Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 9, 2006, Pages 3141-3146

  Chikenji, George ^a,b   Fujitsuka, Yoshimi ^a   Takada, Shoji ^a,c  

^a KOBE UNIVERSITY   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Computational protein design; Energy landscape; Fragment assembly; G model; SIMFOLD

Indexed keywords

CHIMERIC PROTEIN;

ARTICLE; CALCULATION; CHIMERA; COMPUTER PREDICTION; ENERGY; FRAGMENT ASSEMBLY METHOD; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 33644760365     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0508195103     Document Type: Article

References (59)

1. Fersht, A. R. (1999) Structure- and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (Freeman, New York).
2. Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225.
3. Jones, T. A. & Thirup, S. (1986) EMBO J. 5, 819-822.
4. Levitt, M. (1992) J. Mol. Biol. 226, 507-533.
5. Bowie, J. U. & Eisenberg, D. (1994) Proc. Natl. Acad. Sci. USA 91, 4436-4440.
6. Jones, D. T. (1997) Proteins 29, 185-191.
7. Bradley, P., Chivian, D., Meiler, J., Misura, K. M. S., Rohl, C. A., Schief, W. R., Wedemeyer, W. J., Schueler-Furman, O., Murphy, P., Strauss, J., et al. (2003) Proteins 53, 457-468.
8. Jones, D. T. & McGuffin, L. J. (2003) Proteins 53, 480-485.
9. Fang, Q. & Shortle, D. (2003) Proteins 53, 486-490.
10. Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M. & Hughey, R. (2003) Proteins 53, 491-496.
11. Shao, Y. & Bystroff, C. (2003) Proteins 53, 497-502.
12. Bonneau, R. & Baker, D. (2001) Anna. Rev. Biophys. Biomol. Struct. 30, 173-189.
13. Rohl, C., C. E. M. Strauss, K. M. S. Misura & Baker, D. (2004) Methods Enzymol. 383, 66-93.
14. Bryngelson, J. D., Onuchic, J. N., Socci, N. D. & Wolynes, P. G. (1995) Proteins 21, 167-195.
15. Onuchic, J. N. & Wolynes, P. G. (2004) Curr. Opin. Struct. Biol. 14, 70-75.
16. Takada, S., Luthey-Schulten, Z. A. & Wolynes, P. G. (1999) J. Chem. Phys. 110, 11616-11629.
17. Fujitsuka, Y., Takada, S., Luthey-Schulten, Z. A. & Wolynes, P. G. (2004) Proteins 54, 88-103.
18. Chikenji, G., Fujitsuka, Y. & Takada, S. (2003) J. Chem. Phys. 119, 6895-6903.
19. Chikenji, G., Fujitsuka, Y. & Takada, S. (2004) Chem. Phys. 307, 157-162.
20. Blanco, F. J., Rivas, G. & Serrano, L. (1994) Nat. Struct. Biol. 1, 584-590.
21. Yi, Q., Bystroff, C., Rajagopal, P., Klevit, R. E. & Baker, D. (1998) Protein Sci. 283, 293-300.
22. Rotondi, K. S. & Gierasch, L. M. (2003) Biochemistry 42, 7976-7985.
23. Honda, S., Yamasaki, K., Sawada, Y. & Morii, H. (2004) Structure (London) 12, 1507-1518.
24. Zhou, X., Aleber, F., Folkers, G., Gonnet, G. H. & Chelvanayagam, G. (2000) Proteins 41, 248-256.
25. Wang, Y. & Shortle, D. (1997) Folding Des. 2, 93-100.
26. Nakajima, N., Higo, J., Kidera, A. & Nakamura, H. (2000) J. Mol. Biol. 296, 197-216.
27. Higo, J., Ito, N., Kuroda, M., Ono, S., Nakajima, N. & Nakamura, H. (2001) Protein Sci. 10, 1160-1171.
28. Lau, K. F. & Dill, K. A. (1989) Macromolecules 22, 3986-3997.
29. Li, H., Helling, R., Tang, C. & Wingreen, N. (1996) Science 273, 666-669.
30. Wolynes, P. G. (1997) Nat. Struct. Biol. 4, 871-874.
31. Dill, K. A. (1990) Biochemistry 29, 7133-7155.
32. Thomas, P. D. & Dill, K. A. (1993) Protein Sci. 2, 2050-2065.
33. Irbäck, A. & Sandelin, E. (1998) J. Chem. Phys. 108, 2245-2250.
34. Shoemaker, B. A., Wang, J. & Wolynes, P. G. (1997) Proc. Natl. Acad. Sci. USA 94, 777-782.
35. Portman, J. J., Takada, S. & Wolynes, P. G. (1998) Phys. Rev. Lett. 81, 5237-5240.
36. Galzitskaya, O. V. & Finkelstein, A. V. (1999) Proc. Natl. Acad. Sci. USA 96, 11299-11304.
37. Alm, E. & Baker, D. (1999) Proc. Natl. Acad. Sci. USA 96, 11305-11310.
38. Munoz, V. & Eaton, W. A. (1999) Proc. Natl. Acad. Sci. USA 96, 11311-11316.
39. Clementi, C., Nymeyer, H. & Onuchic, J. N. (2000) J. Mol. Biol. 298, 937-953.
40. Koga, N. & Takada, S. (2001) J. Mol. Biol. 313, 171-180.
41. Karaniclas, J. & Brooks, C. L., III (2003) J. Mol. Biol. 334, 309-325.
42. Gō, N. (1983) Annu. Rev. Biophys. Bioeng. 12, 183-210.
43. Dahiyat, B. I. & Mayo, S. L. (1997) Science 278, 82-87.
44. Walsh, S. T. R., Cheng, H., Bryson, J. W., Roder, H. & DeGrado, W. F. (1999) Proc. Natl. Acad. Sci. USA 96, 5486-5491.
45. Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. & Baker, D. (2003) Science 302, 1364-1868.
46. Shakhnovich, E. I. (1998) Folding Des. 3, R45-R58.
47. Jin, W., Kambara, O., Sasakawa, H., Tamura, A. & Takada, S. (2003) Structure (London) 11, 581-590.
48. Smith, L. J., Fiehig, K. M., Schwalbe H. & Dobson, C. M. (1996) Folding Des. 1, R95-R106.
49. Hammarström, P. & Carlsson, U. (2000) Biochem. Biophys. Res. Commun. 276, 393-398.
50. Shortle, D. & Ackerman, M. S. (2001) Science 293, 487-489.
51. Mohana-Borges, R., Goto, N. K., Kroon, G. J., Dyson, H. J. & Wright, P. E. (2004) J. Mol. Biol. 304, 1131-1142.
52. Klimov, D. K., Newfield, D. & Thirumalai, D. (2002) Proc. Natl. Acad. Sci. USA 99, 8019-8024.
53. Zagrovic, B. & Pande, V. S. (2003) Nat. Struct. Biol. 10, 955-961.
54. Jha, A. K., Colubri, A., Freed, K. F. & Sosnick, T. R. (2005) Proc. Natl. Acad. Sci. USA 102, 13099-13104.
55. Chan, H. S. & Dill, K. A. (1990) Proc. Natl. Acad. Sci. USA 87, 6388-6392.
56. Pietrokovski, S. (1996) Nucleic Acids Res. 24, 3836-3845.
57. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
58. Shortle, D., Simons, K. T. & Baker, D. (1998) Proc. Natl. Acad. Sci. USA 95, 11158-11162.
59. Kraulis, P. (1991) J. Appl. Crystallogr. 24, 946-950.