Exploring the interplay between topology and secondary structural formation in the protein folding problem

Journal of Physical Chemistry B

Volumn 107, Issue 40, 2003, Pages 11193-11200

  Cheung, Margaret S ^a   Finke, John M ^a   Callahan, Benjamin ^b   Onuchic, José N ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; HAMILTONIANS; HYDROGEN BONDS; MATHEMATICAL MODELS; TOPOLOGY;

CHYMOTRYPSIN INHIBITOR; PROTEIN FOLDING;

PROTEINS;

EID: 0242368163     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp034441r     Document Type: Article

References (61)

1. Onuchic, J. N. H.; Nymeyer, H.; García, A. E.; Chahine, J.; Socci, N. D. Adv. Protein Chem. 2000, 54, 87-153.
2. Bryngelson, J. D.; Wolynes, P. G. Proc. Natl Acad. Sci. U.S.A. 1987, 84, 7524-7528.
3. Scheraga, H. A. Protein Sci. 1992, 1, 691.
4. Dill, K. A.; Chan, H. S. Nature Struct. Biol. 1997, 4, 10-19.
5. Eaton, W. A.; Munoz, V.; Thompson, P.; Chan, C. K.; Hofrichter, J. Curr. Opin. Struct. Biol. 1997, 7, 10-14.
6. Telford, J. R.; Wittung-Stafshede, P.; Gray, H. B.; Winkler, J. R. Acc. Chem. Res. 1998, 31, 755-763.
7. Gruebele, M. Annu. Rev. Phys. Chem. 1999, 50, 485-516.
8. Shea, J.-E.; Brooks, C. L.; Onuchic, J. N. Annu. Rev. Phys. Chem. 2001, 52, 499-535.
9. Dokholyan, N. V.; Li, L.; Ding, F.; Shakhnovich, E. I. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 8637-8641.
10. Myers, J. K.; Oas, T. G. Annu. Rev. Biochem. 2002, 71, 783-815.
11. Leopold, P. E.; Montal, M.; Onuchic, J. N. Proc. Natl Acad. Sci. U.S.A. 1992, 89, 8721-8725.
12. Jackson, S. E.; el Masry, N.; Fersht, A. R. Biochemistry 1993, 32, 2, 11270-11278.
13. Martinez, J. C.; Serrano, L. Nature Struct. Biol. 1999, 6, 1010-1016.
14. Riddle, D. S.; Grantcharova, V. P.; Santiago, J. V.; Alm, E.; Ruczinski, I.; Baker, D. Nature Struct. Biol. 1999, 6, 1016-1024.
15. Plaxco, K. W.; Simons, K. T.; Baker, D. J. Mol. Biol. 1998, 277, 985-994.
16. Onuchic, J. N.; Wolynes, P. G.; Luthey-Schulten, Z. A.; Socci, N. D. Proc. Natl Acad. Sci. U.S.A. 1995, 92, 3626-3630.
17. Levitt, M.; Warshel, A. Nature 1975, 253, 694-698.
18. Friedrichs, M. S.; Goldstein, R. A.; Wolynes, P. G. J. Mol. Biol. 1991, 222 (4), 1013-1034.
19. Irbäck, A.; Potthast, F. J. Chem. Phys. 1995, 103, 10298-10305.
20. Guo, Z.; Thirumalai, D.; Honeycutt, J. D. J. Chem. Phys. 1992, 97 (1), 525-535.
21. Berry, R. S.; Elmaci, N.; Rose, J. P.; Vekhter, B. Proc. Natl Acad. Sci. U.S.A. 1997, 94, 9520-9524.
22. Guo, Z.; Brooks, C. L. Biopolymers 1997, 42, 745-757.
23. Nymeyer, H.; García, A. E.; Onuchic, J. N. Proc. Natl Acad. Sci. U.S.A. 1998, 95, 5921-5928.
24. Shea, J.-E.; Onuchic, J. N.; Brooks, C. L. J. Chem. Phys. 2000, 113, 7663-7671.
25. Berriz, G. F.; Shakhnovich, E. I. J. Mol. Biol. 2001, 310, 673-685.
26. Karanicolas, J.; Brooks, C. L. Protein Sci. 2002, 11, 2351-2361.
27. Clementi, C.; Nymeyer, H.; Onuchic, J. N. J. Mol. Biol. 2000, 298, 937-953.
28. Clementi, C.; Jennings, P. A.; Onuchic, J. N. J. Mol. Biol. 2001, 311, 879-890.
29. Koga, N.; Takada, S. J. Mol. Biol. 2001, 313, 171-180.
