forth in SEQ ID NO: 1. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a mouse neurofilament NF-H protein having the sequence set forth in SEQ ID NO: 3.
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises a neurofilament NF-H sequence selected from the group consisting of SPEAEK (SEQ ID NO:23), SPAAVK (SEQ ID NO:24), SPAEAK (SEQ ID NO:25), SPAEPK (SEQ ID NO:26), SPAEVK (SEQ ID NO:27), SPATVK (SEQ ID NO:28), SPEKAK (SEQ ID NO:29), SPGEAK (SEQ ID NO:30), SPIEVK (SEQ ID NO:31), SPPEAK (SEQ ID NO:32), SPSEAK (SEQ ID NO:33), SPEKEAK (SEQ ID NO:34), SPAKEKAK (SEQ ID NO:35), SPEKEEAK (SEQ ID NO:36), SPTKEEAK (SEQ ID NO:37), SPVKEEAK (SEQ ID NO:38), SPVKAEAK (SEQ ID NO:39), SPVKEEAK (SEQ ID NO:40), SPVKEEVK (SEQ ID NO:41), SPVKEEEKP (SEQ ID NO:42), SPEKAKTLDVK (SEQ ID NO:43), SPADKFPEKAK (SEQ ID NO:44), SPEAKTPAKEEAR (SEQ ID NO:45), SPEKAKTPVKEGAK (SEQ ID NO:46), SPVKEEAKTPEKAK (SEQ ID NO:47), SPVKEGAKPPEKAKPLDVK (SEQ ID NO:48), SPVKEDIKPPAEAKSPEKAK (SEQ ID NO:49), SPLKEDAKAPEKEIPKKEEVK (SEQ ID NO:50), SPEKEEAKTSEKVAPKKEEVK (SEQ ID NO:51), SPEAQTPVQEEATVPTDIRPPEQVK (SEQ ID NO:52), SPVKEEVKAKEPPKKVEEEKTLPTPKTEAKESKKDE (SEQ ID NO:53).
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises at least 2-100 repeats of a neurofilament NF-H sequence set forth above, or a combination thereof.
According to another particular embodiment of the present invention, an EBD sequence of a fusion polypeptide is derived from a mammalian neurofilament protein NF-M. In a related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a bovine neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 5. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a chicken neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 7. In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a human neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 9. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a mouse neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 11. In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a rat neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 13. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a rabbit neurofilament NF-M protein having the sequence set forth in SEQ ID NO: 15.
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises a neurofilament NF-M sequence selected from the group consisting of SPPK (SEQ ID NO:54), SPVK (SEQ ID NO:55), SPAAK (SEQ ID NO:56), SPAPK (SEQ ID NO:57), SPEAK (SEQ ID NO:58), SPMPK (SEQ ID NO:59), SPPAK (SEQ ID NO:60), SPTAK (SEQ ID NO:61), SPTTK (SEQ ID NO:62), SPVAK (SEQ ID NO:63), SPVAK (SEQ ID NO:64), SPVPK (SEQ ID NO:65), SPVSK (SEQ ID NO:66), SPEKPA (SEQ ID NO:67), SPVEEKAK (SEQ ID NO:68), SPVEEKGK (SEQ ID NO:69), SPVEEVKP (SEQ ID NO:70), SPEKPATPKVT (SEQ ID NO:71), SPEKPRTPEKPA (SEQ ID NO:72), SPEKPTTPEKW (SEQ ID NO:73), SPEKPSSPLKDEKA (SEQ ID NO:74), SPVKEKAVEEMITIT (SEQ ID NO:75), SPVKEEAAEEAATITK (SEQ ID NO:76), SPVPKSPVEEVKPKAEATAG (SEQ ID NO:77), SPVKAESPVKEEVPAKPVKV (SEQ ID NO:78), SPEKEAKEEEKPQEKEKEKEK (SEQ ID NO:79), SPVKATTPEIKEEEGEKEEEGQE (SEQ ID NO:80), SPVEEVKPKPEAKAGKGEQKEE (SEQ ID NO:81), SPEKPATPEKPPTPEKAITPEKVR (SEQ ID NO:82), SPEKPATPEKPRTPEKPATPEKPR (SEQ ID NO:83), SPKEEKVEKKEEKPKDVPKKKAE (SEQ ID NO:84), SPKEEKAEKKEEKPKDVPEKKKAE (SEQ ID NO:85), SPVEEAKSKAEVGKGEQKEEEEKE (SEQ ID NO:86), SPKEEKVEKKEEKPKDVPDKKKAE (SEQ ID NO:87), SPVKEEAVAEVVTITKSVKVHLEKET (SEQ ID NO:88), SSEKDEGEQEEEEGETEAEGEGEEAEAKEEK (SEQ ID NO:89), SPVEEVKPKAEAGAEKGEQKEKVEEEKKEAKE (SEQ ID NO:90), SPVTEQAKAVQKAAAEVGKDQKAEKAAEKAAKEEKAA (SEQ ID NO:91), SPEAKEEEEEGEKEEEEEGQEEEEEEDEGVKSDQAEEGGSEKEG (SEQ ID NO:92).
According to another particular embodiment of the present invention, an EBD sequence of a fusion polypeptide is derived from a phage sequence. In a related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a filamentous phage fd. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises at least one linker region derived from a filamentous phage fd adsorption protein pIII. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises a filamentous phage fd adsorption protein pIII having a sequence set forth in SEQ ID NO: 17. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises a filamentous phage fd adsorption protein pIII sequence selected from the group consisting of EGGGS (SEQ ID NO:93), EGGGT (SEQ ID NO:94), SEGGG (SEQ ID NO:95), GGGSGGG (SEQ ID NO:96), SGGGSGSG (SEQ ID NO:97), and SGGGSEGGG (SEQ ID NO:98).
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises at least 2-100 repeats of A filamentous phage fd adsorption protein pIII sequence set forth above, or a combination thereof.
In another particular embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention is derived from a nuclear pore protein. In a more particular embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from an yeast nuclear pore Nup2p protein having the sequence set forth in SEQ ID NO: 19. In a related embodiment, the EBD is derived from the yeast nucleoporin Nup2p protein and is selected from the group consisting of FSFGTSQPNNTPS (SEQ ID NO:99), FSFSIPSKNTPDASKPS (SEQ ID NO:100), FVFGQAAAKPSLEKSS (SEQ ID NO:101), FSFGVPNSSKNETSKPV (SEQ ID NO:102), FTFGTKHAADSQNNKPS (SEQ ID NO:103), FTFGSSALADNKEDVKKP (SEQ ID NO:104), FSFGINTNTTKTADTKAPT (SEQ ID NO:105), FSFGKTTANLPANSSTSPAPSIPSTG (SEQ ID NO:106), FSFGPKKENRKKDESDSENDIEIKGPE (SEQ ID NO:107), FKFSGTVSSDVFKLNPSTDKNEKKTETNAKP (SEQ ID NO:108), FKFSLPFEQKGSQTTTNDSKEESTTEATGNESQ (SEQ ID NO:109), FTFGSTTIEKKNDENSTSNSKPEKSSDSNDSNPS (SEQ ID NO:110), FSFGISNGSESKDSDKPSLPSAVDGENDKKEATKPA (SEQ ID NO:111), FSFSSATSTTEQTKSKNPLSLTEATKTNVDNNSKAEAS (SEQ ID NO:112) and FSFGAATPSAKEASQEDDNNNVEKPSSKPAFNLISNAGTEKEKESKKDSKPA (SEQ ID NO:113).
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises at least 2-100 repeats of a Nup2p sequence set forth above, or a combination thereof.
According to another particular embodiment of the present invention, an EBD sequence is a sequence derived from a mammalian elastin protein. In another related embodiment, the EBD sequence of a fusion polypeptide of the invention is derived from a mouse elastin having the sequence set forth in SEQ ID NO: 21.
In a related embodiment, the EBD comprises a sequence derived from an elastin protein and is selected from the group consisting of VPGA (SEQ ID NO:114), GAGGL (SEQ ID NO:115), GAGGG (SEQ ID NO:116), VPGVG (SEQ ID NO:117), VPGFGAGA (SEQ ID NO:118), VPGALPGA (SEQ ID NO:119), VPGFGAGAG (SEQ ID NO:120), VPAVPGAGG (SEQ ID NO:121), VPGGVGVGG (SEQ ID NO:122), VGAGGFPGYG (SEQ ID NO:123), VPGAVPGGLPGG (SEQ ID NO:124), VSPAAAAKAAKYGAA (SEQ ID NO:125), VPQVGAGIGAGGKPGK (SEQ ID NO:126), VPGGVGVGGIPGGVGVGG (SEQ ID NO:127), VPGGVGGIGGIGGLGVSTGAV (SEQ ID NO:128), VPGGAAGAAAAYKAAAKAGAGLGGVGG (SEQ ID NO:129), VSPAAAAKAAAKAAKYGARGGVGIPTYG (SEQ ID NO:130), KPPKPYGGALGALGYQGGGCFGKSCGRKRK (SEQ ID NO:131), VPGAGTPAAAAAAAAAKAAAKAGLGPGVGG (SEQ ID NO:132), VPGRVAGAAPPAAAAAAAKAAAKAAQYGLG (SEQ ID NO:133), VPGVGLPGVYPGGVLPGTGARFPGVGVLPG (SEQ ID NO:134), VPTGTGVKAKAPGGGGAFSGIPGVGPFGGQQPG (SEQ ID NO:135), VPGGVYYPGAGIGGLGGGGGALGPGGKPPKPGAG (SEQ ID NO:136), VGAGAGLGGASPAAAAAAAKAAKYGAGGAGALGGL (SEQ ID NO:137), GLGGVLGARPFPGGGVAARPGFGLSPIYPGGGAGGLGVGG (SEQ ID NO:138), VPGSLAASKAAKYGAAGGLGGPGGLGGPGGLGGPGGLGGAG (SEQ ID NO:139), VPGGPGVRLPGAGIPGVGGIPGVGGIPGVGGPGIGGPGIVGGPGA (SEQ ID NO:140), VLPGVGGGGIPGGAGAIPGIGGIAGAGTPAAAAAAKAAAKAAKYGAAGGL (SEQ ID NO:141), VPGGVGPGGVTGIGAGPGGLGGAGSPAAAKSAAKAAAKAQYRAAAGLGAG (SEQ ID NO:142), and VPLGYPIKAPKLPGGYGLPYTNGKLPYGVAGAGGKAGYPTGTGVGSQAAAAAAK AAKYGAGGAG (SEQ ID NO:143).
In yet another related embodiment, the EBD sequence of a fusion polypeptide of the invention comprises at least 2-100 repeats of an elastin sequence set forth above, or a combination thereof.
In another embodiment, the EBD sequence of a fusion polypeptide of the invention comprises a combination of any one or more of the EBD sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H and NF-M sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H and Nup2p sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-M and Nup2p sequence set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-M and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of Nup2p and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H, NF-M and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H, NF-M and Nup2p sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of Nup2p, NF-M and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of NF-H, Nup2p and filamentous phage fd adsorption protein pIII sequences set forth herein.
In yet another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a combination of Nup2p, NF-H, NF-M and filamentous phage fd adsorption protein pIII sequences set forth herein.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a variant version of an amino acid sequence of NF-H described herein, where resulting sequence preserves amino acid composition of the parent sequence.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a variant version of an amino acid sequence of NF-M described herein, where resulting sequence preserves amino acid composition of the parent sequence.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a variant version of an amino acid sequence of Nup2p described herein, where resulting sequence preserves amino acid composition of the parent sequence.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a variant version of an amino acid sequence of filamentous phage fd adsorption protein pIII described herein, where resulting sequence preserves amino acid composition of the parent sequence.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention comprises a variant version of an amino acid sequence of elastin described herein, where resulting sequence preserves amino acid composition of the parent sequence.
According to another embodiment of the invention, an EBD sequence of a fusion polypeptide of the invention generally comprises between about 5-600 amino acid residues, between about 5-300 amino acid residues or between about 5-100 amino acid residues, however other polypeptide lengths may also be used.
In another embodiment, an EBD sequence of a fusion polypeptide of the invention is cleavable, e.g., can be removed and/or separated from the heterologous polypeptide sequence after recombinant expression by, for example, enzymatic or chemical cleavage methods.
In another embodiment, an EBD sequence of a fusion polypeptide of the invention is covalently linked at the N-terminus of the heterologous polypeptide sequence of interest. In another embodiment, an EBD sequence of a fusion polypeptide of the invention is covalently linked at the C-terminus of the heterologous polypeptide sequence of interest. In yet another embodiment, an EBD sequence of a fusion polypeptide of the invention is covalently linked at the N- and C-termini of the heterologous polypeptide sequence of interest.
In another embodiment of the invention, the charge of an EBD sequence of a fusion polypeptide of the invention is modulated by, for example, enzymatic and/or chemical methods, in order to modulate the activity of the EBD sequence. In a particular embodiment, the charge of the EBD sequence is modulated by phosphorylation.
According to another aspect of the invention, an isolated polynucleotide is provided, wherein the polynucleotide encodes a fusion polypeptide as described herein.
According to yet another aspect of the invention, there is provided an expression vector comprising an isolated polynucleotide encoding a fusion polypeptide as described herein. In a related embodiment, an expression vector is provided comprising a polynucleotide encoding an EBD sequence and further comprising a cloning site for insertion of a polynucleotide encoding a heterologous polypeptide of interest.
According to yet another aspect of the invention, there is provided a host cell comprising an expression vector as described herein.
According to yet another aspect of the invention, there is provided a kit comprising an isolated polynucleotide as described herein, an isolated polypeptide as described herein and/or an isolated host cell as described herein.
Yet another aspect of the invention provides a method for producing a recombinant protein comprising the steps of: introducing into a host cell an expression vector comprising a polynucleotide sequence encoding a fusion polypeptide, the fusion polypeptide comprising at least one entropic bristle domain sequence and at least one polypeptide sequence of interest; and expressing the fusion polypeptide in the host cell. In another embodiment, the method further comprises the step of isolating the fusion polypeptide from the host cell. In another related embodiment, the method further comprises the step of removing the entropic bristle domain sequence from the fusion polypeptide before or after isolating the fusion polypeptide from the host cell.
These and other aspects of the present invention will become apparent upon reference to the following detailed description. All references disclosed herein and in the enclosed Application Data Sheet are hereby incorporated by reference in their entirety as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 depicts the average net charge of a 5 residue moving window for residues 422 to 916 of human neurofilament medium (NF-M) protein sequence.

