Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water

Journal of Chemical Physics

Volumn 127, Issue 23, 2007, Pages

  Kamberaj, Hiqmet ^a   Van Der Vaart, Arjan ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDES; SOLVENTS; STATISTICAL METHODS;

BIOMOLECULAR SYSTEMS; CONFORMATIONAL SAMPLING; EXPLICIT WATER; MULTIPLE SCALING REPLICA EXCHANGE; SOLUTE TEMPERING;

BIOMOLECULES;

AMYLOID; PEPTIDE FRAGMENT; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION;

AMYLOID; COMPUTER SIMULATION; MODELS, CHEMICAL; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; WATER;

EID: 37549000521     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2806930     Document Type: Article

References (71)

1. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
2. T. E. Cheatham III and B. R. Brooks, Theor. Chem. Acc. 99, 279 (1998).
3. W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D. P. Geerke, A. Glaättli, P. H. Hnenberger, M. A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt, and H. B. Yu, Angew. Chem., Int. Ed. 45, 4064 (2006).
4. J. B. Clarage, T. Romo, B. K. Andrews, B. M. Pettitt, and G. N. Phillips, Jr., Proc. Natl. Acad. Sci. U.S.A. 92, 3288 (1995).
5. R. G. Palmer, Adv. Phys. 31, 669 (1982).
6. H. Frauenfelder, F. Parak, and R. D. Young, Annu. Rev. Biophys. Biophys. Chem. 17, 451 (1988).
7. D. Kern and E. R. Zuiderweg, Curr. Opin. Struct. Biol. 13, 748 (2003).
8. M. Gerstein, A. M. Lesk, and C. Chothia, Biochemistry 33, 6739 (1994).
9. M. Gerstein and W. Krebs, Nucleic Acids Res. 26, 4280 (1998).
10. M. Karplus, Y. Q. Gao, J. Ma, A. van der Vaart, and W. Yang, Philos. Trans. R. Soc. London, Ser. A 363, 331 (2005).
11. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 7, 181 (1997).
12. A. van der Vaart, Theor. Chem. Acc. 116, 183 (2006).
13. M. E. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. 97, 1990 (1992).
14. G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, Mol. Phys. 87, 1117 (1996).
15. M. E. Tuckerman and G. J. Martyna, J. Phys. Chem. B 104, 159 (2000).
16. P. Minary, G. J. Martyna, and M. E. Tuckerman, Phys. Rev. Lett. 93, 150201 (2004).
17. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
18. P. Amara and J. E. Straub, J. Phys. Chem. 99, 14840 (1995).
19. H. Grubmller and P. Tavan, J. Chem. Phys. 101, 5047 (1994).
20. A. F. Voter, Phys. Rev. Lett. 78, 3908 (1997).
21. A. F. Voter, J. Chem. Phys. 106, 4665 (1997).
22. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
23. X. Wu and S. Wang, J. Chem. Phys. 110, 9401 (1999).
24. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
25. R. K. Hart, R. V. Pappu, and J. W. Ponder, J. Comput. Chem. 21, 531 (2000).
26. D. Hamelberg, J. Mongan, and J. McCammon, J. Chem. Phys. 120, 11919 (2004).
27. F. Rodriguez-Barrios and F. Gago, J. Am. Chem. Soc. 126, 15386 (2004).
28. A. van der Vaart and M. Karplus, J. Chem. Phys. 122, 114903 (2005).
29. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998).
30. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 108, 9236 (1998).
31. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett. 57, 2607 (1986).
32. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
33. M. C. Tesi, E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996).
34. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002).
35. D. Thirumalai, R. D. Mountain, and T. R. Kirkpatrick, J. Chem. Phys. 124, 174093 (2006).
36. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. 51, 129 (2000).
37. R. Zhou and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 99, 12777 (2002).
38. R. Zhou, Proteins 53, 148 (2003).
39. A. E. Garcia and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 100, 13898 (2003).
40. A. Okur, L. Wickstrom, M. Layten, R. Geney, K. Song, V. Hornak, and C. J. Simmerling, J. Chem. Theory Comput. 2, 420 (2006).
41. X. Cheng, G. Cui, V. Hornak, and C. Simmerling, J. Phys. Chem. B 109, 8220 (2005).
42. P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 103, 13749 (2005).
43. K. Srinivasaraghavan and M. Zacharias, Proteins: Struct., Funct., Bioinf. 66, 697 (2007).
44. E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Phys. Rev. Lett. 96, 028105 (2006).
45. P. Liu and G. A. Voth, J. Chem. Phys. 126, 045106 (2007).
46. C. Tsallis, J. Stat. Phys. 52, 479 (1988).
47. U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 56, 2228 (1997).
48. U. H. E. Hansmann, F. Eisenmenger, and Y. Okamoto, Chem. Phys. Lett. 297, 374 (1998).
49. U. H. E. Hansmann and Y. Okamoto, Braz. J. Phys. 29, 187 (1999).
50. I. Andricioaei and J. E. Straub, J. Chem. Phys. 107, 9117 (1997).
51. J. E. Straub and I. Andricioaei, Braz. J. Phys. 29, 179 (1999).
52. T. Whitfield, L. Bu, and J. Straub, Physica A 305, 157 (2002).
53. M. Nauenberg, Phys. Rev. E 67, 036114 (2003).
54. M. Nauenberg, Phys. Rev. E 69, 038102 (2004).
55. D. H. Zanette and M. A. Montemurro, Phys. Lett. A 316, 184 (2003).
56. D. H. Zanette and M. A. Montemurro, Phys. Lett. A 324, 383 (2004).
57. C. Tsallis, Phys. Rev. E 69, 038101 (2004).
58. X. Huang, M. Hagen, B. Kim, R. A. Friesner, R. Zhou, and B. J. Berne, J. Phys. Chem. B 111, 5405 (2007).
59. A. MacKerell, M. Feig, and C. Brooks, J. Comput. Chem. 25, 1400 (2004).
60. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
61. E. Gallicchio, M. Andrec, A. K. Felts, and R. Levy, J. Phys. Chem. B 109, 6722 (2005).
62. J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. 3, 26 (2007).
63. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 25, 1400 (2004).
64. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. Pedersen, J. Chem. Phys. 103, 8577 (1995).
65. A. Mascione, F. Porcelli, U. Ilangovan, A. Ramamoorthy, and G. Veglia, Biopolymers 69, 29 (2003).
66. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
67. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
68. G. J. Martyna, M. E. Tuckerman, and M. L. Klein, J. Chem. Phys. 97, 2635 (1992).
69. D. Thirumalai, R. D. Mountain, and T. R. Kirkpatrick, Phys. Rev. A 39, 3563 (1989).
70. H. G. Katzgraber, S. Trebst, D. A. Huse, and M. Troyer, J. Stat. Mech.: Theory Exp. 3, 1742 (2006).
71. S. C. Lovell, I. W. Davis, W. B. Arendall III, P. Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, and D. C. Richardson, Proteins 50, 437 (2003).