Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36

Journal of Chemical Physics

Volumn 118, Issue 10, 2003, Pages 4733-4747

  Mukherjee, Arnab ^a   Bagchi, Biman ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ATOMS; COMPUTER SIMULATION; ELECTRON ENERGY LEVELS; GRAPH THEORY; HYDROPHOBICITY; MOLECULAR STRUCTURE; MONTE CARLO METHODS; NUMERICAL ANALYSIS; PROBABILITY DISTRIBUTIONS; PROTEINS; QUENCHING;

BENDING POTENTIAL; BONDING POTENTIAL; BROWNIAN DYNAMICS SIMULATION; HELIX POTENTIAL; HYDROPHOBIC TOPOLOGICAL CONTACT; NONBONDING POTENTIAL; PROTEIN FOLDING; RELATIVE CONTACT ORDER; TORSIONAL POTENTIAL;

MOLECULAR DYNAMICS;

EID: 0037426218     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1542599     Document Type: Article

References (71)

1. C. B. Anfinsen, Science 181, 223 (1973)
2. M. Sela, F. H. White, and C. B. Anfinsen, ibid. 125, 691 (1957).
3. K. A. Dill, D. O. V. Alonso, and K. Hutchinson, Biochemistry 28, 5439 (1989).
4. P. E. Leopold, M. Montal, and J. N. Onuchi, Proc. Natl. Acad. Sci. U.S.A. 89, 8721 (1992).
5. J. D. Bryngelson, J. N. Onuchi, N. D. Socci, and P. G. Wolynes, Proteins: Struct. Funct., Genet. 21, 167 (1995).
6. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524 (1987)
7. J. Phys. Chem. 93, 6902 (1989).
8. B. A. Shoemaker, J. Wang, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 94, 777 (1997).
9. C. Levinthal, in Mossbauer Spectroscopy in Biological Systems, in Proceedings of a Meeting held at Allerton House, Monticello, Illinois, edited by P. Debrunner, J. C. M. Tsibris, and E. Munck (University of Illinois Press, Urbana), p. 22.
10. R. Zwanzig, A. Szabo, and B. Bagchi, Proc. Natl. Acad. Sci. U.S.A. 89, 20 (1992).
11. H. Frauenfelder, S. G. Sligar, and P. G. Wolynes, Science 254, 1598 (1991).
12. J. N. Onuchic, P. G. Wolynes, Z. Luthey-Schulten, and N. D. Socci, Proc. Natl. Acad. Sci. U.S.A. 92, 3626 (1995).
13. J. N. Onuchic, N. D. Socci, Z. Luthey-Schulten, and P. G. Wolynes, Folding Des. 1, 441 (1996).
14. K. Yue and K. A. Dill, Phys. Rev. E 48, 226 (1993)
15. H. S. Chan and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 87, 6368 (1990).
16. K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10, (1997).
17. H. Nymeyer, N. D. Socci, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 97, 634 (2000).
18. R. Zwanzig, Proc. Natl. Acad. Sci. U.S.A. 92, 9801 (1995).
19. J. J. Portman, S. Takada, and P. G. Wolynes, Phys. Rev. Lett. 81, 5237 (1998).
20. J. J. Portman, S. Takada, and P. G. Wolynes, J. Chem. Phys. 114, 5069 (2001)
21. 114, 5082 (2001).
22. M. Levitt and A. Warshel, Nature (London) 253, 694 (1975).
23. J. Skolnick, and A. Kolinski, Science 250, 1121 (1990).
24. A. Kolinski, W. Galazaka, and J. Skolnick, Proteins 26, 271 (1996).
25. G. Srinivas and B. Bagchi, J. Chem. Phys. 116, 8579 (2002).
26. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 87, 3526 (1990)
27. Biopolymers 32, 695 (1992).
28. M. Levitt, J. Mol. Biol. 104, 59 (1976).
29. A. Liwo, S. Oldziej, M. R. Pincus, R. J. Wawak, S. Rackovsky, and H. A. Scheraga, J. Comput. Chem. 18, 850 (1997).