BRIEF DESCRIPTION OF THE SEQUENCE IDENTIFIERS

SEQ ID NO: 1 is the amino acid sequence of a human NF-H protein, Swiss-Prot accession number P12036, having an illustrative EB-domain corresponding to residues 414-1026.
SEQ ID NO: 2 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 1, GenBank accession number BC073969, having an illustrative EB-domain corresponding to residues 1242-3081.
SEQ ID NO: 3 is the amino acid sequence of a mouse NF-H protein, Swiss-Prot accession number P19246, having an illustrative EB domain corresponding to residues 409-1087.
SEQ ID NO: 4 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 3, GenBank accession number M35131, having an illustrative EB-domain corresponding to residues 1227-3219.
SEQ ID NO: 5 is the amino acid sequence of a bovine NF-M protein, Swiss-Prot accession number 077788; having an illustrative EB domain corresponding to residues 412-925.
SEQ ID NO: 6 is a polynucleotide sequence encoding protein residues 116-925 of bovine NF-M, GenBank accession number AF091342, having an illustrative EB domain corresponding to residues 891-2433.
SEQ ID NO: 7 is the amino acid sequence of a chicken NF-M protein, Swiss-Prot accession number P16053, having an illustrative EB domain corresponding to residues 407-857.
SEQ ID NO: 8 is a polynucleotide sequence encoding the protein fragment 259-857 of chicken NF-M, GenBank accession number X05558, having an illustrative EB domain corresponding to residues 177-1530.
SEQ ID NO: 9 is the amino acid sequence of a human NF-M protein, Swiss-Prot accession number P07197, having an illustrative EB domain corresponding to residues 412-915.
SEQ ID NO: 10 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 9, GenBank accession number Y00067, having an illustrative EB domain corresponding to residues 1236-2751.
SEQ ID NO: 11 is the amino acid sequence of a mouse NF-M protein, Swiss-Prot accession number P08553, having an illustrative EB domain corresponding to residues 411-848.
SEQ ID NO: 12 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 11, GenBank accession number X05640, having an illustrative EB domain corresponding to residues 1233-2550.
SEQ ID NO: 13 is the amino acid sequence of a rat NF-M protein, Swiss-Prot accession number P12839, having an illustrative EB domain corresponding to residues 411-845.
SEQ ID NO: 14 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 13, GenBank accession number Z12152, having an illustrative EB domain corresponding to residues 1233-2538.
SEQ ID NO: 15 is the amino acid sequence of a rabbit NF-M protein, Swiss-Prot accession number P54938, having an illustrative EB domain corresponding to residues 198-644.
SEQ ID NO: 16 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 15, GenBank accession number Z47378, having an illustrative EB domain corresponding to residues 594-1938.
SEQ ID NO: 17 is the amino acid sequence of a phage fd pill protein, Swiss-Prot accession number P69168, having illustrative EB-domains corresponding to residues 86-104 and 236-274.
SEQ ID NO: 18 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 17, GenBank accession number V00604, having illustrative EB domains corresponding to residues 258-312 and 708-822.
SEQ ID NO: 19 is the amino acid sequence of a Yeast Nup2p protein, Swiss-Prot accession number P32499, having an illustrative EB-domain corresponding to residues 189-582.
SEQ ID NO: 20 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 19, GenBank accession number X69964, having an illustrative EB domain corresponding to residues 567-1748.
SEQ ID NO: 21 is the amino acid sequence of a mouse elastin protein, Swiss-Prot accession number P54320, the entire sequence of which represents an illustrative EB domain.
SEQ ID NO: 22 is a polynucleotide sequence encoding the amino acid sequence of SEQ ID NO: 21, GenBank accession number U08210.
SEQ ID Nos: 23 to 144 represent further illustrative EBD sequences according to the present invention.

