Simulation of protein folding by reaction path annealing

Journal of Chemical Physics

Volumn 114, Issue 8, 2001, Pages 3823-3841

  Eastman, Peter ^a   Grønbech Jensen, Niels ^b,c   Doniach, Sebastian ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LANGEVIN EQUATION; ONSAGER-MACHLUP ACTION FUNCTIONAL; PROTEIN FOLDING; REACTION PATH ANNEALING;

CALCULATIONS; COMPUTER SIMULATION; HYDROGEN BONDS; MOLECULAR DYNAMICS; POLYPEPTIDES; PROTEINS; SIMULATED ANNEALING; SOLVENTS;

BIOCHEMISTRY;

EID: 0035250027     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1342162     Document Type: Article

References (75)

1. A. R. Fersht, Curr. Opin. Struct. Biol. 7, 3 (1997).
2. E. I. Shakhnovich, Curr. Opin. Struct. Biol. 7, 29 (1997).
3. H. S. Chan and K. A. Dill, Proteins 30, 2 (1998).
4. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
5. F. Kano and N. Go, Biopolymers 21, 565 (1982).
6. H. Taketomi, F. Kano, and N. Go, Biopolymers 27, 527 (1988).
7. V. Daggett and M. Levitt, J. Mol. Biol. 232, 600 (1993).
8. M. H. Hao, M. R. Pincus, S. Rackovsky, and H. A. Scheraga, Biochemistry 32, 9614 (1993).
9. W. VanGunsteren, P. Hunenberger, H. Kovacs, A. Mark, and C. Schiffer, Philos. Trans. R. Soc. London, Ser. B 348, 49 (1995).
10. B. Wroblowski, J. Diaz, K. Heremans, and Y. Engelborghs, Proteins: Struct., Funct., Genet. 25, 446 (1996).
11. T. Lazaridis and M. Karplus, Science 278, 1928 (1997).
12. L. Wang, Y. Duan, R. Shortle, B. Imperiali, and P. Kollman, Protein Sci. 8, 1292 (1999).
13. J. Tsai, M. Levitt, and D. Baker, J. Mol. Biol. 291, 215 (1999).
14. K. F. Fulton, E. R. G. Main, V. Daggett, and S. E. Jackson, J. Mol. Biol. 291, 445 (1999).
15. A. V. Finkelstein, Protein Eng. 10, 843 (1997).
16. S. Chandrasekhar, Rev. Mod. Phys. 15, 1 (1943).
17. L. Onsager and S. Machlup, Phys. Rev. 91, 1505 (1953).
18. L. R. Pratt, J. Chem. Phys. 85, 5045 (1986).
19. R. Elber and M. Karplus, Chem. Phys. Lett. 139, 375 (1987).
20. R. Olender and R. Elber, J. Chem. Phys. 105, 9299 (1996).
21. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998).
22. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 110, 6617 (1999).
23. S. Huo and J. E. Straub, J. Chem. Phys. 107, 5000 (1997).
24. D. M. Zuckerman and T. B. Woolf, J. Chem. Phys. 111, 9475 (1999).
25. S. Huo and J. E. Straub, Proteins 36, 249 (1999).
26. R. Elber, J. Meller, and R. Dlender, J. Phys. Chem. B 103, 899 (1999).
27. L. S. Itzhaki, D. E. Otzen, and A. R. Fersht, J. Mol. Biol. 254, 260 (1995).
28. V. P. Grantcharova, D. S. Riddle, J. V. Santiago, and D. Baker, Nat. Struct. Biol. 5, 714 (1998).
29. M. Oliveberg, Y. J. Tan, M. Silow, and A. R. Fersht, J. Mol. Biol. 277, 933 (1998).
30. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Biophys. J. 75, 662 (1998).
31. F. S. Csajka and D. Chandler, J. Chem. Phys. 109, 1125 (1998).
32. J.-P. Hansen and I. R. McDonald, Theory of Simple Liquids, 2nd ed. (Academic, New York, 1986).
33. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
34. H. Risken, The Fokker-Planck Equation: Methods of Solution and Applications, 2nd ed. (Springer, Berlin, 1989).
35. G. Parisi, Statistical Field Theory (Addison-Wesley, Redwood City, CA, 1988).
36. R. Elber and D. Shalloway, J. Chem. Phys. 112, 5539 (2000).