30. J. Pillardy, C. Czaplewski, A. Liwo, et al., Proc. Natl. Acad. Sci. U.S.A. 98, 2329 (2001)
31. ibid. 96, 2025 (1999).
32. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
33. U. H. E. Hansmann and L. T. Wille, Phys. Rev. Lett. 88, 068105 (2002).
34. V. Grantcharova, E. J. Alm, D. Baker, and A. L. Horwich, Curr. Opin. Struct. Biol. 11, 70 (2001).
35. K. A. Dill, Biochemistry 29, 7133 (1990).
36. W. Kauzmann, Adv. Protein Chem. 14, 1 (1959).
37. C. Tanford, The Hydrophobic Effect: Formation of Micelles and Biological Membranes, 2nd ed. (Wiley, New York, 1980).
38. E. S. Huang, S. Subbiah, and M. Levitt, J. Mol. Biol. 252, 709 (1995).
39. J. Janin, Nature (London) 277, 491 (1979).
40. G. Rose, A. Geselowitz, G. Lesser, R. Lee, and M. Zehfus, Science 229, 834 (1985).
41. R. Wolfenden, L. Andersson, P. Cullis, and C. Southgate, Biochemistry 20, 849 (1981).
42. J. Kyte and R. F. Doolittle, J. Mol. Biol. 157, 105 (1982).
43. D. F. Sickle, L. G. Presta, K. A. Dill, and G. D. Rose, J. Mol. Biol. 226, 1143 (1992).
44. P. Y. Chou and G. Fasman, Biochemistry 13, 211, (1974).
45. A. Chakrabartty, and R. L. Baldwin, Adv. Protein Chem. 46, 141 (1995).
46. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959).
47. J. P. Hansen and I. R. McDonald, Theory of Simple Liquids (Academic, New York, 1986).
48. (a) H. Noguchi and K. Yoshikawa, J. Chem. Phys. 113, 854 (2000)
49. (b) 109, 5070 (1998).
50. C. N. Pace and J. M. Scholtz, Biophys. J. 75, 422 (1998).
51. G. C. A. M. Mooij, D. Frenkel, and B. Smit, J. Phys.: Condens. Matter 4, L255 (1992)
52. D. Frenkel and B. Smit, Mol. Phys. 75, 983 (1992).
53. J. J. De Pablo, M. Laso, J. I. Siepmann, and U. Suter, Mol. Phys. 80, 55 (1993).
54. N. Madras and A. D. Sokal, J. Stat. Phys. 50, 109 (1988).
55. S. Consta, T. J. H. Vlugt, J. W. Hoeth, B. Smith, and D. Frenkel, Mol. Phys. 97, 1243 (1999)
56. S. Consta, N. B. Wilding, D. Frenkel, and Z. Alexandrowicz, J. Chem. Phys. 110, 3220 (1999).
57. S. Santos and U. W. Sutter, J. Chem. Phys. 14. 9772 (2001).
58. M. G. Martin and J. I. Siepmann, J. Phys. Chem. B 103, 4508 (1999).
59. T. J. H. Vlugt, R. Krishna, and B. Smit, J. Phys. Chem. B 103, 1102 (1999).
60. M. Dijkstra, J. Chem. Phys. 107, 3277 (1997).
61. D. L. Ermak and J. A. McCammon, J. Chem. Phys. 69, 1352 (1978).
62. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, Oxford, 2001).
63. J. U. Bowie, R. Luthy, and D. Eisenberg, Science 253, 164 (1991)
64. L. Zhang and J. Skolnick, Protein Sci. 7, 1201 (1998).
65. D. Shortle, W. E. Stites, and A. K. Meeker, Biochemistry 29, 8033 (1990).
66. K. W. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. 277, 985 (1998).
67. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol. 112, 535 (1977).
68. C. J. McKnight, D. S. Doering, P. T. Matsudaria, and P. S. Kim, J. Mol. Biol. 260, 126 (1996).
69. G. Srinivas and B. Bagchi, Theor. Chem. Acc. (to be published).
70. A. Mukherjee and B. Bagchi, Phys. Rev. Lett. (to be published).
71. R. Zwanzig and B. Baguchi (unpublished work).