Quantifying β-sheet stability by phage display

Journal of Molecular Biology

Volumn 322, Issue 1, 2002, Pages 179-188

  Distefano, Mark D ^a,b   Zhong, Alan ^b   Cochran, Andrea G ^b  

^a University of Minnesota   (United States)

^b GENENTECH INC   (United States)

Author keywords

Combinatorial mutagenesis; Phage display; Protein stability; Side chain interactions; sheet propensity

Indexed keywords

ALANINE;

ARTICLE; BETA SHEET; ENERGY; METHODOLOGY; MUTATIONAL ANALYSIS; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; SEQUENCE ANALYSIS; THERMOSTABILITY;

EID: 0036970470     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00738-6     Document Type: Article

References (42)

1. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34, 167-339.
2. Salemme, F. R. (1983). Structural properties of protein β-sheets. Prog. Biophys. Mol. Biol. 42, 95-133.
3. Smith, C. K. & Regan, L. (1997). Construction and design of β-sheets. Accts Chem. Res. 30, 153-161.
4. Gellman, S. H. (1998). Minimal model systems for β sheet secondary structure in proteins. Curr. Opin. Chem. Biol. 2, 717-725.
5. Lacroix, E., Kortemme, T., Lopez de la Paz, M. & Serrano, L. (1999). The design of linear peptides that fold as monomeric β-sheet structures. Curr. Opin. Struct. Biol. 9, 487-493.
6. Hutchinson, E. G. & Thornton, J. M. (1994). A revised set of potentials for β-turn formation in proteins. Protein Sci. 3, 2207-2216.
7. Lifson, S. & Sander, C. (1980). Specific recognition in the tertiary structure of β-sheets of proteins. J. Mol. Biol. 139, 627-639.
8. 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.
9. 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.
10. Gunasekaran, K., Ramakrishnan, C. & Balaram, P. (1997). β-Hairpins in proteins revisited: lessons for de novo design. Protein Eng. 10, 1131-1141.
11. Smith, C. K. & Regan, L. (1995). Guidelines for protein design: the energetics of β sheet side-chain interactions. Science, 270, 980-982.
12. Merkel, J. S. & Regan, L. (1998). Aromatic rescue of glycine in β sheets. Fold. Des. 3, 449-455.
13. 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.
14. Blasie, C. A. & Berg, J. M. (1997). Electrostatic interactions across a β-sheet. Biochemistry, 36, 6218-6222.
15. Russell, S. J. & Cochran, A. G. (2000). Designing stable β-hairpins: energetic contributions from cross-strand residues. J. Am. Chem. Soc. 122, 12600-12601.
16. Zaremba, S. M. & Gregoret, L. M. (1999). Context-dependence of amino acid residue pairing in anti-parallel β-sheets. J. Mol. Biol. 291, 463-479.
17. Merkel, J. S. & Regan, L. (2000). Modulating protein folding rates in vivo and in vitro by side-chain interactions between the parallel β strands of green fluorescent protein. J. Biol. Chem. 275, 29200-29206.
18. 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.
19. Woolfson, D. N. (2001). Core-directed protein design. Curr. Opin. Struct. Biol. 11, 464-471.
20. Sidhu, S. S., Lowman, H. B., Cunningham, B. C. & Wells, J. A. (2000). Phage display for selection of novel binding peptides. Methods Enzymol. 328, 333-363.
21. 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.
22. Morrison, K. L. & Weiss, G. A. (2001). Combinatorial alanine scanning. Curr. Opin. Chem. Biol. 5, 302-307.
23. Vajdos, F. F., Adams, C. A., 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.
24. 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.
25. Zhou, H. X., Hoess, R. H. & DeGrado, W. F. (1996). In vitro evolution of thermodynamically stable turns. Nature Struct. Biol. 3, 446-450.
26. Sauer-Eriksson, A. E., Kleywegt, G. J., Uhlen, M. & Jones, T. A. (1995). Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure, 3, 265-278.
27. Minor, D. L., Jr & Kim, P. S. (1994). Measurement of the β-sheet-forming propensities of the amino acids. Nature, 367, 660-663.
28. Minor, D. L., Jr & Kim, P. S. (1994). Context is a major determinant of β-sheet propensity. Nature, 371, 264-267.
29. Wells, J. A. (1990). Additivity of mutational effects in proteins. Biochemistry, 29, 8509-8517.
30. Mandel-Gutfreund, Y., Zaremba, S. M. & Gregoret, L. M. (2001). Contributions of residue pairing to β-sheet formation: covariation of amino acid residue pairs on antiparallel β-strands. J. Mol. Biol. 305, 1145-1159.
31. Kim, C. A. & Berg, J. M. (1993). Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature, 362, 267-270.
32. Chothia, C. (1983). Coiling of β-pleated sheets. J. Mol. Biol. 163, 107-117.
33. Muñoz, V. & Serrano, L. (1994). Intrinsic secondary structure propensities of the amino acids, using statistical φ-ψ matrices: comparison with experimental scales. Proteins: Struct. Funct. Genet. 20, 301-311.
34. Bai, Y. & Englander, S. W. (1994). Hydrogen bond strength and β-sheet propensities: the role of a side-chain blocking effect. Proteins: Struct. Funct. Genet. 18, 262-266.
35. Avbelj, F. & Baldwin, R. L. (2002). Role of backbone solvation in determining thermodynamic β-propensities of the amino acids. Proc. Natl Acad. Sci. USA, 99, 1309-1313.
36. Street, A. G. & Mayo, S. L. (1999). Intrinsic β-sheet propensities result from van der Waals interactions between side-chains and the local backbone. Proc. Natl Acad. Sci. USA, 96, 9074-9076.
37. Otzen, D. E. & Fersht, A. R. (1995). Side-chain determinants of β-sheet stability. Biochemistry, 34, 5718-5724.
38. McCallister, E. L., Alm, E. & Baker, D. (2000). Critical role of β-hairpin formation in protein G folding. Nature Struct. Biol. 7, 669-673.
39. Kim, D. E., Gu, H. & Baker, D. (1998). The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proc. Natl Acad. Sci. USA, 95, 4982-4986.
40. 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: Struct. Funct. Genet. 21, 11-21.
41. Deshayes, K., Schaffer, M., Skelton, N. J., Nakamura, G., Kadkhodayan, S. & Sidhu, S. S. (2002). Rapid identification of small binding motifs with high-throughput phage display: the discovery of peptidic antagonists of IGF-1 function. Chem. Biol. 9, 495-505.
42. 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.