37. A. Kitao, S. Hayward, and N. Go, Proteins 33, 496 (1998).
38. C. U. Brooks, J. Phys. Chem. 100, 2536 (1996).
39. P Eastman and S. Doniach, Proteins 30, 215 (1998).
40. P Eastman, M. Pellegrini, and S. Doniach, J. Chem. Phys. 110, 10141 (1999)
41. I P Ma and M. Karplus, J. Mol. Biol. 274, 114 (1997).
42. D. Vitkup, G. A. Petsko, and M. Karplus, Nat. Struct. Biol. 4, 202 (1997).
43. W. Wriggers and K. Schulten, Biophys. J. 73, 624 (1997).
44. P. J. Steinbach and B. R. Brooks, Proc. Natl. Acad. Sci. U.S.A. 90, 9135 (1993).
45. M. Pellegrini, N. Gronbech-Jensen, and S. Doniach, Physica A 239, 244 (1997).
46. T. Ooi, M. Oobatake, G. Nemethy, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 84, 3086 (1987).
47. L. Wesson and D. Eisenberg, Protein Sci. 1, 227 (1992).
48. J. D. Augspurger and H. A. Scheraga, J. Comput. Chem. 17, 1549 (1996).
49. K. A. Sharp and B. Honig, J. Phys. Chem. 94, 7684 (1990).
50. S. R. Kimura, R. C. Brower, C. Zhang, and M. Sugimori, J. Chem. Phys. 112, 7723 (2000).
51. S. Nakamura, M. Ikeguchi, and K. Shimizu, J. Comput. Chem. 19, 1716 (1998).
52. A. M. Gronenborn, D. R. Filpula, N. Z. Essig, A. Achari, M. Whitlow, P. T. Wingfield, and G. M. Clore, Science 253, 657 (1991).
53. T. L. Blundell, J. E. Pitts, I. J. Tickle, S. P. Wood, and C.-W. Wu, Proc. Natl. Acad. Sci. U.S.A. 78, 4175 (1981).
54. J. A. Rupley and G. Careri, Adv. Protein Chem. 41, 37 (1991).
55. W. F. van Gunsteren and M. Karplus, Macromolecules 15, 1528 (1982).
56. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, J. Am. Chem. Soc. 106, 765 (1984).
57. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc. 110, 1657 (1988).
58. B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, J. Comput. Chem. 18, 1463 (1997).
59. Kundert (available from Netlib at www.netlib.com, 1988).
60. S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, Biochemistry 35, 691 (1996).
61. P. A. Thompson, W. A. Eaton, and J. Hofrichter, Biochemistry 36, 9200 (1997).
62. G. L. Millhauser, C. J. Stenland, P. Hanson, K. A. Bolin, and F. J. M. Vandeven, J. Mol. Biol. 267, 963 (1997).
63. W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983).
64. G. L. Millhauser, Biochemistry 34, 3873 (1995).
65. J. M. Scholtz, Q. Hong, E. J. York, J. M. Stewart, and R. L. Baldwin, Biopolymers 31, 1463 (1991).
66. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959).
67. V. Muñoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Nature (London) 390, 196 (1997).
68. V. S. Pande and D. S. Rokhsar, Proc. Natl. Acad. Sci. U.S.A. 96, 9062 (1999).
69. D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 97, 2544 (2000).
70. S. Takada, Z. Luthey-Schulten, and P. G. Wolynes, J. Chem. Phys. 110, 11616 (1999).
71. R. A. Abagyan and M. M. Totrov, J. Mol. Biol. 268, 678 (1997).
72. V. S. Pande, A. Grosberg, T. Tanaka, and D. S. Rokhsar, Curr. Opin. Struct. Biol. 8, 68 (1998).
73. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, J. Mol. Biol. 296, 1183 (2000).
74. J. C. Martinez, M. T. Pisabarro, and L. Serrano, Nat. Struct. Biol. 5, 721 (1998).
75. F. Chiti, N. Taddei, P. M. White, M. Bucciantini, F. Magherini, M. Stefani, and C. M. Dobson, Nat. Struct. Biol. 6, 1005 (1999).