Thoroughly sampling sequence space: Large-scale protein design of structural ensembles

Protein Science

Volumn 11, Issue 12, 2002, Pages 2804-2813

  Larson, Stefan M ^a   England, Jeremy L ^b   Desjarlais, John R ^c   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

^b HARVARD COLLEGE   (United States)

^c Xencor Inc   (United States)

Author keywords

Backbone flexibility; Designability; Distributed computing; Protein design; Sequence space

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENTROPY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; PLIABILITY; PROTEIN CONFORMATION;

PROTEIN;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENTROPY; MODELS, MOLECULAR; PLIABILITY; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEINS;

EID: 0036892389     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0203902     Document Type: Article

References (54)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Baldwin, E.P., Hajiseyedjavadi, O., Baase, W.A., and Matthews, B.W. 1993. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science 262: 1715-1718.
3. Bateman, A., Bimey, E., Durbin, R., Eddy, S.R., Howe, K.L., and Sonnhammer, E.L. 2000. The Pfam protein families database. Nucleic Acids Res. 28: 263-266.
4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein data bank. Nucleic Acids Res. 28: 235-242.
5. Bornscheuer, U.T. and Pohl, M. 2001. Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5: 137-143.
6. Brenner, S.E., Chothia, C., and Hubbard, T.J. 1997. Population statistics of protein structures: Lessons from structural classifications. Curr. Opin. Struct. Biol. 7: 369-376.
7. Buchler, N.E. and Goldstein, R.A. 1999. Effect of alphabet size and foldability requirements on protein structure designability. Proteins 34: 113-124.
8. Cedrone, F., Menez, A., and Quemeneur, E. 2000. Tailoring new enzyme functions by rational redesign. Curr. Opin. Struct. Biol. 10: 405-410.
9. Chothia, C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357: 543-544.
10. Dahiyat, B.I. 1999. In silico design for protein stabilization. Curr. Opin. Biotechnol. 10: 387-390.
11. Desjarlais, J.R. and Clarke, N.D. 1998. Computer search algorithms in protein modification and design. Curr. Opin. Struct. Biol. 8: 471-475.
12. Desjarlais, J.R. and Handel, T.M. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci. 4: 2006-2018.
13. -. 1999. Side-chain and backbone flexibility in protein core design. J. Mol. Biol. 290: 305-318.
14. Eisenberg, D. and McLachlan, A.D. 1986. Solvation energy in protein folding and binding. Nature 319: 199-203.
15. Eriksson, A.E., Baase, W.A., Zhang, X.J., Heinz, D.W., Blaber, M., Baldwin, E.P., and Matthews, B.W. 1992. Response of a protein structure to cavitycreating mutations and its relation to the hydrophobic effect. Science 255: 178-183.
16. Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T., and Kim, P.S. 1998. Highresolution protein design with backbone freedom. Science 282: 1462-1467.
17. Helling, R., Li, H., Melin, R., Miller, J., Wingreen, N., Zeng, C., and Tang, C. 2001. The designability of protein structures. J. Mol. Graph. Model 19: 157-167.
18. Henikoff, S. and Henikoff, J.G. 1994. Protein family classification based on searching a database of blocks. Genomics 19: 97-107.
19. Jorgensen, W.L. and Tirado-Rives, J. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110: 1657-1666.
20. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
21. Kazlauskas, R.J. 2000. Molecular modeling and biocatalysis: Explanations, predictions, limitations, and opportunities. Curr. Opin. Chem. Biol. 4: 81-88.
22. Koehl, P. and Delarue, M. 1994. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239: 249-275.
23. Koehl, P. and Levitt, M. 1999a. De novo protein design. I. In search of stability and specificity. J. Mol. Biol. 293: 1161-1181.
24. -. 1999b. De novo protein design. II. Plasticity in sequence space. J. Mol. Biol. 293: 1183-1193