DETAILED DESCRIPTION OF THE INVENTION

The practice of the present invention will employ, unless indicated specifically to the contrary, conventional methods of molecular biology and recombinant DNA techniques within the skill of the art, many of which are described below for the purpose of illustration. Such techniques are explained fully in the literature. See, e.g., Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Maniatis et al., Molecular Cloning: A Laboratory Manual (1982); DNA Cloning: A Practical Approach, vol. I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., 1984); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., 1985); Transcription and Translation (B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R. Freshney, ed., 1986); Perbal, A Practical Guide to Molecular Cloning (1984).
All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.
As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural references unless the content clearly dictates otherwise.
As used herein, the terms “polypeptide” and “protein” are used interchangeably, unless specified to the contrary, and according to conventional meaning, i.e., as a sequence of amino acids. Polypeptides are not limited to a specific length, e.g., they may comprise a full length protein sequence or a fragment of a full length protein, and may include post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring. Polypeptides of the invention may be prepared using any of a variety of well known recombinant and/or synthetic techniques, illustrative examples of which are further discussed below.
As noted above, the present invention, in a general aspect, relates to isolated fusion polypeptides comprising at least one entropic bristle domain (EBD) sequence and at least one heterologous polypeptide sequence. By providing an EBD sequence which sweeps out the three-dimensional space surrounding a newly synthesized heterologous polypeptide, the EBD sequences of the invention effectively exclude other polypeptides and thereby minimize aggregation with other newly synthesized heterologous polypeptides during recombinant polypeptide production.
In addition, an EBD sequence of the invention can provide steric stabilization to recombinant polypeptides, a property that is relatively independent of concentration, and can thus minimize problems associated with high-level recombinant production of polypeptides and proteins (e.g., precipitation, toxicity and/or inclusion body formation). Thus, EBD fusion polypeptides described herein exhibit both steric effects (via the entropic bristle's motion) and electrostatic effects (via the bristle's highly charged sequence) to minimize interactions between recombinant polypeptides expressed as fusions according to the present invention. These characteristics allow EBD polypeptide sequences to more effectively solubilize recombinantly expressed polypeptides than, for example, other fusion partners which do not have a steric exclusion component that contributes to their activity.
Therefore, according to one embodiment of the invention, fusion polypeptides comprising an EBD sequence and a heterologous polypeptide are provided which exhibit improved solubility relative to the corresponding heterologous polypeptide in the absence of the EBD sequence. In one embodiment, for example, the fusion polypeptide has at least 5% increased solubility relative to the heterologous polypeptide sequence alone. In another related embodiment, the fusion polypeptide has at least 25% increased solubility relative to the heterologous polypeptide sequence. In yet another related embodiment, the fusion polypeptide has at least 50% increased solubility relative to the heterologous polypeptide sequence.
The extent of improved solubility provided by an EBD sequence described herein can be determined using any of a number of available approaches (see for example, Kapust, R. B. and D. S. Waugh, Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci, 1999. 8:1668-74; Fox, J. D., et al., Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers. FEBS Lett, 2003. 537:53-7; Dyson M R, Shadbolt S P, Vincent K J, Perera R L, McCafferty J. Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression. BMC Biotechnol. 2004 Dec. 14; 4(1):32).
Cells from single, drug resistant colony of E. coli overproducing the fusion polypeptide are grown to saturation in LB broth (Miller J H. 1972. Experiments in molecular genetics. Cold Spring Harbor, N.Y.: Cold Spring Harbor Press. p 433) supplemented with 100 mg/mL ampicillin and 30 mg/mL chloramphenicol at 37° C. The saturated cultures are diluted 50-fold in the same medium and grown in shake-flasks to mid-log phase (A₆₀₀˜0.5-0.7), at which time IPTG is added to a final concentration of 1 mM. After 3 h, the cells are recovered by centrifugation. The cell pellets are resuspended in 0.1 culture volumes of lysis buffer (50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA), and disrupted by sonication. A total protein sample is collected from the cell suspension after sonication, and a soluble protein sample is collected from the supernatant after the insoluble debris is pelleted by centrifugation (20,000×g). These samples are subjected to SDS-PAGE and proteins are visualized by staining with Coomassie Brilliant Blue. At least three independent experiments are typically performed to obtain numerical estimates of the solubility of each fusion protein in E. coli. Coomassie-stained gels will be scanned with a gel-scanning densitometer and the pixel densities of the bands corresponding to the fusion proteins are obtained directly by volumetric integration. In each lane, the collective density of all E. coli proteins that are larger than the largest fusion protein are also determined by volumetric integration and used to normalize the values in each lane relative to the others. The percent solubility of each fusion protein is calculated by dividing the amount of soluble fusion protein by the total amount of fusion protein in the cells, after first subtracting the normalized background values obtained from negative control lanes (cells containing no expression vector). Descriptive statistical data (e.g., the mean and standard deviation) is then generated using standard methods.
The presence of an EBD sequence in fusion polypeptides of the present invention can also serve to reduce the extent of aggregation of a heterologous polypeptide sequence. In one embodiment, for example, the fusion polypeptide exhibits at least 10% reduced aggregation relative to the heterologous polypeptide. In another embodiment, the fusion polypeptide has at least 25% reduced aggregation relative to the heterologous polypeptide.
The extent of reduced aggregation provided by the fusion polypeptides of the present invention can be determined using any of a number of available techniques (see for example, Kapust, R. B. and D. S. Waugh, Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci, 1999. 8:1668-74; Fox, J. D., et al., Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers. FEBS Lett, 2003. 537:53-7).
Cells from single, drug resistant colony of E. coli overproducing the fusion polypeptide are grown to saturation in LB broth (Miller J H. 1972. Experiments in molecular genetics. Cold Spring Harbor, N.Y.: Cold Spring Harbor Press. p 433) supplemented with 100 mg/mL ampicillin and 30 mg/mL chloramphenicol at 37° C. The saturated cultures are diluted 50-fold in the same medium and grown in shake-flasks to mid-log phase (A₆₀₀˜0.5-0.7), at which time IPTG is added to a final concentration of 1 mM. After 3 h, the cells are recovered by centrifugation. The cell pellets are resuspended in 0.1 culture volumes of lysis buffer (50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA), and disrupted by sonication. A total protein sample is collected from the cell suspension after sonication, and an insoluble protein sample is collected from the pellet after the centrifugation (20,000×g). These samples are subjected to SDS-PAGE and proteins are visualized by staining with Coomassie Brilliant Blue. At least three independent experiments are typically performed to obtain numerical estimates of the solubility of each fusion protein in E. coli. Coomassie-stained gels are scanned with a gel-scanning densitometer and the pixel densities of the bands corresponding to the fusion proteins are obtained directly by volumetric integration. In each lane, the collective density of all insoluble E. coli proteins that are larger than the largest fusion protein is also determined by volumetric integration and used to normalize the values in each lane relative to the others. The percent insolubility of each fusion protein is calculated by dividing the amount of insoluble fusion protein by the total amount of fusion protein in the cells, after first subtracting the normalized background values obtained from negative control lanes (cells containing no expression vector). Descriptive statistical data (e.g., the mean and standard deviation) is generated by standard methods.
The presence of an EBD sequence in the fusion polypeptides of the present invention can also serve to improve the folding characteristics of the fusion polypeptides relative to the corresponding heterologous polypeptide, e.g., by minimizing interference caused by interaction with other proteins.
Assays for evaluating the folding characteristics of a fusion polypeptide of the invention can be carried out using conventional techniques, such as circular dichroism spectroscopy in far ultra-violet region, circular dichroism in near ultra-violet region, nuclear magnetic resonance spectroscopy, infra-red spectroscopy, Raman spectroscopy, intrinsic fluorescence spectroscopy, extrinsic fluorescence spectroscopy, fluorescence resonance energy transfer, fluorescence anisotropy and polarization, steady-state fluorescence, time-domain fluorescence, numerous hydrodynamic techniques including gel-filtration, viscometry, small-angle X-ray scattering, small angle neutron scattering, dynamic light scattering, static light scattering, scanning microcalorimetry, and limited proteolysis.
In another embodiment of the invention, an EBD comprises an amino acid sequence that maintains a substantially random coil conformation. Whether a given amino acid sequence maintains a substantially random coil conformation can be determined by circular dichroism spectroscopy in far ultra-violet region, nuclear magnetic resonance spectroscopy, infra-red spectroscopy, Raman spectroscopy, fluorescence spectroscopy, numerous hydrodynamic techniques including gel-filtration, viscometry, small-angle X-ray scattering, small angle neutron scattering, dynamic light scattering, static light scattering, scanning microcalorimetry, and limited proteolysis.
In another embodiment of the invention, an EBD sequence comprises an amino acid sequence that is substantially mutually repulsive. This property of being mutually repulsive can be determined by simple calculations of charge distribution within the polypeptide sequence.
In yet another embodiment of the invention, an EBD sequence comprises an amino acid sequence that remains in substantially constant motion, particularly in an aqueous environment. The property of being in substantially constant motion can be determined by nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, small angle neutron scattering, dynamic light scattering, intrinsic fluorescence spectroscopy, extrinsic fluorescence spectroscopy, fluorescence resonance energy transfer, fluorescence anisotropy and polarization, steady-state fluorescence, time-domain fluorescence.
