Describing protein folding kinetics by molecular dynamics simulations. 1. Theory

Journal of Physical Chemistry B

Volumn 108, Issue 21, 2004, Pages 6571-6581

  Swope, William C ^a   Pitera, Jed W ^a   Suits, Frank ^b  

^a IBM ALMADEN RESEARCH CENTER   (United States)

^b IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FUNCTIONS; HYDROPHILICITY; HYDROPHOBICITY; MARKOV PROCESSES; MOLECULAR DYNAMICS; NANOTECHNOLOGY; PROBLEM SOLVING;

DRIVING FORCE; PROTEIN FOLDING; STATE-TO-STATE TRANSITIONS; TEMPORAL RESOLUTION;

PROTEINS;

EID: 2942567954     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp037421y     Document Type: Article

References (49)

1. Swope, W. C.; Pitera, J. W.; Suits, F.; Pitman, M. C.; 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.
2. Capaldi, A. P.; Radford, S. E. Curr. Opin. Struct. Biol. 1998, 8, 86.
3. Eaton, W. A.; Munoz, V.; Thompson, P. A.; Henry, E. R.; Hofrichter, J. Acc. Chem. Res. 1998, 31, 745.
4. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220.
5. Martin Gruebele, M. In Mechanisms of Protein Folding, 2nd ed.; Pain, R. H., Ed.; Oxford University Press: New York, 2000.
6. Roder, H.; Elove, G. A.; Shastry, M. C. R. In Mechanisms of Protein Folding, 2nd ed.; Pain, R. H., Ed.; Oxford University Press: New York, 2000.
7. Duan, Y.; Kollman, P. Science 1998, 252, 740.
8. Snow, C. D.; Nguyen, H.; Pande, V. S.; Gruebele, M. Nature 2002, 420, 102.
9. Snow, C. D.; Zagrovic, B.; Pande, V. S. J. Am. Chem. Soc. 2002, 124, 14548.
10. Daura, X.; Juan, B.; Seebach, D.; v. Gunsteren, W. F.; Mark, A. E. J. Mol. Biol. 1998, 280, 925.
11. Sheinerman, F.; Brooks, C., III. J. Mol. Biol. 1998, 278, 439.
12. Pitera, J. W.; Swope, W. C. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7587.
13. Yang, W. Y.; Pitera, J. W.; Swope, W. C.; Gruebele, M. Nature Struct. Biol., submitted.
14. Mayor, U.; Johnson, C. M.; Daggett, V.; Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13518.
15. Dobson, C. M.; Karplus, M. Curr. Opin. Struct. Biol. 1999, 9, 92.
16. Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Trends Biochem. Sci. 2000, 25, 331.
17. Mayor, M.; Guydosh, N. R.; Johnson, C. M.; Grossmann, J. G.; Sato, S.; Jas, G. S.; Freund, S. M. V.; Alonso, D. O. V.; Daggett, V.; Fersht, A. R. Nature 2003, 421, 863.
18. Phillips, J.; Zheng, G.; Kumar, S.; Kale, L. Supercomputing 2002 Proceedings 2002, http://www.sc2002.org/paperpdfs/pap.pap277.pdf.
19. Makino, J.; Taiji, M. Scientific simulations with special-purpose computers; John Wiley and Sons: Chichester, U.K., 1998.
20. Shirts, M.; Pande, V. S. Science 2000, 290, 1903.
21. Shirts, M. R.; Pande, V. S. Phys. Rev. Lett. 2001, 86, 4983.
22. Folding@Home home page. http://folding.stanford.edu.
23. Globus Alliance home page. http://www.globus.org.
24. BlueGene project home page. http://www.research.ibm.com/bluegene/.
25. Allen, F.; et al. IBM Syst. J. 2001, 40, 310.
26. Fitch, B. G.; Germain, R. S.; Mendell, M.; Pitera, J. W.; Pitman, M. C.; Rayshubski, A.; Sham, Y.; Suits, F.; Swope, W. C.; Ward, T. J. C.; Zhestkov, Y.; Zhou, R. J. Parallel Distributed Computing 2003, 63, 759.
27. Adiga, N.; et al. Supercomputing 2002 Proceedings 2002, http://www.sc-2002.org/paperpdfs/pap.pap207.pdf.
28. Mitsutake, A.; Sugita, Y.; Okamoto, Y. Biopolymers 2001, 60, 96.
29. Garcia, A. E.; Sanbonmatsu, K. Y. Proteins 2002, 42, 345.
30. Zhou, R.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14931.
31. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. J. Chem. Phys. 2003, 119, 5740.
32. Ozkan, S. B.; Bahar, I.; Dill, K. A. Nature Struct. Biol. 2001, 8, 765.
33. Ozkan, S. B.; Dill, K. A.; Bahar, I. Biopolymers 2003, 68, 35.
34. Zhang, W.; Chen, S. J. Chem. Phys. 2003, 118, 3413.
35. Levy, Y.; Jortner. J.; Berry, R. S. Phys. Chem. Chem. Phys. 2002, 4, 5052.
36. Hummer, G.; Kevrekidis, I. G. J. Chem. Phys. 2003, 118, 10762.
37. de Groot, B. L.; Daura, X.; Mark, A. E.; Grubmuller, H. J. Mol. Biol. 2001, 309, 299.
38. Becker, O. M.; Karplus, M J. Chem. Phys. 1997, 106, 1495.
39. Buchholz, P. J. Appl. Probability 1994, 31, 59.
40. Jernigan, R. W.; Baran, R. H. Statistics Probability Lett. 2003, 64, 17.
41. Huisinga, W.; Schutte, C.; Stuart, A. M. Cummun Pure Appl. Math. 2003, 56, 234.
42. Fersht, A. R. Structure and Mechanism in Protein Science; W. H. Freeman: New York, 1999.
43. Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 14122.
44. Oppenheim, I.; Shuler, K. E.; Weiss, G. H. Stochastic Processes In Chemical Physics: The Master Equation; The MIT Press: Cambridge MA, 1977.
45. Van Kampen, N. G. Stochastic Processes in Physics and Chemistry; North-Holland Physics Publishing: New York, 1987.
46. decay = -τ/ln(μ).
47. Andersen, H. C. J. Chem. Phys. 1980, 72, 2384.
48. Hansmann, U. H. E. Chem. Phys. Lett. 1997, 281, 140.
49. In evaluating this expression we adopt a convention where we assume that if the trajectory had gone one time step longer, it would have left the state it was in at the end of the simulation. Similarly, we assume that the state immediately before the first time step produced during the simulation is in a different state than that of the first step of the simulation.