25. -. 2002a. Improved recognition of native-like protein structures using a family of designed sequences. Proc. Natl. Acad. Sci. 99: 691-696.
26. -. 2002b. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. 99: 1280-1285.
27. Kono, H. and Saven, J.G. 2001. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J. Mol. Biol. 306: 607-628.
28. Kuhlman, B. and Baker, D. 2000. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. 97: 10383-10388.
29. Larson, S.M., Di Nardo, A.A., and Davidson, A.R. 2000. Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303: 433-446.
30. Lee, C. 1994. Predicting protein mutant energetics by self-consistent ensemble optimization. J. Mol. Biol. 236: 918-939.
31. Li, H., Helling, R., Tang, C., and Wingreen, N. 1996. Emergence of preferred structures in a simple model of protein folding. Science 273: 666-669.
32. Li, H., Tang, C., and Wingreen, N.S. 1998. Are protein folds atypical? Proc. Natl. Acad. Sci. 95: 4987-4990.
33. Madej, T., Gibrat, J.F., and Bryant, S.H. 1995. Threading a database of protein cores. Proteins 23: 356-369.
34. Malakauskas, S.M. and Mayo, S.L. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5: 470-475.
35. Miller, J., Zeng, C., Wingreen, N.S., and Tang, C. 2002. Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins. 47: 506-512.
36. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995, SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
37. Musacchio, A., Saraste, M., and Wilmanns, M. 1994. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nat. Struct. Biol. 1: 546-551.
38. Orengo, C.A., Jones, D.T., and Thornton, J.M. 1994. Protein superfamilies and domain superfolds. Nature 372: 631-634.
39. Pabo, C. 1983. Molecular technology. Designing proteins and peptides. Nature 301: 200.
40. Pande, V.S., Grosberg, A.Y., and Tanaka, T. 1997. Statistical mechanics of simple models of protein folding and design. Biophys J. 73: 3192-3210.
41. Plaxco. K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
42. Pokala, N. and Handel, T.M. 2001. Review: Protein design - Where we were, where we are, where we're going. J. Struct. Biol. 134: 269-281.
43. Raha, K., Wollacott, A.M., Italia, M.J., and Desjarlais, J.R. 2000. Prediction of amino acid sequence from structure. Protein Sci. 9:1106-1119.
44. Shakhnovich, E.I. 1998. Protein design: A perspective from simple tractable models. Fold, Des. 3: R45-R58.
45. Shenkin, P.S., Erman, B., and Mastrandrea, L.D. 1991. Information-theoretical entropy as a measure of sequence variability. Proteins 11:297-313.
46. Shirts, M. and Pande, V.S. 2000. COMPUTING: Screen savers of the world unite! Science 290; 1903-1904.
47. Su, A. and Mayo, S.L. 1997. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6: 1701-1707.
48. Tobin, M.B., Gustafsson, C., and Huisman, G.W. 2000. Directed evolution: The "rational" basis for "irrational" design. Curr. Opin. Struct. Biol. 10: 421-427.
49. Voigt, C.A., Gordon, D.B., and Mayo, S.L. 2000. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol. 299: 789-803.
50. Voigt, C.A., Mayo, S.L., Arnold, F.H., and Wang, Z.G. 2001. Computational method to reduce the search space for directed protein evolution. Proc. Natl. Acad. Sci. 98; 3778-3783.
51. Wang, Y., Addess, K.J., Geer, L., Madej, T., Marchler-Bauer, A., Zimmerman, D., and Bryant, S.H. 2000. MMDB: 3D structure data in Entrez. Nucleic Acids Res. 28: 243-245.
52. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., and Weiner, P. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106: 765-784.
53. Wernisch, L., Hery S., and Wodak, S.J. 2000. Automatic protein design with all atom force-fields by exact and heuristic optimization. J. Mol. Biol. 301; 713-736.
54. Zou, J. and Saven, J.G. 2000. Statistical theory of combinatorial libraries of folding proteins: Energetic discrimination of a target structure. J. Mol. Biol. 296: 281-294.