According to a more particular embodiment of the present invention, an EBD sequence is derived from one of the three subunits that make up mammalian axon neurofilaments (including human, bovine, chicken, rabbit, mouse, and rat neurofilaments). Axon neurofilaments are major cytoskeletal components of the axonal cell. One of the functions of neurofilaments is to maintain the bore of the axon. Spacing between the filaments is maintained by the action of an entropic brush formed by entropic bristles carried by certain of the neurofilament subunits. The combination of the entropic bristles along the length of the fiber results in the formation of an entropic brush that functions to sterically exclude interfiber contact by thermally-driven motion, thereby maintaining the bore of the axon. Interfilament spacing is thought to be maintained by long-range interactions between the entropic brushes formed by the EBDs that project from the NF-M and NF-H monomers (Brown and Hoh, 1997).
Therefore, in another embodiment of the invention, an EBD sequence of the invention comprises a C-terminal entropic bristle sequence of an NF-M or NF-H neurofilament protein. For example, in one embodiment, an EBD sequence of the invention comprises at least one amino acid sequence, SPEAEK (SEQ ID NO:23), derived from the neurofilament triplet H protein. In a related embodiment, multiple repeats of the SPEAEK (SEQ ID NO:23) sequence are provided within the same isolated fusion polypeptide. In a more particular embodiment, about 1-10, 1-50 or 1-100 repeats of the sequence SPEAEK (SEQ ID NO:23) are provide in a polypeptide.
In another embodiment of the invention, an EBD sequence is a sequence derived from a phage protein. In a more particular embodiment, the EBD sequence comprises at least one sequence derived from the linker region of a filamentous phage, such as the filamentous phage fd. In a more particular embodiment, the EBD sequence comprises at least one sequence derived from the linker region derived from the filamentous phage fd adsorption protein pIII. In a more particular embodiment, the EBD sequence comprises at least one sequence derived from the 36 amino acid linker region derived from filamentous phage fd adsorption protein pIII. In a more particular embodiment, an EBD sequence of the invention comprises between about 1-10, 1-50 or 1-100 repeats of the amino acid sequence EGGGS (SEQ ID NO:93), derived from the linker region of a filamentous phage fd adsorption protein pIII.
In another embodiment of the invention, an EBD sequence is a sequence derived from nucleoporin. In eukaryotic cells, the translocation of biomolecules between the nucleus and cytosol occurs through nuclear pore complexes (NPCs), supramolecular protein structures embedded in the double lipid membrane of the nuclear envelope (Nakielny, S., and Dreyfuss, G. (1999) Cell 99, 677-690; Pemberton, L. F., Blobel, G., and Rosenblum, J. S. (1998) Curr. Opin. Cell Biol. 10, 392-399; Rout, M., and Aitchison, J. (2001) J. Biol. Chem. 276, 16593-16596). For example, the Saccharomyces cerevisiae NPC is a 60-MDa structure (Yang, Q., Rout, M. P., and Akey, C. W. (1998) Mol. Cell. 1, 223-234) formed by 30 different nucleoporins present in multiple copies per NPC (Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000) J. Cell Biol. 148, 635-651). The yeast NPC contains a core ring structure with 8-fold symmetry measuring 95 nm in diameter and 35 nm in depth (Yang, Q., Rout, M. P., and Akey, C. W. (1998) Mol. Cell. 1, 223-234). It is believed that nucleoporins form a barrier meshwork that excludes most macromolecules larger than a threshold size from entering the NPC (Rout, M., and Aitchison, J. (2001) J. Biol. Chem. 276, 16593-16596; Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000) J. Cell Biol. 148, 635-651; Denning D P, Uversky V, Patel S S, Fink A L, Rexach M (2002) The Saccharomyces cerevisiae nucleoporin Nup2p is a natively unfolded protein. J Biol. Chem. 277(36):33447-55).
Therefore, in another embodiment of the invention, an EBD sequence of the invention comprises a central fragment of yeast nucleoporin Nup2p, such as those described herein. For example, in one embodiment, an EBD sequence of the invention comprises at least one amino acid sequence, FSFGTSQPNNTPS (SEQ ID NO:99), derived from the yeast nucleoporin porin protein Nup2p. In a related embodiment, multiple repeats of the FSFGTSQPNNTPS (SEQ ID NO:99) sequence are provided within the same isolated fusion polypeptide. In a more particular embodiment, about 1-10, 1-50 or 1-100 repeats of the sequence FSFGTSQPNNTPS (SEQ ID NO:99) are provide in a polypeptide.
In another embodiment of the invention, an EBD sequence is a sequence derived from an elastin-like polypeptide (ELP). ELPs comprise multiple repeats of the elastin-derived pentamer VPGXG (SEQ ID NO:144) where x, the guest residue, is not proline. ELPs are disordered and highly solvated at normal temperatures. They undergo inverse transition at elevated temperatures (the T_tof a particular ELP sequence). The conformation of ELPs transitions from extended to collapsed and is dependent on temperature and salt concentration. Purification of proteins using ELPs may be carried out using inverse transition cycling. The ELP is soluble at temperatures below its T_tand insoluble at temperatures above its T_t. Using ELPs to purify protein may be accomplished by making a fusion construct that includes the target heterologous protein and a suitable ELP multimer, e.g., comprising about 5-100 residues.
As will be understood by those skilled in the art, the propensity of a polypeptide chain to maintain a substantially random coil and flexible conformation is encoded in its amino acid composition rather than in its amino acid sequence (Uversky V N, Gillespie J R, Fink A L (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins. 41(3):415-27). This means that polypeptides sharing similar amino acid compositions will be similarly unfolded. The function of EBDs to increase protein solubility is based at least in part on their random coil and flexible conformation. Therefore, in one preferred embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence of a mammalian NF-H protein. In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence of a mammalian NF-M protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence of a Nup2 protein. In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence of a mammalian elastin protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence of a filamentous phage fd adsorption protein pIII.
In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any combination of fragments derived from sequence of a mammalian NF-H protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any combination of fragments derived from sequence of a mammalian NF-M protein. In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any combination of fragments derived from sequence of a Nup2p protein. In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any combination of fragments derived from sequence of an elastin protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any combination of fragments derived from sequence of a filamentous phage fd adsorption protein pIII.
In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any combination of fragments derived from sequence of a mammalian NF-H protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any combination of fragments derived from sequence of a mammalian NF-M protein. In one more embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any combination of fragments derived from sequence of a Nup2p protein. In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any combination of fragments derived from sequence of an elastin protein. In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any combination of fragments derived from sequence of a filamentous phage fd adsorption protein pIII.
In another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to any pairwise or multiple combinations of fragments derived from sequence of a mammalian NF-H protein, a mammalian NF-M protein, a Nup2p protein, an elastin protein and a filamentous phage fd adsorption protein pIII.
In yet another embodiment of the invention, an EBD sequence of the invention comprises a scrambled variant sequence corresponding to multiple repeats of any pairwise or multiple combinations of fragments derived from sequence of a mammalian NF-H protein, a mammalian NF-M protein, a Nup2p protein, an elastin protein and a filamentous phage fd adsorption protein pIII.
In another embodiment, the fusion polypeptides of the invention further comprise independent cleavable linkers, which allow an EBD sequence, for example at either the N or C terminus, to be easily cleaved from a heterologous polypeptide sequence of interest. Such cleavable linkers are known and available in the art. This embodiment thus provides improved isolation and purification of a heterologous polypeptide sequence and facilitates downstream high-throughput processes.
The present invention also provides polypeptide fragments of an EBD polypeptide sequence described herein, wherein the fragment comprises at least about 5, 10, 15, 20, 25, 50, or 100 contiguous amino acids, or more, including all intermediate lengths, of an EBD polypeptide sequence set forth herein, or those encoded by a polynucleotide sequence set forth herein. In a preferred embodiment, an EBD fragment provides similar or improved activity relative to the activity of the EBD sequence from which it is derived (wherein the activity includes, for example, one or more of improved solubility, improved folding, reduced aggregation and/or improved yield, when in fusion with a heterologous polypeptide sequence of interest.
In another aspect, the present invention provides variants of an EBD polypeptide sequence described herein. EBD polypeptide variants will typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity (e.g., determined as described below), along its length, to an EBD polypeptide sequence set forth herein. Preferably the EBD variant provides similar or improved activity relative to the activity of the EBD sequence from which the variant was derived (wherein the activity includes one or more of improved solubility, improved folding, reduced aggregation and/or improved yield, when in fusion with a heterologous polypeptide sequence of interest.
An EBD polypeptide variant thus refers to a polypeptide that differs from an EBD polypeptide sequence disclosed herein in one or more substitutions, deletions, additions and/or insertions. Such variants may be naturally occurring or may be synthetically generated, for example, by modifying one or more of the EBD polypeptide sequences of the invention and evaluating their activity as described herein and/or using any of a number of techniques well known in the art.
In many instances, a variant will contain conservative substitutions. A “conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. As described above, modifications may be made in the structure of the EBD polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable activity. When it is desired to alter the amino acid sequence of an EBD polypeptide to create an equivalent or an improved EBD variant or EBD fragment, one skilled in the art can readily change one or more of the codons of the encoding DNA sequence, for example according to Table 1.
For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of desired activity. It is thus contemplated that various changes may be made in the EBD polypeptide sequences of the invention, or corresponding DNA sequences which encode said EBD polypeptide sequences, without appreciable loss of their desired activity.

