Enhanced sampling and applications in protein folding in explicit solvent

Journal of Chemical Physics

Volumn 132, Issue 24, 2010, Pages

  Zhang, Cheng ^a   Ma, Jianpeng ^a,b  

^a Rice University   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA CARBON; COMPLEX SYSTEMS; CONTINUOUS TEMPERATURE; EXPLICIT SOLVENTS; FOLDED CONFORMATION; INTEGRAL IDENTITIES; LENNARD-JONES LIQUID SYSTEMS; NATIVE STATE; RANDOM WALK; ROOT MEAN SQUARE DEVIATIONS; RUNTIME ESTIMATES; THERMAL AVERAGES; THREE SYSTEMS; TWO-DIMENSIONAL ISING MODEL; VILLIN HEADPIECE;

PROTEIN FOLDING;

ISING MODEL;

ACTIN BINDING PROTEIN; PEPTIDE; PROTEIN; SOLVENT; TRP CAGE PEPTIDE; TRP-CAGE PEPTIDE; TRPZIP2 PROTEIN; VILLIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; TEMPERATURE; THERMODYNAMICS;

AMINO ACID SEQUENCE; MICROFILAMENT PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOLVENTS; TEMPERATURE; THERMODYNAMICS;

EID: 77954209324     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3435332     Document Type: Article

References (71)

1. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsovvelyaminov, J. Chem. Phys. JCPSA6 0021-9606 96, 1776 (1992) 10.1063/1.462133
2. E. Marinari and G. Parisi, Europhys. Lett. EULEEJ 0295-5075 19, 451 (1992) 10.1209/0295-5075/19/6/002
3. C. Zhang and J. Ma, Phys. Rev. E PLEEE8 1063-651X 76, 036708 (2007) 10.1103/PhysRevE.76.036708 (Pubitemid 47477048)
4. H. Li, M. Fajer, and W. Yang, J. Chem. Phys. JCPSA6 0021-9606 126, 024106 (2007) 10.1063/1.2424700 (Pubitemid 46105650)
5. Y. Q. Gao, J. Chem. Phys. JCPSA6 0021-9606 128, 064105 (2008); 10.1063/1.2825614 (Pubitemid 351264556)
6. J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. PRLTAO 0031-9007 97, 050601 (2006). 10.1003/PhysRevLett.97.050601
7. C. Zhang and J. Ma, J. Chem. Phys. JCPSA6 0021-9606 130, 194112 (2009). 10.1063/1.3139192
8. C. J. Geyer, Proceedings of the 23rd Symposium on the Interface (American Statistical Association, New York, 1991)
9. U. H. E. Hansmann, Chem. Phys. Lett. CHPLBC 0009-2614 281, 140 (1997) 10.1016/S0009-2614(97)01198-6
10. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. JUPSAU 0031-9015 65, 1604 (1996) 10.1143/JPSJ.65.1604
11. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett. PRLTAO 0031-9007 57, 2607 (1986); 10.1103/PhysRevLett.57.2607
12. J. Kim, J. E. Straub, and T. Keyes, J. Chem. Phys. JCPSA6 0021-9606 132, 224107 (2010). 10.1063/1.3432176
13. E. Darve and A. Pohorille, J. Chem. Phys. JCPSA6 0021-9606 115, 9169 (2001) 10.1063/1.1410978 (Pubitemid 33128021)
14. M. Fasnacht, R. H. Swendsen, and J. M. Rosenberg, Phys. Rev. E PLEEE8 1063-651X 69, 056704 (2004). 10.1103/PhysRevE.69.056704
15. A. B. Adib and C. Jarzynski, J. Chem. Phys. JCPSA6 0021-9606 122, 014114 (2005). 10.1063/1.1829631 (Pubitemid 41047757)
16. C. Zhang and J. Ma, arXiv:1005.0170 (2010).
17. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 61, 2635 (1988) 10.1103/PhysRevLett.61.2635
18. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
19. A. E. Ferdinand and M. E. Fisher, Phys. Rev. PRVAAH 0096-8250 185, 832 (1969). 10.1103/PhysRev.185.832
20. P. D. Beale, Phys. Rev. Lett. PRLTAO 0031-9007 76, 78 (1996). 10.1103/PhysRevLett.76.78
21. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. Berendsen, J. Comput. Chem. JCCHDD 0192-8651 26, 1701 (2005) 10.1002/jcc.20291 (Pubitemid 43076182)
22. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008) 10.1021/ct700301q
23. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. JMOBAK 0022-2836 7, 306 (2001)
24. H. J. C. Berendsen and D. van der Spoel, Comput. Phys. Commun. CPHCBZ 0010-4655 91, 43 (1995). 10.1016/0010-4655(95)00042-E
25. E. J. Sorin and V. S. Pande, Biophys. J. BIOJAU 0006-3495 88, 2472 (2005). 10.1529/biophysj.104.051938 (Pubitemid 40976118)
26. J. C. W. L. Jorgensen, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. JCPSA6 0021-9606 79, 926 (1983). 10.1063/1.445869
27. U. Essman, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 103, 8577 (1995). 10.1063/1.470117
28. G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. JCPSA6 0021-9606 126, 014101 (2007). 10.1063/1.2408420 (Pubitemid 46068390)
29. S. Miyamoto and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 13, 952 (1992). 10.1002/jcc.540130805
30. B. Hess, J. Chem. Theory Comput. JCTCCE 1549-9618 4, 116 (2008). 10.1021/ct700200b
31. A. G. Cochran, N. J. Skelton, and M. A. Starovasnik, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 98, 5578 (2001). 10.1073/pnas.091100898 (Pubitemid 32435684)
32. J. Zhang, M. Qin, and W. Wang, Proteins 18PLAF 0887-3585 62, 672 (2006) 10.1002/prot.20813 (Pubitemid 43191254)
33. J. W. Pitera, I. Haque, and W. C. Swope, J. Chem. Phys. JCPSA6 0021-9606 124, 141102 (2006). 10.1063/1.2190226
34. L. Yang, Q. Shao, and Y. Q. Gao, J. Phys. Chem. B JPCBFK 1089-5647 113, 803 (2009) 10.1021/jp803160f
35. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 4077 (2004) 10.1073/pnas. 0305260101 (Pubitemid 38405886)
36. A. E. Roitberg, A. Okur, and C. Simmerling, J. Phys. Chem. B JPCBFK 1089-5647 111, 2415 (2007) 10.1021/jp068335b (Pubitemid 46548721)
37. C. Chen and Y. Xiao, Bioinformatics BOINFP 1367-4803 24, 659 (2008) 10.1093/bioinformatics/btn029 (Pubitemid 351321209)
38. W. Y. Yang, J. W. Pitera, W. C. Swope, and M. Gruebele, J. Mol. Biol. JMOBAK 0022-2836 336, 241 (2004). 10.1016/j.jmb.2003.11.033 (Pubitemid 38102345)
