Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

Chemical Physics Letters

Volumn 400, Issue 1-3, 2004, Pages 258-263

  Watanabe, Yukihisa S ^a   Kim, Jae Gil ^a,c   Fukunishi, Yoshifumi ^d   Nakamura, Haruki ^b,d  

^a Japan Biological Information Research Center   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; WATER;

ARTICLE; CHEMICAL STRUCTURE; COMPARATIVE STUDY; CONFORMATION; ENERGY; FORCE; FREQUENCY MODULATION; HYDROGEN BOND; MOLECULAR DYNAMICS; SIMULATION;

EID: 9644303223     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2004.10.118     Document Type: Article

References (35)

1. W.C. Still, A. Tempczyk, R.C. Hawley, and T. Hendrickson J. Am. Chem. Soc. 112 1990 6127
2. M. Schaefer, and M. Karplus J. Phys. Chem. 100 1996 1578
3. A. Onufriev, D. Bashford, and D.A. Case J. Phys. Chem. B 104 2000 3712
4. D.G. Hawkins, J.C. Cramer, and G.D. Truhlar Chem. Phys. Lett. 246 1995 122
5. D.G. Hawkins, J.C. Cramer, and G.D. Truhlar J. Phys. Chem. 100 1996 19824
6. B.D. Bursulaya, and C.L. Brooks III J. Phys. Chem. B 104 2000 12378
7. R. Zhou, and B.J. Berne Proc. Natl. Acad. Sci. USA 99 2002 12777
8. H. Nymeyer, and A.E. Garcia Proc. Natl. Acad. Sci. USA 100 2003 13934
9. J.W. Pitera, and W. Swope Proc. Natl. Acad. Sci. USA 100 2003 7587
10. R. Zhou Proteins 53 2003 148
11. M. Feig, and C.L. Brooks III Curr. Opin. Struct. Biol. 14 2004 217
12. B.A. Berg, and T. Neuhaus Phys. Rev. Lett. 68 1992 9
13. U.H.E. Hansmann, and Y. Okamoto J. Comp. Chem. 14 1993 1333
14. N. Nakajima, A. Kidera, and H. Nakamura J. Phys. Chem. B 101 1997 817
15. Y. Sugita, and Y. Okamoto Chem. Phys. Lett. 314 1999 141
16. N. Nakajima, J. Higo, A. Kidera, and H. Nakamura J. Mol. Biol. 296 2000 197
17. I. Fukuda, and H. Nakamura Phys. Rev. E 65 2002 026105
18. Y. Fukunishi, Y. Mikami, and H. Nakamura J. Phys. Chem. B 107 2003 13201
19. N. Kamiya, J. Higo, and H. Nakamura Protein Sci. 11 2002 2297
20. Y.S. Watanabe, Y. Fukunishi, and H. Nakamura J. Mol. Graph. Model. 23 2004 59
21. N. Nakajima, J. Higo, A. Kidera, and H. Nakamura Chem. Phys. Lett. 278 1997 297
22. J.G. Kim, Y. Fukunishi, A. Kidera, and H. Nakamura Phys. Rev. E 68 2003 021110
23. A.M. Ferrenberg, and R.H. Swendsen Phys. Rev. Lett. 63 1989 1195
24. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein J. Chem. Phys. 79 1983 926
25. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman J. Am. Chem. Soc. 117 1995 5179
26. P.A. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot, and A. Pohorille Comp. Simulat. Biomol. Sys. 3 1997 83
27. J. Wang, P. Cieplak, and P.A. Kollman J. Comp. Chem. 21 2000 1049
28. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen J. Comp. Phys. 23 1977 327
29. T.J. Richmond J. Mol. Biol. 178 1984 63
30. A.R. Kinjo, A. Kidera, H. Nakamura, and K. Nishikawa Eur. Biophys. J. 30 2001 1
31. J.W. Ponder, and D.A. Case Adv. Protein Chem. 66 2003 27
32. S. Ono, N. Nakajima, J. Higo, and H. Nakamura J. Comp. Chem. 21 2000 748
33. T. Yoda, Y. Sugita, and Y. Okamoto Chem. Phys. Lett. 386 2004 460
34. S. Ono, M. Kuroda, J. Higo, N. Nakajima, and H. Nakamura J. Comp. Chem. 23 2002 470
35. J. Higo, N. Ito, M. Kuroda, S. Ono, N. Nakajima, and H. Nakamura Protein Sci. 10 2001 1160