TABLE 1

Amino Acids	Codons

Alanine	Ala	A	GCA	GCC	GCG	GCU
Cysteine	Cys	C	UGC	UGU
Aspartic acid	Asp	D	GAC	GAU
Glutamic acid	Glu	E	GAA	GAG
Phenylalanine	Phe	F	UUC	UUU
Glycine	Gly	G	GGA	GGC	GGG	GGU
Histidine	His	H	CAC	CAU
Isoleucine	Ile	I	AUA	AUC	AUU
Lysine	Lys	K	AAA	AAG
Leucine	Leu	L	UUA	UUG	CUA	CUC	CUG	CUU
Methionine	Met	M	AUG
Asparagine	Asn	N	AAC	AAU
Proline	Pro	P	CCA	CCC	CCG	CCU
Glutamine	Gln	Q	CAA	CAG
Arginine	Arg	R	AGA	AGG	CGA	CGC	CGG	CGU
Serine	Ser	S	AGC	AGU	UCA	UCC	UCG	UCU
Threonine	Thr	T	ACA	ACC	ACG	ACU
Valine	Val	V	GUA	GUC	GUG	GUU
Tryptophan	Trp	W	UGG
Tyrosine	Tyr	Y	UAC	UAU

In making such changes, the hydropathic index of amino acids may also be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporated herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn has potential bearing on the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte and Doolittle, 1982). These values are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).
Therefore, according to certain embodiments, amino acids within an EBD sequence of the invention may be substituted by other amino acids having a similar hydropathic index or score. Preferably, any such changes result in an EBD sequence with a similar level of activity as the unmodified EBD sequence. In making such changes, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred. It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). Thus, an amino acid can be substituted for another having a similar hydrophilicity value and in many cases still retain a desired level of activity. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.
As outlined above, amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
In addition, any polynucleotide of the invention, such as a polynucleotide encoding an EBD polypeptide sequence, or a vector comprising a polynucleotide encoding an EBD polypeptide sequence, may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
Amino acid substitutions within an EBD sequence of the invention may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also, or alternatively, contain nonconservative changes.
In an illustrative embodiment, a variant EBD polypeptide differs from the corresponding unmodified EBD sequence by substitution, deletion or addition of five percent of the original amino acids or fewer. Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the desired activity.
A polypeptide of the invention may further comprise a signal (or leader) sequence at the N-terminal end of the polypeptide, which co-translationally or post-translationally directs transfer of the protein. The polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support.
As noted above, the present invention provides EBD polypeptide variant sequences which share some degree of sequence identity with an EBD polypeptide specifically described herein, such as those having at least 40%, 50%, 60%, 70%, 80%, 90% or 95% identity with an EBD polypeptide sequence described herein. When comparing polypeptide sequences to evaluate their extent of shared sequence identity, two sequences are said to be “identical” if the sequence of amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity.
A “comparison window” as used herein, refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O., (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes, pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M., CABIOS 5:151-153 (1989); Myers, E. W. and Muller W., CABIOS 4:11-17 (1988); Robinson, E. D., Comb. Theor 11:105 (1971); Saitou, N. Nei, M., Mol. Biol. Evol. 4:406-425 (1987); Sneath, P. H. A. and Sokal, R. R., Numerical Taxonomy—the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif. (1973); Wilbur, W. J. and Lipman, D. J., Proc. Natl. Acad., Sci. USA 80:726-730 (1983).
Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman, Add. APL. Math 2:482 (1981), by the identity alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity methods of Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
One preferred example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nucl. Acids Res. 25:3389-3402 (1977), and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
In one preferred approach, the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
In another aspect of the invention, there is provided an isolated polynucleotide sequence encoding a fusion polypeptide, the fusion polypeptide comprising at least one entropic bristle domain sequence and at least one heterologous polypeptide sequence of interest. In a related aspect, the invention provides expression vectors comprising a polynucleotide encoding an EBD fusion polypeptide of the invention. In another related aspect, an expression vector of the invention comprises a polynucleotide encoding one or more EBD sequence and further comprises a multiple cloning site for the insertion of a polynucleotide encoding a heterologous polypeptide sequence of interest.
Polynucleotides compositions of the present invention may be identified, prepared and/or manipulated using any of a variety of well established techniques (see generally, Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989, and other like references).
The terms “DNA” and “polynucleotide” are used essentially interchangeably herein to refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species. “Isolated”, as used herein, means that a polynucleotide is substantially away from other coding sequences, and that the DNA molecule does not contain large portions of unrelated coding DNA, such as large chromosomal fragments or other functional genes or polypeptide coding regions. Of course, this refers to the DNA molecule as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.
As will be understood by those skilled in the art, the polynucleotide compositions of this invention can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.
As will also be recognized, polynucleotides of the invention may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules may include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
In addition to the EBD polynucleotide sequences set forth herein, the present invention also provides EBD polynucleotide variants having substantial identity to an EBD polynucleotide sequence disclosed herein, for example those comprising at least 50% sequence identity, preferably at least, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% or higher, sequence identity compared to an EBD polynucleotide sequence of this invention using the methods described herein, (e.g., BLAST analysis using standard parameters, as described below). One skilled in this art will recognize that these values can be appropriately adjusted to determine corresponding identity of polypeptides encoded by two polynucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like.
Typically, EBD polynucleotide variants will contain one or more substitutions, additions, deletions and/or insertions, preferably such that the activity (e.g., improved folding, reduced aggregation and/or improved yield, when in fusion with a heterologous sequence of interest) of the polypeptide encoded by the variant polynucleotide is not substantially diminished relative to the corresponding unmodified polynucleotide sequence.
In additional embodiments, the present invention provides polynucleotide fragments comprising or consisting of various lengths of contiguous stretches of sequence identical to or complementary to one or more of the EBD polynucleotide sequences disclosed herein. For example, polynucleotides are provided by this invention that comprise or consist of at least about 10, 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguous nucleotides of one or more of the sequences disclosed herein as well as all intermediate lengths there between. It will be readily understood that “intermediate lengths”, in this context, means any length between the quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30, 31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151, 152, 153, etc.; including all integers through 200-500; 500-1,000, and the like. A polynucleotide sequence as described here may be extended at one or both ends by additional nucleotides not found in the native sequence. This additional sequence may consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides at either end of the disclosed sequence or at both ends of the disclosed sequence. Preferably, an EBD polynucleotide fragment of the invention encodes a fusion polypeptide that retains one or more desired activities, e.g., improved folding, reduced aggregation and/or improved yield, when in fusion with a heterologous sequence of interest.
The EBD polynucleotides of the present invention, or fragments thereof, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol. For example, illustrative polynucleotide segments with total lengths of about 10,000, about 5000, about 3000, about 2,000, about 1,000, about 500, about 200, about 100, about 50 base pairs in length, and the like, (including all intermediate lengths) are contemplated to be useful in many implementations of this invention.
It will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that will encode a polypeptide as described herein. Some of these polynucleotides bear minimal homology to the native polynucleotide sequence. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention. Further, different alleles of an EBD polynucleotide sequence provided herein are within the scope of the present invention. Alleles are endogenous sequences that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides. The resulting mRNA and protein may, but need not, have an altered structure or function. Alleles may be identified using standard techniques (such as hybridization, amplification and/or database sequence comparison).
In another embodiment of the invention, a mutagenesis approach, such as site-specific mutagenesis, may be employed for the preparation of variants and/or derivatives of the EBD polynucleotides and polypeptides described herein. By this approach, for example, specific modifications in a polypeptide sequence can be made through mutagenesis of the underlying polynucleotides that encode them. These techniques provides a straightforward approach to prepare and test sequence variants, for example, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the polynucleotide.
Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Mutations may be employed in a selected polynucleotide sequence to improve, alter, decrease, modify, or otherwise change the properties of the polynucleotide itself, and/or alter the properties, activity, composition, stability, or primary sequence of the encoded polypeptide.
In certain embodiments, the present invention contemplates the mutagenesis of the disclosed polynucleotide sequences to alter one or more activities/properties of the encoded polypeptide. The techniques of site-specific mutagenesis are well-known in the art, and are widely used to create variants of both polypeptides and polynucleotides. For example, site-specific mutagenesis is often used to alter a specific portion of a DNA molecule. In such embodiments, a primer comprising typically about 14 to about 25 nucleotides or so in length may be employed, with about 5 to about 10 residues on both sides of the junction of the sequence being altered.
As will be appreciated by those of skill in the art, site-specific mutagenesis techniques have often employed a phage vector that exists in both a single stranded and double stranded form. Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage are readily commercially-available and their use is generally well-known to those skilled in the art. Double-stranded plasmids are also routinely employed in site directed mutagenesis that eliminates the step of transferring the gene of interest from a plasmid to a phage.
In general, site-directed mutagenesis in accordance herewith is performed by first obtaining a single-stranded vector or melting apart of two strands of a double-stranded vector that includes within its sequence a DNA sequence that encodes the desired peptide. An oligonucleotide primer bearing the desired mutated sequence is prepared, generally synthetically. This primer is then annealed with the single-stranded vector, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation. This heteroduplex vector is then used to transform appropriate cells, such as E. coli cells, and clones are selected which include recombinant vectors bearing the mutated sequence arrangement.
The preparation of sequence variants of the selected peptide-encoding DNA segments using site-directed mutagenesis provides a means of producing potentially useful species and is not meant to be limiting as there are other ways in which sequence variants of peptides and the DNA sequences encoding them may be obtained. For example, recombinant vectors encoding the desired peptide sequence may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants. Specific details regarding these methods and protocols are found in the teachings of Maloy et al., 1994; Segal, 1976; Prokop and Bajpai, 1991; Kuby, 1994; and Maniatis et al., 1982, each incorporated herein by reference, for that purpose.
As used herein, the term “oligonucleotide directed mutagenesis procedure” refers to template-dependent processes and vector-mediated propagation which result in an increase in the concentration of a specific nucleic acid molecule relative to its initial concentration, or in an increase in the concentration of a detectable signal, such as amplification. As used herein, the term “oligonucleotide directed mutagenesis procedure” is intended to refer to a process that involves the template-dependent extension of a primer molecule. The term template dependent process refers to nucleic acid synthesis of an RNA or a DNA molecule wherein the sequence of the newly synthesized strand of nucleic acid is dictated by the well-known rules of complementary base pairing (see, for example, Watson, 1987). Typically, vector mediated methodologies involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided by U.S. Pat. No. 4,237,224, specifically incorporated herein by reference in its entirety.
In another approach for the production of polypeptide variants of the present invention, recursive sequence recombination, as described in U.S. Pat. No. 5,837,458, may be employed. In this approach, iterative cycles of recombination and screening or selection are performed to “evolve” individual polynucleotide variants of the invention wherein one or more desired activities is improved or modified.
In other embodiments of the present invention, the polynucleotide sequences provided herein can be advantageously used as probes or primers for nucleic acid hybridization. As such, it is contemplated that nucleic acid segments that comprise or consist of a sequence region of at least about a 15 nucleotide long contiguous sequence that has the same sequence as, or is complementary to, a 15 nucleotide long contiguous sequence disclosed herein may be used. Longer contiguous identical or complementary sequences, e.g., those of about 20, 30, 40, 50, 100, 200, 500, 1000 (including all intermediate lengths) and even up to full length sequences will also be of use in certain embodiments.