39. J. P. Ulmschneider, M. B. Ulmschneider, and A. Di Nola, J. Phys. Chem. B JPCBFK 1089-5647 110, 16733 (2006). 10.1021/jp061619b (Pubitemid 44373403)
40. J. Wang, P. Cieplak, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 21, 1049 (2000). 10.1002/1096-987X(200009)21:12<1049::AID-JCC33.0.CO;2-F
41. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins 18PLAF 0887-3585 65, 712 (2006). 10.1002/prot.21123 (Pubitemid 44583220)
42. J. W. Neidigh, R. M. Fesinmeyer, and N. H. Andersen, Nat. Struct. Biol. NSBIEW 1072-8368 9, 425 (2002). 10.1038/nsb798 (Pubitemid 34568786)
43. L. Qiu, S. A. Pabit, A. E. Roitberg, and S. J. Hagen, J. Am. Chem. Soc. JACSAT 0002-7863 124, 12952 (2002). 10.1021/ja0279141 (Pubitemid 35247099)
44. R. Zhou, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 13280 (2003) 10.1073/pnas.2233312100 (Pubitemid 37444733)
45. D. Paschek, S. Hempel, and A. E. Garcia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 17754 (2008) 10.1073/pnas.0804775105
46. J. Juraszek and P. G. Bolhuis, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 15859 (2006); 10.1073/pnas.0606692103 (Pubitemid 44657557)
47. S. Kannan and M. Zacharias, Proteins 76, 448 (2008). 10.1002/prot.22359
48. R. Day, D. Paschek, and A. E. Garcia, Proteins 18PLAF 0887-3585 78, 11 (2010).
49. L. Yang, M. P. Grubb, and Y. Q. Gao, J. Chem. Phys. JCPSA6 0021-9606 126, 125102 (2007) 10.1063/1.2709639 (Pubitemid 46517175)
50. C. Simmerling, B. Strockbine, and A. E. Roitberg, J. Am. Chem. Soc. JACSAT 0002-7863 124, 11258 (2002) 10.1021/ja0273851
51. S. Chowdhury, M. C. Lee, G. Xiong, and Y. Duan, J. Mol. Biol. JMOBAK 0022-2836 327, 711 (2003) 10.1016/S0022-2836(03)00177-3 (Pubitemid 36300811)
52. C. D. Snow, B. Zagrovic, and V. S. Pande, J. Am. Chem. Soc. JACSAT 0002-7863 124, 14548 (2002) 10.1021/ja028604l (Pubitemid 35425023)
53. J. W. Pitera and W. Swope, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 7587 (2003). 10.1073/pnas.1330954100 (Pubitemid 36760013)
54. W. W. Streicher and G. I. Makhatadze, Biochemistry BICHAW 0006-2960 46, 2876 (2007). 10.1021/bi602424x (Pubitemid 46417925)
55. Y. Duan and P. A. Kollman, Science SCIEAS 0036-8075 282, 740 (1998). 10.1126/science.282.5389.740 (Pubitemid 28489385)
56. T. K. Chiu, J. Kubelka, R. Herbst-Irmer, W. A. Eaton, J. Hofrichter, and D. R. Davies, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 7517 (2005). 10.1073/pnas.0502495102 (Pubitemid 40741003)
57. G. Jayachandran, V. Vishal, and V. S. Pande, J. Chem. Phys. JCPSA6 0021-9606 124, 164902 (2006). 10.1063/1.2186317
58. H. Lei, C. Wu, H. Liu, and Y. Duan, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 104, 4925 (2007). 10.1073/pnas.0608432104 (Pubitemid 47186153)
59. D. L. Ensign, P. M. Kasson, and V. S. Pande, J. Mol. Biol. JMOBAK 0022-2836 374, 806 (2007) 10.1016/j.jmb.2007.09.069 (Pubitemid 350019606)
60. C. D. Snow, H. Nguyen, V. S. Pande, and M. Gruebele, Nature (London) NATUAS 0028-0836 420, 102 (2002) 10.1038/nature01160 (Pubitemid 35291448)
61. M. Y. Shen and K. F. Freed, Proteins 18PLAF 0887-3585 49, 439 (2002) 10.1002/prot.10230 (Pubitemid 35388130)
62. A. Fernández, M. Y. Shen, A. Colubri, T. R. Sosnick, R. S. Berry, and K. F. Freed, Biochemistry BICHAW 0006-2960 42, 664 (2003) 10.1021/bi026510i (Pubitemid 36133290)
63. B. Zagrovic, C. D. Snow, M. R. Shirts, and V. S. Pande, J. Mol. Biol. JMOBAK 0022-2836 323, 927 (2002). 10.1016/S0022-2836(02)00997-X (Pubitemid 35341065)
64. P. L. Freddolino and K. Schulten, Biophys. J. BIOJAU 0006-3495 97, 2338 (2009). 10.1016/j.bpj.2009.08.012
65. J. Kubelka, W. A. Eaton, and J. Hofrichter, J. Mol. Biol. JMOBAK 0022-2836 329, 625 (2003). 10.1016/S0022-2836(03)00519-9 (Pubitemid 36629358)
66. M. Wang, Y. Tang, S. Sato, L. Vugmeyster, C. J. McKnight, and D. P. Raleigh, J. Am. Chem. Soc. JACSAT 0002-7863 125, 6032 (2003). 10.1021/ja028752b (Pubitemid 36582956)
67. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, J. Comput. Chem. JCCHDD 0192-8651 24, 1999 (2003). 10.1002/jcc.10349
68. R. B. Best, N. V. Buchete, and G. Hummer, Biophys J 95, L07 (2008) 10.1529/biophysj.108.132696
69. R. B. Best and G. Hummer, J. Phys. Chem. B JPCBFK 1089-5647 113, 9004 (2009) 10.1021/jp901540t
70. E. J. Thompson, A. J. DePaul, S. S. Patel, and E. J. Sorin, PLoS ONE ZZZZZZ 1932-6203 5, e10056 (2010). 10.1371/journal.pone.0010056
71. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graph. 14, 33 (1996). 10.1016/0263-7855(96)00018-5 0263-7855 (Pubitemid 26152973)