Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer

Journal of Chemical Physics

Volumn 110, Issue 23, 1999, Pages 11616-11629

  Takada, Shoji ^a,b   Luthey Schulten, Zaida ^b   Wolynes, Peter G ^b  

^a KOBE UNIVERSITY   (Japan)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOND STRENGTH (CHEMICAL); COMPUTER SIMULATION; CONFORMATIONS; HYDROGEN BONDS; MOLECULAR DYNAMICS; PERMITTIVITY; SOLVENTS;

FOLDING DYNAMICS; HETEROPOLYMERS; PEPTIDES;

PROTEINS;

EID: 0032606941     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.479101     Document Type: Article

References (45)

1. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 84, 7524 (1987).
2. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins: Struct., Funct., Genet. 21, 167 (1995).
3. P. G. Wolynes, Z. Luthey-Schulten, and J. N. Onuchic, Chem. Biol. 3, 425 (1996).
4. B. Nölting, R. Golbik, and A. R. Fersht, Proc. Natl. Acad. Sci. USA 92, 10668 (1995).
5. L. A. Itzhaki, D. E. Otzen, and A. R. Fersht, J. Mol. Biol. 254, 260 (1995).
6. R. M. Ballew, J. Sabelko, and M. Gruebele, Proc. Natl. Acad. Sci. USA 93, 5759 (1996).
7. R. E. Burton, G. S. Huang, M. A. Daugherty, P. W. Fullbright, and T. G. Oas, J. Mol. Biol. 263, 1996 (311).
8. V. Muñoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Nature (London) 390, 196 (1997).
9. W. A. Eaton, P. A. Thompson, C. Chan, S. J. Hagen, and J. Hofrichter, Structure 4, 1996 (1133).
10. S. J. Hagen, J. Hofrichter, A. Szabo, and W. A. Eaton, Proc. Natl. Acad. Sci. USA 93, 11615 (1996).
11. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
12. A. Godzik, A. Kolinski, and J. Skolnick, J. Comput. Chem. 14, 1194 (1993).
13. H. Nymeyer, A. E. Garcia, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA 95, 5921 (1998).
14. G. F. Berriz, A. M. Gutin, and E. I. Shakhnovich, J. Chem. Phys. 106, 9276 (1997).
15. B. M. Pettitt and M. Karplus, Chem. Phys. Lett. 121, 194 (1985).
16. M. Pellegrini, N. Gronbech-Jensen, and S. Doniach, J. Chem. Phys. 104, 8639 (1996).
17. D. Eisenberg and A. D. McLachlan, Nature (London) 319, 199 (1986).
18. N. Go, Annu. Rev. Biophys. Bioeng. 12, 183 1983;
19. H. Abe and N. Gō, Biopolymers 20, 1013 (1980).
20. N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys. 104, 5860 (1996).
21. D. Thirumalai and Z. Guo, Biopolymers 35, 137 (1995);
22. Z. Guo and D. Thirumalai, Biopolymers ibid. 36, 83 (1995).
23. M. Sasai, Proc. Natl. Acad. Sci. USA 92, 8438 (1995).
24. C. Hardin, Z. A. Luthey-Schulten, and P. G. Wolynes, Proteins: Struct. Func., Genet. 34, 281 (1999).
25. B. Honig and A. Yang, Adv. Protein Chem. 46, 27 (1995).
26. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
27. H. A. Scheraga, Macromolecules 10, 1 (1977).
28. For example, CHARMM, B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
29. Z. Guo and D. Thirumalai, J. Mol. Biol. 263, 323 (1996).
30. L. Regan and W. F. DeGrado, Science 241, 976 (1988).
31. See, for example, D. E. Smith and A. D. J. Haymet, J. Chem. Phys. 98, 6445 (1993).
32. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
33. W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983).
34. P. J. Kraulis, Molscript, J. Appl. Crystallogr. 24, 946 (1991).
35. D. S. Riddle, J. V. Santiago, S. T. Bray-Hall, N. Doshi, V. P. Grantcharova, Q. Yi, and D. Baker, Nature, Struct. Biol. 4, 805 (1997);
36. P. G. Wolynes, Nature, Struct. Biol. ibid. , 871 (1997).
37. D. Hamada, S. Segewa, and Y. Goto, Nature, Struct. Biol. 3, 868 (1996).
38. E. M. Boczko and C. L. Brooks III, Science 269, 393 (1995).
39. Z. Guo, C. L. Brooks III, and E. M. Boczko, Proc. Natl. Acad. Sci. USA 94, 10161 (1997).
40. U. H. E. Hansmann, Y. Okamoto, and J. N. Onuchic, Proteins: Struct. Func., Genet. 34, 472 (1999).
41. M. Schaefer, C. Bartels, and M. Karplus, J. Mol. Biol. 284, 835 (1998).
42. M. Mezard, G. Parisi, and M. A. Virasoro, Spin Glass Theory and Beyond (World Scientific, Singapore, 1987).
43. S. Takada and P. G. Wolynes, Phys. Rev. E 55, 4562 (1997).
44. J. J. Portman, S. Takada, and P. G. Wolynes, Phys. Rev. Lett. 81, 5237 (1998).
45. J. N. Onuchic, J. Wang, and P. G. Wolynes, J. Chem. Phys. (in press).