Many template dependent processes are available to amplify a target sequences of interest present in a sample. One of the best known amplification methods is the polymerase chain reaction (PCR™) which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, each of which is incorporated herein by reference in its entirety. Briefly, in PCR™, two primer sequences are prepared which are complementary to regions on opposite complementary strands of the target sequence. An excess of deoxynucleoside triphosphates is added to a reaction mixture along with a DNA polymerase (e.g., Taq polymerase). If the target sequence is present in a sample, the primers will bind to the target and the polymerase will cause the primers to be extended along the target sequence by adding on nucleotides. By raising and lowering the temperature of the reaction mixture, the extended primers will dissociate from the target to form reaction products, excess primers will bind to the target and to the reaction product and the process is repeated. Preferably reverse transcription and PCR™ amplification procedure may be performed in order to quantify the amount of mRNA amplified. Polymerase chain reaction methodologies are well known in the art.
Any of a number of other template dependent processes, many of which are variations of the PCR™ amplification technique, are readily known and available in the art. Illustratively, some such methods include the ligase chain reaction (referred to as LCR), described, for example, in Eur. Pat. Appl. Publ. No. 320,308 and U.S. Pat. No. 4,883,750; Qbeta Replicase, described in PCT Intl. Pat. Appl. Publ. No. PCT/US87/00880; Strand Displacement Amplification (SDA) and Repair Chain Reaction (RCR). Still other amplification methods are described in Great Britain Pat. Appl. No. 2 202 328, and in PCT Intl. Pat. Appl. Publ. No. PCT/US89/01025. Other nucleic acid amplification procedures include transcription-based amplification systems (TAS) (PCT Intl. Pat. Appl. Publ. No. WO 88/10315), including nucleic acid sequence based amplification (NASBA) and 3SR. Eur. Pat. Appl. Publ. No. 329,822 describes a nucleic acid amplification process involving cyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, and double-stranded DNA (dsDNA). PCT Intl. Pat. Appl. Publ. No. WO 89/06700 describes a nucleic acid sequence amplification scheme based on the hybridization of a promoter/primer sequence to a target single-stranded DNA (“ssDNA”) followed by transcription of many RNA copies of the sequence. Other amplification methods such as “RACE” (Frohman, 1990), and “one-sided PCR” (Ohara, 1989) are also well-known to those of skill in the art.
As noted, the EBD fusion polynucleotides, polypeptides and vectors of the present invention are advantageous in the context of recombinant polypeptide production, particularly where it is desired to achieve, for example, improved solubility, improved yield, improved folding and/or reduced aggregation of a heterologous polypeptide to which an EBD polypeptide sequence has been operably fused. Therefore, another aspect of the invention provides methods for producing a recombinant protein, for example by introducing into a host cell an expression vector comprising a polynucleotide sequence encoding a fusion polypeptide as described herein, e.g., a fusion polypeptide comprising at least one EBD sequence and at least one heterologous polypeptide sequence of interest; and expressing the fusion polypeptide in the host cell. In a related embodiment, the method further comprises the step of isolating the fusion polypeptide from the host cell. In another embodiment, the method further comprises the step of removing an entropic bristle domain sequence from the fusion polypeptide before or after isolating the fusion polypeptide from the host cell.
For recombinant production of a fusion polypeptide of the invention, DNA sequences encoding the polypeptide components of a fusion polypeptide (e.g., one or more EBD sequences and a heterologous polypeptide sequence of interest) may be assembled using conventional methodologies. In one example, the components may be assembled separately and ligated into an appropriate expression vector. For example, the 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the activities of both component polypeptides.
A peptide linker sequence may be employed to separate an EBD polypeptide sequence from a heterologous polypeptide sequence by some defined distance, for example a distance sufficient to ensure that the advantages of the invention are achieved, e.g, advantages such as improved folding, reduced aggregation and/or improved yield. Such a peptide linker sequence may be incorporated into the fusion polypeptide using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based, for example, on the factors such as: (1) their ability to adopt a flexible extended conformation; and (2) their inability to adopt a secondary structure that could interfere with the activity of the EBD sequence. Illustrative peptide linker sequences, for example, may contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258-8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length, for example.
The ligated DNA sequences of a fusion polynucleotide are operably linked to suitable transcriptional and/or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.
The EBD and heterologous polynucleotide sequences may comprise a sequence as described herein, or may comprise a sequence that has been modified to facilitate recombinant polypeptide production. As will be understood by those of skill in the art, it may be advantageous in some instances to produce polypeptide-encoding polynucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
Moreover, the polynucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter polypeptide encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product. For example, DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. In addition, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and so forth.
In a particular embodiment, a fusion polynucleotide is engineered to further comprise a cleavage site located between the EBD polypeptide-encoding sequence and the heterologous polypeptide sequence, so that the hetereolous polypeptide may be cleaved and purified away from an EBD polypeptide sequence at any desired stage following expression of the fusion polypeptide. Illustratively, a fusion polynucleotide of the invention may be designed to include heparin, thrombin, or factor Xa protease cleavage sites.
In order to express a desired polypeptide, the nucleotide sequences encoding the polypeptide, or functional equivalents, may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of an inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y., and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York. N.Y.
A variety of expression vector/host systems may be utilized to contain and express polynucleotide sequences of the present invention. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.
The “control elements” or “regulatory sequences” present in an expression vector are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the pBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or pSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
In bacterial systems, any of a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide. For example, when large quantities are needed, for example for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be used. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as pBLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of .beta.-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509); and the like. Proteins made in such systems may be designed to include heparin, thrombin, or factor Xa protease cleavage sites so that the cloned polypeptide of interest can be released from the EBD moiety at will.
In the yeast, Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al. (supra) and Grant et al. (1987) Methods Enzymol. 153:516-544.
In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311. Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, for example, Hobbs, S. or Murry, L. E. in McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York, N.Y.; pp. 191-196).
An insect system may also be used to express a polypeptide of interest. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which the polypeptide of interest may be expressed (Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. 91:3224-3227).
In mammalian host cells, a number of viral-based expression systems are generally available. For example, in cases where an adenovirus is used as an expression vector, sequences encoding a polypeptide of interest may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan, J. and Shenk, T. (1984) Proc. Natl. Acad. Sci. 81:3655-3659). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162).
In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as CHO, COS, HeLa, MDCK, HEK293, and WI38, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
For long-term, high-yield production of recombinant proteins, stable expression is generally preferred. For example, cell lines which stably express a polynucleotide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11:223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1990) Cell 22:817-23) genes which can be employed in tk.sup.- or aprt.sup.-cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. 85:8047-51). The use of visible markers has gained popularity with such markers as anthocyanins, beta-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes, C. A. et al. (1995) Methods Mol. Biol. 55:121-131).
Although the presence/absence of marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed. For example, if the sequence encoding a polypeptide is inserted within a marker gene sequence, recombinant cells containing sequences can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a polypeptide-encoding sequence under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
Alternatively, host cells that contain and express a desired polynucleotide sequence may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include, for example, membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein.
A variety of protocols for detecting and measuring the expression of polynucleotide-encoded products, using either polyclonal or monoclonal antibodies specific for the product are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on a given polypeptide may be preferred for some applications, but a competitive binding assay may also be employed. These and other assays are described, among other places, in Hampton, R. et al. (1990; Serological Methods, a Laboratory Manual, APS Press, St Paul. Minn.) and Maddox, D. E. et al. (1983; J. Exp. Med. 158:1211-1216).
A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide. Alternatively, the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits. Suitable reporter molecules or labels, which may be used include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the polypeptide from cell culture. The polypeptide produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides of the invention may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to polynucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.). The inclusion of cleavable linker sequences such as those specific for Factor Xa or enterokinase (Invitrogen. San Diego, Calif.) between the purification domain and the encoded polypeptide may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing a polypeptide of interest and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromatography) as described in Porath, J. et al. (1992, Prot. Exp. Purif. 3:263-281) while the enterokinase cleavage site provides a means for purifying the desired polypeptide from the fusion protein. Further discussion of vectors which comprise fusion proteins can be found in Kroll, D. J. et al. (1993; DNA Cell Biol. 12:441-453).
In addition to recombinant production methods, polypeptides of the invention, and fragments thereof, may be produced by direct peptide synthesis using solid-phase techniques (Merrifield J. (1963) J. Am. Chem. Soc. 85:2149-2154). Polypeptide synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.
According to another aspect, the present invention further provides binding agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to an EBD sequence according to the present invention, or to a portion, variant or derivative thereof. Such binding agents may be used, for example, to detect the presence of a polypeptide comprising an EBD sequence, to facilitate purification of a polypeptide comprising an EBD sequence, and the like. An antibody, or antigen-binding fragment thereof, is said to “specifically bind” to a polypeptide if it reacts at a detectable level (within, for example, an ELISA assay) with the polypeptide, and does not react detectably with unrelated polypeptides under similar conditions.
Antibodies and other binding agents can be prepared using conventional methodologies. For example, monoclonal antibodies specific for a polypeptide of interest may be prepared using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.
Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. The polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
A number of “humanized” antibody molecules comprising an antigen-binding site derived from a non-human immunoglobulin have been described, including chimeric antibodies having rodent V regions and their associated CDRs fused to human constant domains (Winter et al. (1991) Nature 349:293-299; Lobuglio et al. (1989) Proc. Nat. Acad. Sci. USA 86:4220-4224; Shaw et al. (1987) J. Immunol. 138:4534-4538; and Brown et al. (1987) Cancer Res. 47:3577-3583), rodent CDRs grafted into a human supporting FR prior to fusion with an appropriate human antibody constant domain (Riechmann et al. (1988) Nature 332:323-327; Verhoeyen et al. (1988) Science 239:1534-1536; and Jones et al. (1986) Nature 321:522-525), and rodent CDRs supported by recombinantly veneered rodent FRs (European Patent Publication No. 519,596, published Dec. 23, 1992). These “humanized” molecules are designed to minimize unwanted immunological response toward rodent antihuman antibody molecules which limits the duration and effectiveness of therapeutic applications of those moieties in human recipients.
Yet another aspect of the invention provides kits comprising one or more compositions described herein, e.g., an isolated EBD polynucleotide, polypeptide, antibody, vector, host cell, etc. In a particular embodiment, the invention provides a kit containing an expression vector comprising a polynucleotide sequence encoding an EBD polypeptide sequence and a multiple cloning site for easily introducing into the vector a polynucleotide sequence encoding a heterologous polypeptide sequence of interest. In another embodiment, the expression vector further comprises an engineered cleavage site to facilitate separation of the an EBD polypeptide sequence from the hetereologous polypeptide sequence of interest following recombinant production.
The following Examples are offered by way of illustration and not by way of limitation.

