Coarse master equations for peptide folding dynamics

Journal of Physical Chemistry B

Volumn 112, Issue 19, 2008, Pages 6057-6069

  Buchete, Nicolae Viorel ^a,b   Hummer, Gerhard ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; CORRELATION METHODS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; NANOFLUIDICS; QUANTUM CHEMISTRY; RATE CONSTANTS; RELAXATION PROCESSES; SYSTEMS ANALYSIS;

ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; COARSE MASTER EQUATIONS; CONFORMATIONAL DYNAMICS; CONFORMATIONAL RELAXATION; CONFORMATIONAL STATES; CORRELATION FUNCTIONS; EIGENVECTORS; HELIX-COIL TRANSITIONS; MASTER EQUATIONS; MOLECULAR COORDINATES; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANISMS; NON-MARKOVIAN DYNAMICS; PEPTIDE FOLDING; STATE MODELING; TIME SCALING; TRANSITION PATHS; TRANSITION RATE MATRIX; TWO-STATE;

DYNAMICS;

PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; TEMPERATURE; TIME;

COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE; TIME FACTORS;

EID: 44949178407     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0761665     Document Type: Article

References (84)

1. Mohanty, D.; Elber, R.; Thirumalai, D.; Beglov, D.; Roux, B. J. Mol. Biol. 1997, 272, 423-442.
2. Schütte, C.; Fischer, A.; Huisinga, W.; Deuflhard, P. J. Comput. Phys. 1999, 151, 146-168.
3. Huisinga, W.; Schütte, C.; Stuart, A. M. Commun. Pure Appl. Math 2003, 56, 234-269.
4. Swope, W. C.; Pitera, J. W.; Suits, F. J. Phys. Chem B 2004, 108, 6571-6581.
5. Swope, W. C.; Pitera, J. W.; Suits, F.; Pitman, M.; Eleftheriou, M.; Fitch, B. G.; Germain, R. S.; Rayshubski, A.; Ward, T. J. C.; Zhestkov, Y.; Zhou, R. J. Phys. Chem B 2004, 108, 6582-6594.
6. Levy, Y.; Jortner, J.; Berry, R. S. Phys. Chem. Chem Phys. 2002, 4, 5052-5058.
7. Chekmarev, D. S.; Ishida, T.; Levy, R. M. J. Phys. Chem B 2004, 108, 19487-19495.
8. de Groot, B. L.; Daura, X.; Mark, A. E.; Grubmüller, H. J. Mol. Biol. 2001, 309, 299-313.
9. Becker, O. M.; Karplus, M. J. Chem Phys. 1997, 106, 1495-1517.
10. Sriraman, S.; Kevrekidis, I. G.; Hummer, G. J. Phys. Chan. B 2005, 109, 6479-6484.
11. Zwanzig, R. J. Stat. Phys. 1983, 30, 255-262.
12. Zwanzig, R.; Szabo, A.; Bagchi, B. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 20-22.
13. Bryngelson, J. D.; Wolynes, P. G. J. Phys. Chem 1989, 93, 6902-6915.
14. Schonbrun, J.; Dill, K. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12678-12682.
15. Bicout, D. J.; Szabo, A. J. Chem Phys. 1998, 109, 2325-2338.
16. Hummer, G. New J. Phys. 2005, 7, 34.
17. Best, R. B.; Hummer, G. Phys. Rev. Lett. 2006, 96, 228104.
18. Hummer, G.; Kevrekidis, I. G. J. Chem. Phys. 2003, 118, 10762-10773.
19. Bolhuis, P. G.; Dellago, C.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5877-5882.
20. Ma, A.; Dinner, A. R. J. Phys. Chem B 2005, 109, 6769-6779.
21. Hummer, G. J. Chem Phys. 2004, 120, 516.
22. Rhee, Y. M.; Pande, V. S. J. Phys. Chem B 2005, 109, 6780-6786.
23. Ren, W.; Vanden-Eijnden, E.; Maragakis, P.; E, W. J. Chem Phys. 2005, 123, 134109.
24. Elmer, S. P.; Park, S.; Pande, V. S. J. Chem Phys. 2005, 123, 114902.
25. Elmer, S. P.; Park, S.; Pande, V. S. J. Chem Phys. 2005, 123, 114903.
26. Snow, C. D.; Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 43-69.
27. Singhal, N.; Pande, V. S. J. Chem Phys. 2005, 123, 204909.
28. Singhal, N.; Snow, C. D.; Pande, V. S. J. Chem Phys. 2004, 121, 415.
29. van der Spoel, D.; Seibert, M. M. Phys. Rev. Lett. 2006, 96, 238102.
30. Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Dill, K. A. Multiscale Model. Sim. 2006, 5, 1214-1226.
31. Noe, F.; Horenko, I.; Schütte, C.; Smith, J. C. J. Chem. Phys. 2007, 126, 155102.
32. Kube, S.; Weber, M. J. Chem. Phys. 2007, 126, 024103.
33. Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. J. Chem. Phys. 2007, 126, 155101.
