Phage-display as a tool for quantifying protein stability determinants

European Journal of Biochemistry

Volumn 271, Issue 9, 2004, Pages 1623-1629

  Kotz, Joanne D ^a   Bond, Christopher J ^b   Cochran, Andrea G ^a,b  

^a Department of Protein Engineering ^*  (United States)

^b GENENTECH INC   (United States)

Author keywords

Beta sheet; Hydrophobic core; Phage display; Protein G; Protein stability

Indexed keywords

BETA SHEET; COMBINATORIAL CHEMISTRY; COMPUTER MODEL; DNA SEQUENCE; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SHORT SURVEY; STATISTICAL ANALYSIS; WILD TYPE;

BACTERIAL PROTEINS; COMPLEMENTARITY DETERMINING REGIONS; IMMUNOGLOBULIN HEAVY CHAINS; PEPTIDE LIBRARY; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

CAMELIDAE;

EID: 2342627978     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04076.x     Document Type: Short Survey

References (34)

1. Hoess, R.H. (2001) Protein design and phage display. Chem. Rev. 101, 3205-3218.
2. Forrer, P., Jung, S. & Plückthun, A. (1999) Beyond binding: Using phage display to select for structure, folding and enzymatic activity in proteins. Curr. Opin. Struct. Biol. 9, 514-520.
3. O'Neil, K.T., Hoess, R.H., Raleigh, D.P. & DeGrado, W.F. (1995) Thermodynamic genetics of the folding of the B1 immunoglobulin-binding domain from Streptococcal protein G. Proteins 21, 11-21.
4. Gu, H., Yi, Q., Bray, S.T., Riddle, D.S., Shiau, A.K. & Baker, D. (1995) A phage display system for studying the sequence determinants of protein folding. Protein Sci. 4, 1108-1117.
5. Sidhu, S.S., Lowman, H.B. & Wells, J.A. (2000) Phage display for selection of novel binding peptides. Methods Enzymol. 328, 333-363.
6. Sieber, V., Plückthun, A. & Schmid, F.X. (1998) Selecting proteins with improved stability by phage-based methods. Nat. Biotechnol. 16, 955-960.
7. Zhou, H.X., Hoess, R.H. & DeGrado, W.F. (1996) In vitro evolution of thermodynamically stable turns. Nat. Struct. Biol. 3, 446-451.
8. Jung, S., Honegger, A. & Plückthun, A. (1999) Selection for improved protein stability by phage display. J. Mol. Biol. 294, 163-180.
9. Martin, A., Sieber, V. & Schmid, F.X. (2001) In-vitro selection of highly stabilized protein variants with optimized surface. J. Mol. Biol. 309, 717-726.
10. Bai, Y. & Feng, H. (2004) Selection of stably folded proteins by phage-display with proteolysis. Eur. J. Biochem. 271, 1609-1614.
11. Dahiyat, B.I. & Mayo, S.L. (1997) Probing the role of packing specificity in protein design. Proc. Natl Acad. Sci. USA 94, 10172-10177.
12. Malakauskas, S.M. & Mayo, S.L. (1998) Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5, 470-475.
13. Ross, S.A., Sarisky, C.A., Su, A. & Mayo, S.L. (2001) Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification. Protein Sci. 10, 450-454.
14. Su, A. & Mayo, S.L. (1997) Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6, 1701-1707.
15. HH domain stability and the design of mono-body scaffolds for naive antibody libraries. J. Mol. Biol. 332, 643-655.
16. Distefano, M.D., Zhong, A. & Cochran, A.G. (2002) Quantifying β-sheet stability by phage display. J. Mol. Biol. 322, 179-188.
17. Dahiyat, B.I. & Mayo, S.L. (1996) Protein design automation. Protein Sci. 5, 895-903.
18. Weiss, G.A., Watanabe, C.K., Zhong, A., Goddard, A. & Sidhu, S.S. (2000) Rapid mapping of protein functional epitopes by combinatorial alanine scanning. Proc. Natl Acad. Sci. USA 97, 8950-8954.
19. Vajdos, F.F., Adams, C.W., Breece, T.N., Presta, L.G., de Vos, A.M. & Sidhu, S.S. (2002) Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J. Mol. Biol. 320, 415-428.
20. Morrison, K.L. & Weiss, G.A. (2001) Combinatorial alanine-scanning. Curr. Opin. Chem. Biol. 5, 302-307.
21. Smith, C.K. & Regan, L. (1995) Guidelines for protein design: The energetics of β-sheet side chain interactions. Science 270, 980-982.
22. Smith, C.K., Withka, J.M. & Regan, L. (1994) A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33, 5510-5517.
23. Minor, D.L. Jr & Kim, P.S. (1994) Context is a major determinant of β-sheet propensity. Nature 371, 264-267.
24. Minor, D.L. Jr & Kim, P.S. (1994) Measurement of the β-sheet-forming propensities of amino acids. Nature 367, 660-663.
25. Lifson, S. & Sander, C. (1980) Specific recognition in the tertiary structure of β-sheets of proteins. J. Mol. Biol. 139, 627-639.
26. Wouters, M.A. & Curmi, P.M.G. (1995) An analysis of side-chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and non-hydrogen bonded pairs. Proteins: Struct. Funct. Genet. 22, 119-131.
27. Hutchinson, E.G., Sessions, R.B., Thornton, J.M. & Woolfson, D.N. (1998) Determinants of strand register in antiparallel β-sheets of proteins. Protein Sci. 7, 2287-2300.
28. Ruan, B., Hoskins, J., Wang, L. & Bryan, P.N. (1998) Stabilizing the subtilisin BPN′ pro-domain by phage display selection: How restrictive is the amino acid code for maximum protein stability? Protein Sci. 7, 2345-2353.
29. Merkel, J.S., Sturtevant, J.M. & Regan, L. (1999) Sidechain interactions in parallel β-sheets: The energetics of cross-strand pairings. Structure 7, 1333-1343.
30. Lassila, K.S., Datta, D. & Mayo, S.L. (2002) Evaluation of the energetic contribution of an ionic network to beta-sheet stability. Protein Sci. 11, 688-690.
31. Lahr, S.J., Broadwater, A., Carter, C.W. Jr, Collier, M.L., Hensley, L., Waldner, J.C., Pielak, G.J. & Edgell, M.H. (1999) Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure. Proc. Natl Acad. Sci. USA 96, 14860-14865.
32. Sauer, R.T. (1996) Protein folding from a combinatorial perspective. Fold. Des. 1, R27-R30.
33. Gronenborn, A.M., Filpula, D.R., Essig, N.Z., Achari, A., Whitlow, M., Wingfield, P.T. & Clore, G.M. (1991) A novel, highly stable fold of the immunoglobulin binding domain of Streptococcal protein G. Science 253, 657-661.
34. Graille, M., Stura, E.A., Corper, A.L., Sutton, B.J., Taussig, M.J., Charbonnier, J.-B. & Silverman, G.J. (2000) Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity. Proc. Natl Acad. Sci. USA 97, 5399-5404.