EXAMPLES

Example 1

Use of Neurofilament Triplet M Protein (NF-M) in an Entropic Bristle Domain Vector

The heterogeneity in the charge distribution of the human NF-M protein sequence was determined (shown below). The observed heterogeneity of the sequence suggests that EBDs with different characteristics may result for different regions of the sequence. For example, a 422-600 fragment is predominantly negatively charged. This fragment could be used as a basis to design EBDs for negatively charged proteins. The charge distribution in the 601-916 fragment is very heterogeneous. It can be used as a basis to design EBDs both for positively- and negatively-charged proteins.
Cloning of EBD sequence: We obtained the full-length cDNA for human NF-M from Origene Technologies (Rockville, Md.) and cloned the coding region for a 494-residue EBD sequence (residues 422 to 916 of the NF-M protein) into a pMALc2E vector from which the maltose-binding protein coding region had been deleted. (See FIG. 1.) Restriction sites suitable for cloning the test proteins were engineered at the appropriate locations. The proximity of the start codon in the cloned target sequences to the Shine Delgarno sequence of the vector was the same as that in pMALc2E. This construct is referred to as pEBDM.
Preparation of heterologous sequence: The coding region of a heterologous sequence of interest may be examined for rare E. Coli codons and restrictions sites for a suitable cloning strategy. Prior to cloning, incompatible codons and restriction sites may be altered by site directed mutagenesis. The heterologous protein coding region, not including the stop codon, is PCR-amplified using primers containing the relevant restriction sites for the 5′ and the 3′ ends of the test protein open reading frame respectively.
Assembly of EBD expression vector: The PCR-amplified open reading frame of the heterologous polypeptide sequence of interest is ligated into the pEBDM vector backbone following digestion with appropriate restriction enzymes. In addition to cloning the heterologous sequence into an EBD expression vector, the test proteins may be cloned, for example, into an MBP expression vector (e.g., pMAL™-c2E, which already contains a maltose-binding protein coding region) as well as a control vector. The pMAL™-c2E serves as a positive control. To construct the control vector backbone, a KpnI site is added to pMAL™-c2E at base 1524 by site-directed mutagenesis of 4 bases. This allows excision of the MBP coding region (including the start codon) by KpnI digestion and re-ligation.
Protein expression and solubility analysis are carried out essentially according to the procedures of Kapust and Waugh. Briefly, the construct is transformed into E. Coli BL21/DE3 cells (Stratagene, LaJolla, Calif.). This cell line provides increased protein stability due to its deficiency in both the OmpT and Lon proteases. The transformed cells are grown at 37° C. with shaking in LB broth supplemented with the appropriate antibiotics, diluted 50 fold, and grown to an OD₆₀₀of 0.6 before induction. Recombinant protein productions is induced by adding IPTG to a final concentration of 1 mM, grown for more 3 hours, and harvested by centrifugation. The pellets are resuspended in 0.1 volume of lysis buffer and sonicated to disrupt cells. A sample of this crude lysate is reserved and used for total protein analyses. After the crude lysate is cleared by centrifugation, a sample of the cleared lysate will be used for soluble protein analyses. These samples are run on SDS-PAGE gels using standard procedures and visualized by Coomassie staining. The non-degraded soluble recombinant protein is apparent as a heavy band of the appropriate size.
The stained gels are scanned using an Epson Perfection 3200 scanner (Epson, Long Beach, Calif.) and the density of the protein bands is quantified using Total Lab image analysis software (Nonlinear Dynamics, Newcastle upon Tyne, UK). The densities of the bands corresponding to the fusion protein are normalized by dividing by the combined density of all the E. coli proteins larger than the largest fusion protein. Percent solubility is calculated by dividing the normalized density of the fusion protein band in the cleared lysate (soluble protein) lane by the normalized density of the fusion protein band in the crude lysate (total protein) protein lane after subtracting the normalized background density obtained from lanes containing equivalent protein extracts from E. Coli cells grown with an empty vector. Mean and standard deviation are calculated for at least three independent experiments.

Claims

1. An isolated fusion polypeptide comprising at least one entropic bristle domain (EBD) sequence and at least one heterologous polypeptide sequence, wherein the fusion polypeptide has increased solubility relative to the heterologous polypeptide sequence, reduced aggregation relative to the heterologous polypeptide sequence and/or improved folding relative to the heterologous polypeptide sequence.

2. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mammalian neurofilament protein.

3. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mammalian neurofilament NF-H protein.

4. The polypeptide according to claim 1, wherein the EBD sequence is derived from a human neurofilament NF-H protein having a sequence set forth in SEQ ID NO: 1 or 3.

5. The polypeptide according to claim 1, wherein the EBD sequence comprises a neurofilament NF-H sequence selected from the group consisting of SPEAEK (SEQ ID NO:23), SPAAVK (SEQ ID NO:24), SPAEAK (SEQ ID NO:25), SPAEPK (SEQ ID NO:26), SPAEVK (SEQ ID NO:27), SPATVK (SEQ ID NO:28), SPEKAK (SEQ ID NO:29), SPGEAK (SEQ ID NO:30), SPIEVK (SEQ ID NO:31), SPPEAK (SEQ ID NO:32), SPSEAK (SEQ ID NO:33), SPEKEAK (SEQ ID NO:34), SPAKEKAK (SEQ ID NO:35), SPEKEEAK (SEQ ID NO:36), SPTKEEAK (SEQ ID NO:37), SPVKEEAK (SEQ ID NO:38), SPVKAEAK (SEQ ID NO:39), SPVKEEAK (SEQ ID NO:40), SPVKEEVK (SEQ ID NO:41), SPVKEEEKP (SEQ ID NO:42), SPEKAKTLDVK (SEQ ID NO:43), SPADKFPEKAK (SEQ ID NO:44), SPEAKTPAKEEAR (SEQ ID NO:45), SPEKAKTPVKEGAK (SEQ ID NO:46), SPVKEEAKTPEKAK (SEQ ID NO:47), SPVKEGAKPPEKAKPLDVK (SEQ ID NO:48), SPVKEDIKPPAEAKSPEKAK (SEQ ID NO:49), SPLKEDAKAPEKEIPKKEEVK (SEQ ID NO:50), SPEKEEAKTSEKVAPKKEEVK (SEQ ID NO:51), SPEAQTPVQEEATVPTDIRPPEQVK (SEQ ID NO:52), SPVKEEVKAKEPPKKVEEEKTLPTPKTEAKESKKDE (SEQ ID NO:53), or a combination thereof.

6. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mammalian neurofilament protein NF-M.

7. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mammalian neurofilament NF-M protein having the sequence set forth in any one of SEQ ID NOs: 5, 7, 9, 11, 13 or 15.

8. The polypeptide according to claim 1, wherein the EBD sequence comprises a neurofilament NF-M sequence selected from the group consisting of SPPK (SEQ ID NO:54), SPVK (SEQ ID NO:55), SPAAK (SEQ ID NO:56), SPAPK (SEQ ID NO:57), SPEAK (SEQ ID NO:58), SPMPK (SEQ ID NO:59), SPPAK (SEQ ID NO:60), SPTAK (SEQ ID NO:61), SPTTK (SEQ ID NO:62), SPVAK (SEQ ID NO:63), SPVAK (SEQ ID NO:64), SPVPK (SEQ ID NO:65), SPVSK (SEQ ID NO:66), SPEKPA (SEQ ID NO:67), SPVEEKAK (SEQ ID NO:68), SPVEEKGK (SEQ ID NO:69), SPVEEVKP (SEQ ID NO:70), SPEKPATPKVT (SEQ ID NO:71), SPEKPRTPEKPA (SEQ ID NO:72), SPEKPTTPEKW (SEQ ID NO:73), SPEKPSSPLKDEKA (SEQ ID NO:74), SPVKEKAVEEMITIT (SEQ ID NO:75), SPVKEEAAEEAATITK (SEQ ID NO:76), SPVPKSPVEEVKPKAEATAG (SEQ ID NO:77), SPVKAESPVKEEVPAKPVKV (SEQ ID NO:78), SPEKEAKEEEKPQEKEKEKEK (SEQ ID NO:79), SPVKATTPEIKEEEGEKEEEGQE (SEQ ID NO:80), SPVEEVKPKPEAKAGKGEQKEE (SEQ ID NO:81), SPEKPATPEKPPTPEKAITPEKVR (SEQ ID NO:82), SPEKPATPEKPRTPEKPATPEKPR (SEQ ID NO:83), SPKEEKVEKKEEKPKDVPKKKAE (SEQ ID NO:84), SPKEEKAEKKEEKPKDVPEKKKAE (SEQ ID NO:85), SPVEEAKSKAEVGKGEQKEEEEKE (SEQ ID NO:86), SPKEEKVEKKEEKPKDVPDKKKAE (SEQ ID NO:87), SPVKEEAVAEVVTITKSVKVHLEKET (SEQ ID NO:88), SSEKDEGEQEEEEGETEAEGEGEEAEAKEEK (SEQ ID NO:89), SPVEEVKPKAEAGAEKGEQKEKVEEEKKEAKE (SEQ ID NO:90), SPVTEQAKAVQKAAAEVGKDQKAEKAAEKAAKEEKAA (SEQ ID NO:91), SPEAKEEEEEGEKEEEEEGQEEEEEEDEGVKSDQAEEGGSEKEG (SEQ ID NO:92), or a combination thereof.

9. The polypeptide according to claim 1, wherein the EBD sequence is derived from a phage sequence.

10. The polypeptide according to claim 1, wherein the EBD sequence is derived from a filamentous phage fd.

11. The polypeptide according to claim 1, wherein the EBD sequence comprises at least one linker region derived from a filamentous phage fd adsorption protein pIII having a sequence set forth in SEQ ID NO: 17.

12. The polypeptide according to claim 1, wherein the EBD sequence comprises a filamentous phage fd adsorption protein pIII sequence selected from the group consisting of EGGGS (SEQ ID NO:93), EGGGT (SEQ ID NO:94), SEGGG (SEQ ID NO:95), GGGSGGG (SEQ ID NO:96), SGGGSGSG (SEQ ID NO:97), and SGGGSEGGG (SEQ ID NO:98), or a combination thereof.

13. The polypeptide according to claim 1, wherein the EBD sequence is derived from a nuclear pore Nup2p protein having a sequence set forth in SEQ ID NO: 19.

14. The polypeptide according to claim 1, wherein the EBD sequence comprises a yeast nucleoporin Nup2p sequence selected from the group consisting of FSFGTSQPNNTPS (SEQ ID NO:99), FSFSIPSKNTPDASKPS (SEQ ID NO:100), FVFGQAAAKPSLEKSS (SEQ ID NO:101), FSFGVPNSSKNETSKPV (SEQ ID NO:102), FTFGTKHAADSQNNKPS (SEQ ID NO:103), FTFGSSALADNKEDVKKP (SEQ ID NO:104), FSFGINTNTTKTADTKAPT (SEQ ID NO:105), FSFGKTTANLPANSSTSPAPSIPSTG (SEQ ID NO:106), FSFGPKKENRKKDESDSENDIEIKGPE (SEQ ID NO:107), FKFSGTVSSDVFKLNPSTDKNEKKTETNAKP (SEQ ID NO:108), FKFSLPFEQKGSQTTTNDSKEESTTEATGNESQ (SEQ ID NO:109), FTFGSTTIEKKNDENSTSNSKPEKSSDSNDSNPS (SEQ ID NO:110), FSFGISNGSESKDSDKPSLPSAVDGENDKKEATKPA (SEQ ID NO:111), FSFSSATSTTEQTKSKNPLSLTEATKTNVDNNSKAEAS (SEQ ID NO:112) and FSFGAATPSAKEASQEDDNNNVEKPSSKPAFNLISNAGTEKEKESKKDSKPA (SEQ ID NO:113), or a combination thereof.

15. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mammalian elastin protein.

16. The polypeptide according to claim 1, wherein the EBD sequence is derived from a mouse elastin protein having a sequence set forth in SEQ ID NO: 21.

17. The polypeptide according to claim 1, wherein the EBD sequence is an elastin sequence selected from the group consisting of VPGA (SEQ ID NO:114), GAGGL (SEQ ID NO:115), GAGGG (SEQ ID NO:116), VPGVG (SEQ ID NO:117), VPGFGAGA (SEQ ID NO:118), VPGALPGA (SEQ ID NO:119), VPGFGAGAG (SEQ ID NO:120), VPAVPGAGG (SEQ ID NO:121), VPGGVGVGG (SEQ ID NO:122), VGAGGFPGYG (SEQ ID NO:123), VPGAVPGGLPGG (SEQ ID NO:124), VSPAAAAKAAKYGAA (SEQ ID NO:125), VPQVGAGIGAGGKPGK (SEQ ID NO:126), VPGGVGVGGIPGGVGVGG (SEQ ID NO:127), VPGGVGGIGGIGGLGVSTGAV (SEQ ID NO:128), VPGGAAGAAAAYKAAAKAGAGLGGVGG (SEQ ID NO:129), VSPAAAAKAAAKAAKYGARGGVGIPTYG (SEQ ID NO:130), KPPKPYGGALGALGYQGGGCFGKSCGRKRK (SEQ ID NO:131), VPGAGTPAAAAAAAAAKAAAKAGLGPGVGG (SEQ ID NO:132), VPGRVAGAAPPAAAAAAAKAAAKAAQYGLG (SEQ ID NO:133), VPGVGLPGVYPGGVLPGTGARFPGVGVLPG (SEQ ID NO:134), VPTGTGVKAKAPGGGGAFSGIPGVGPFGGQQPG (SEQ ID NO:135), VPGGVYYPGAGIGGLGGGGGALGPGGKPPKPGAG (SEQ ID NO:136), VGAGAGLGGASPAAAAAAAKAAKYGAGGAGALGGL (SEQ ID NO:137), GLGGVLGARPFPGGGVAARPGFGLSPIYPGGGAGGLGVGG (SEQ ID NO:138), VPGSLAASKAAKYGAAGGLGGPGGLGGPGGLGGPGGLGGAG (SEQ ID NO:139), VPGGPGVRLPGAGIPGVGGIPGVGGIPGVGGPGIGGPGIVGGPGA (SEQ ID NO:140), VLPGVGGGGIPGGAGAIPGIGGIAGAGTPAAAAAAKAAAKAAKYGAAGGL (SEQ ID NO:141), VPGGVGPGGVTGIGAGPGGLGGAGSPAAAKSAAKAAAKAQYRAAAGLGAG (SEQ ID NO:142), and VPLGYPIKAPKLPGGYGLPYTNGKLPYGVAGAGGKAGYPTGTGVGSQAAAAAAK AAKYGAGGAG (SEQ ID NO:143), or a combination thereof.

18. The polypeptide according to claim 1, wherein the polypeptide further comprises a cleavable linker.

19. An isolated polynucleotide encoding a fusion polypeptide according to claim 1.

20. An expression vector comprising an isolated polynucleotide according to claims 19.

21. A host cell comprising an expression vector according to claim 20.

22. A kit comprising an isolated polynucleotide according to claim 19.

23. A kit comprising an expression vector according to claim 20.

24. A kit comprising a host cell according to claim 21.

25. A method for producing a recombinant protein comprising the steps of: (a) introducing into a host cell a polynucleotide according to claim 19 or an expression vector according to claim 20; and (b) expressing in the host cell a fusion polypeptide comprising at least one EBD sequence and at least one heterologous polypeptide sequence.