Protein folding kinetics and thermodynamics from atomistic simulations

Physical Review Letters

Volumn 96, Issue 23, 2006, Pages

  Van Der Spoel, David ^a   Seibert, M Marvin ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC PHYSICS; COMPUTER SIMULATION; FREE ENERGY; INFORMATION ANALYSIS; MOLECULAR DYNAMICS; THERMODYNAMIC PROPERTIES;

ATOMISTIC SIMULATIONS; MULTIPLE SIMULATION TRAJECTORIES; PROTEIN FOLDING KINETICS;

PROTEINS;

EID: 33745184030     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.96.238102     Document Type: Article

References (34)

1. M. Seibert, A. Patriksson, B. Hess, and D. van der Spoel, J. Mol. Biol. 354, 173 (2005). JMOBAK 0022-2836 10.1016/j.jmb.2005.09.030
2. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996). JUPSAU 0031-9015 10.1143/JPSJ.65.1604
3. T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami, Chem. Phys. Lett. 335, 435 (2001). CHPLBC 0009-2614 10.1016/S0009-2614(01)00055-0
4. Y. Okamoto, J. Molec. Graph. Model. 22, 425 (2004).
5. R. Zhou, B.J. Berne, and R. Germain, Proc. Natl. Acad. Sci. U.S.A. 98, PNASA6 0027-8424 14931 (2001). 10.1073/pnas.201543998
6. R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, PNASA6 0027-8424 13280 (2003). 10.1073/pnas.2233312100
7. J.W. Pitera and W. Swope, Proc. Natl. Acad. Sci. U.S.A. 100, PNASA6 0027-8424 7587 (2003). 10.1073/pnas.1330954100
8. F. Rao and A. Caflisch, J. Chem. Phys. 119, 4035 (2003). JCPSA6 0021-9606 10.1063/1.1591721
9. D. Paschek and A.E. Garcia, Phys. Rev. Lett. 93, 238105 (2004). PRLTAO 0031-9007 10.1103/PhysRevLett.93.238105
10. W. Zhang, C. Wu, and Y. Duan, J. Chem. Phys. 123, 154105 (2005). JCPSA6 0021-9606 10.1063/1.2056540
11. A. Luzar and D. Chandler, Nature (London) 379, NATUAS 0028-0836 55 (1996). 10.1038/379055a0
12. D. van der Spoel, P.J. van Maaren, P. Larsson, and N. Timneanu, J. Phys. Chem. B 110, 4393 (2006). JPCBFK 1520-6106 10.1021/jp0572535
13. E. Lindahl, B.A. Hess, and D. van der Spoel, J. Mol. Mod. 7, 0948-5023 306 (2001).
14. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen, J. Comput. Chem. 26, JCCHDD 0192-8651 1701 (2005). 10.1002/jcc.20291
15. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, J. Chem. Phys. 79, 926 (1983). JCPSA6 0021-9606 10.1063/1.445869
16. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996). JACSAT 0002-7863 10.1021/ja9621760
17. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen, J. Chem. Phys. 103, 8577 (1995). JCPSA6 0021-9606 10.1063/1.470117
18. D. van der Spoel and P.J. van Maaren, J. Chem. Theor. Comp. 2, 1549-9618 1 (2006). 10.1021/ct0502256
19. J.A. Nelder and R. Mead, Computer J. 7, 0010-4620 308 (1965).
20. S. Honda, K. Yamasaki, Y. Sawada, and H. Morii, Structure Fold. Des. 12, 1507 (2004).
21. Y. Xu, R. Oyola, and F. Gai, J. Am. Chem. Soc. 125, 15388 (2003). JACSAT 0002-7863 10.1021/ja037053b
22. V. Munoz, P.A. Thompson, J. Hofrichter, and W.A. Eaton, Nature (London) 390, NATUAS 0028-0836 196 (1997). 10.1038/36626
23. D. Du, Y. Zhu, C. Huang, and F. Gai, Proc. Natl. Acad. Sci. U.S.A. 101, PNASA6 0027-8424 15915 (2004). 10.1073/pnas.0405904101
24. L.D. Barron, L. Hecht, and G. Wilson, Biochemistry 36, BICHAW 0006-2960 13143 (1997). 10.1021/bi971323j
25. F. Xu and T.A. Cross, Proc. Natl. Acad. Sci. U.S.A. 96, PNASA6 0027-8424 9057 (1999). 10.1073/pnas.96.16.9057
26. Y.M. Rhee, E.J. Sorin, G. Jayachandran, E. Lindahl, and V.S. Pande, Proc. Natl. Acad. Sci. U.S.A. 101, PNASA6 0027-8424 6456 (2004). 10.1073/pnas. 0307898101
27. M.R. Shirts and V.S. Pande, Phys. Rev. Lett. 86, 4983 (2001). PRLTAO 0031-9007 10.1103/PhysRevLett.86.4983
28. P. Bradley, K.M.S. Misura, and D. Baker, Science 309, 1868 (2005). SCIEAS 0036-8075 10.1126/science.1113801
29. O. Schueler-Furman, C. Wang, P. Bradley, K. Misura, and D. Baker, Science 310, 638 (2005). SCIEAS 0036-8075 10.1126/science.1112160
30. D. van der Spoel and E. Lindahl, J. Phys. Chem. B 107, 11178 (2003). JPCBFK 1520-6106 10.1021/jp034108n
31. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 PNASA6 0027-8424 (2002). 10.1073/pnas.202427399
32. G. Bussi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 96, 090601 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.96.090601
33. I. Daidone, M. D'Abramo, A. Di Nola, and A. Amadei, J. Am. Chem. Soc. 127, 14825 (2005). JACSAT 0002-7863 10.1021/ja053383f
34. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg, J. Comput. Chem. 13, JCCHDD 0192-8651 1011 (1992). 10.1002/jcc.540130812