34. Poland, D. C.; Scheraga, H. A. Theory of the helix-coil transition; Academic Press: New York, 1970.
35. Scheraga, H. A.; Vila, J. A.; Ripoll, D. R. Biophys. Chem. 2002, 101, 255-265.
36. Graf, J.; Nguyen, P. H.; Stock, G.; Schwalbe, H. J. Am. Chem. Soc. 2007, 129, 1179-1189.
37. Wang, T.; Du, D.; Gai, F. Chem. Phys. Lett. 2003, 370, 842-848.
38. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200-9210.
39. Doshi, U.; Muñoz, V. Chem. Phys. 2004, 307, 129-136.
40. Buchete, N. V.; Straub, J. E. J. Phys. Chem. B 2001, 105, 6684-6697.
41. van Giessen, A. E.; Straub, J. E. J. Chem. Phys. 2005, 122, 024904.
42. van Giessen, A. E.; Straub, J. E. J. Chem. Theory Comput. 2006, 2, 674-684.
43. Daidone, I.; D'Abramo, M.; Di Nola, A.; Amadei, A. J. Am. Chem. Soc. 2005, 127, 14825-14832.
44. Hummer, G.; García, A. E.; Garde, S. Phys. Rev. Lett. 2000, 85, 2637-2640.
45. Hummer, G.; García, A. E.; Garde, S. Proteins 2001, 42, 77-84.
46. Nymeyer, H.; García, A. E. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13934-13939.
47. Margulis, C. J.; Stern, H. A.; Berne, B. J. J. Phys. Chem. B 2002, 106, 10748-10752.
48. Bicout, D. J.; Szabo, A. Protein Sci. 2000, 9, 452-465.
49. Deuflhard, P.; Huisinga, W.; Fischer, A.; Schütte, C. Linear Algebra Appl. 2000, 315, 39-59.
50. Deuflhard, P.; Weber, M. Linear Algebra Appl. 2005, 398, 161-184.
51. Belkin, M.; Niyogi, P. Neural Comput. 2003, 15, 1373-1396.
52. Coifman, R. R.; Lafon, S.; Lee, A. B.; Maggioni, M.; Nadler, B.; Warner, F.; Zucker, S. Proc. Natl. Acad. Sci. U.S.A. 2004, 102, 7426-7431.
53. Onsager, L. Phys. Rev. 1938, 54, 554-557.
54. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. S. J. Chem. Phys. 1998, 108, 334-350.
55. Geissler, P. L.; Dellago, C.; Chandler, D. J. Phys. Chem. B 1999, 103, 3706-3710.
56. Best, R. B.; Hummer, G. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6732-6737.
57. Snow, C. D.; Rhee, Y. M.; Pande, V. S. Biophys. J. 2006, 91, 14-24.
58. Berezhkovskii, A.; Szabo, A. J. Chem. Phys. 2006, 125, 104902.
59. Berezhkovskii, A.; Szabo, A. J. Chem. Phys. 2004, 122, 014503.
60. Wales, D. J. Mol. Phys. 2002, 100, 3285-3305.
61. Dellago, C.; Bolhuis, P. G.; Chandler, D. J. Chem. Phys. 1999, 110, 6617-6625.
62. van Erp, T. S.; Moroni, D.; Bolhuis, P. G. J. Chem. Phys. 2003, 118, 7762-7774.
63. Hummer, G. J. Chem. Phys. 2004, 120, 516-523.
64. Andrec, M.; Levy, R. M.; Talaga, D. S. J. Phys. Chem. A 2003, 107, 7454-7464.
65. Kou, S. C.; Xie, X. S.; Liu, J. S. Appl. Stat. 2005, 54, 1-28.
66. McSharry, P. E.; Smith, L. A. Phys. Rev. Lett. 1999, 83, 4285-4288.
67. Meyer, R.; Christensen, N. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2000, 62, 3535-3542.
68. Hinrichs, N. S.; Pande, V. S. J. Chem. Phys. 2007, 126, 244101.
69. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718.
70. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
71. Sorin, E. J.; Pande, V. S. Biophys. J. 2005, 88, 2472-2493.
72. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
73. García, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782-2787.
74. Darden, T.; York, D.; Pedersen, L. J. Chem Phys. 1993, 95, 10089-10092.
75. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
76. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
77. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
78. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
79. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
80. Jayachandran, G.; Vishal, V.; Pande, V. S. J. Chem. Phys. 2006, 124, 164902.
81. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291-318.
82. Tobias, D. J.; Brooks, C. L. Biochemistry 1991, 30, 6059-6070.
83. Andrec, M.; Felts, A. K.; Gallicchio, E.; Levy, R. M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6801-6806.
84. Buchete, N.-V.; Hummer, G. Submitted, [http://arxiv.org/abs/0710.5533].