30. Cheung, M. S.; García, A. E.; Onuchic, J. N. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 685-690.
31. Lim, W. A.; Sauer, R. T. Nature 1989, 339, 31-36.
32. Sandberg, W. S.; Terwilliger, T. C. Science 1989, 245, 54-57.
33. Dahiyat, B. I.; Mayo, S. L. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10172-10177.
34. Gonzalez, L., Jr.; Plecs, J. J.; Alber, T. Nature Struct. Biol. 1996, 3, 510-515.
35. Walsh, S. T. R.; Sukharev, V. I.; Betz, S. T.; Vekshin, N. L.; DeGrado, W. F. J. Mol. Biol. 2001, 305, 361-373.
36. Mittermaier, A.; Varani L.; Muhandiram, D. R.; Kay, L. E.; Varani, G. J. Mol. Biol. 1999, 294, 967-979.
37. Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nature Struct. Biol. 2000, 7, 72-77.
38. Vieth, M.; Kolinski, A.; Brooks, C. L.; Skolnick, J. J. Mol. Biol. 1995, 251, 448-467.
39. Takada, S.; Luthey-Schulten, Z.; Wolynes, P. G. J. Chem. Phys. 1999, 110, 11616-11629.
40. Klimov, D. K.; Thirumalai, D. Proc. Natl. Acad. U.S.A. 2000, 97, 2544-2549.
41. Irbäck, A.; Sjunnesson, F.; Wallin, S. Proc. Natl Acad. Sci. U.S.A. 2000, 97, 13614-13618.
42. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323-2347.
43. Guo, C.; Cheung, M. S.; Levine, H.; Kessler, D. A. J. Chem. Phys. 2002, 116, 4353-4365.
44. Ding, F.; Dokholyan, N. V.; Buldyrev, S. V.; Stanley, H. E.; Shakhnovich, E. I. Biophys. J. 2002, 83, 3525-3532.
45. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2001, 115, 1414-1421.
46. Cordier, F.; Wang, C.; Grzesiek, S.; Nicholson, L. K. J. Mol. Biol. 2000, 304, 497-505.
47. Krantz, B. A.; Srivastrava, A. K.; Nauli, S.; Baker, D.; Sauer, R. T.; Sosnick, T. R. Nature Struct. Biol. 2002, 9, 458-463.
48. Leach, A. R. In Molecular modelling: principles and applications; Longman: Harlow, U.K., 1996.
49. Go, N. J. Stat. Phys. 1983, 30 (2), 413-423.
50. Amber6. Case, D. A.; Pearlman, D.; Caldwell, J. W.; T. E. Cheatam, I.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; et al. ALC Press: Lake Oswegoo, OR, 1999.
51. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81 (8), 3684-3690.
52. Ferrenberg, A. M.; Swendsen, R. H. Phys. Rev. Lett. 1988, 61, 2635-2638.
53. Kumar, S.; Bouzida, D.; Swendsen, R. H. Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13 (8), 1011-1021.
54. Plotkin, S. S.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6509-6514.
55. Hardin, C.; Luthey-Schulten Z.; Wolynes, P. G. Proteins 1999, 34, 281-294.
56. Klimov, D. K.; Betancourt, M. R.; Thirumalai, D. Fold. Des. 1998, 3, 481-496.
57. Ilkowski, B.; Skolnick, J.; Kolinski, A. Macromol. Theory. Simul. 2000, 9, 523-533.
58. Fernández, A.; Scheraga, H. A. Proc. Natl Acad. Sci. U.S.A. 2003, 100 (1), 113-118.
59. Kuwata, K.; Shastry, R.; Cheng, H.; Hoshino, M.; Batt, C. A.; Goto, Y.; Roder, H. Nature Struct. Biol. 2001, 8, 151-155.
60. i-1,i+4,i+5) is 0.465999 (rad).
61. The route number, R(Q) = <σ>/Q(1 -Q), where σ is the distribution (variance) of probabilities of the contact formation for each native contact, and