Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian

Biophysical Chemistry

Volumn 137, Issue 2-3, 2008, Pages 116-125

  Xu, Weixin ^a   Mu, Yuguang ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Ab initio protein folding; Replica exchange simulation method with hybrid Hamiltonian; Trpcage

Indexed keywords

PEPTIDE; TRPCAGE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ALPHA HELIX; ARTICLE; HYBRID; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; ROOM TEMPERATURE; SIMULATION; THERMODYNAMICS;

CIRCULAR DICHROISM; HYDROPHOBICITY; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STATIC ELECTRICITY; THERMODYNAMICS; TRANSITION TEMPERATURE; WATER;

EID: 51649103970     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2008.08.002     Document Type: Article

References (69)

1. Duan Y., and Kollman P.A. Science 282 (1998) 740-744
2. Schmidt J.M.e.a. J. Am. Chem. Soc. 115 (1993) 8747-8756
3. Bursulaya B.D., and Brooks C.L. J. Phys. Chem. B. 104 (2000) 12378-12383
4. Yang W.Y., Pitera J.W., Swope W.C., and Gruebele M. J. Mol. Biol. 336 (2004) 241-251
5. Hubner I.A., Deeds E.J., and Shakhnovich E.I. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 17747-17752
6. Jayachandran G., Vishal V., and Pande V.S. J. Chem. Phys. 124 (2006) 164902
7. Mitsutake A., Sugita Y., and Okamoto Y. Biopolymers 60 (2001) 96-123
8. Berg B.A., and Neuhaus T. Phys. Rev. Lett. 68 (1992) 9-12
9. Lyubartsev A.P., Martsinovski A.A., Shevkunov S.V., and Vorontsov-Velyaminov P.N. J. Chem. Phys. 96 (1992) 1776-1783
10. Hansmann U.H.E. Chem. Phys. Lett. 281 (1997) 140-150
11. Garcia A.E., and Onuchic J.N. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 13898-13903
12. Zhou R., and Germain B.J. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 14931-14936
13. Zhang J., Qin M., and Wang W. Proteins 62 (2006) 672-685
14. Mu Y.G., Nordenskiold L., and Tam J.P. Biophys. J 90 (2006) 3983-3992
15. Fukunishi H., Watanabe O., and Takada S. J. Chem. Phys. 116 (2002) 9058-9067
16. Liu P., Kim B., Friesner R.A., and Berne B.J. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 13749-13754
17. Lwin T.Z., and Luo R. J. Chem. Phys. 123 (2005) 194904.1-194904.10
18. Cheng X., Cui G., Hornak V., and Simmerling C. J. Phys. Chem. B 109 (2005) 8220-8230
19. Lyman E., Ytreberg F.M., and Zuckerman D.M. Phys. Rev. Lett. 96 (2006) 028105.1-028105.4
20. Okur A., Wickstrom L., Layten M., Geney R., Song K., Hornak V., and Simmerling C. J. Chem. Theory. Comput. 2 (2006) 420-433
21. Mu Y.G., Yang Y., and Xu W.X. J. Chem. Phys. 127 (2007) 084119
22. Xu W.X., Lai T.F., Yang Y., and Mu Y.G. J. Chem. Phys. 128 (2008) 175105
23. Mu Y.G., Yang Y., and Xu W.X. J. Theor. Comput. Chem. 7 (2008) 177-187
24. Xu W.X., Yang Y., Mu Y.G., and Nordenskiold L. Mol. Simul. 34 (2008) 575-590
25. Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. J. Phys. Chem. B 105 (2001) 6474
26. Blundell T.L.e.a. Proc. Natl. Acad. Sci. U. S. A 78 (1981) 41754179
27. McKnight C.J., Matsudaira P.T., and Kim P.S. Nat. Struct. Biol. 4 (1997) 180184
28. Zarrinpar A., and Lim W.A. Nat. Struct. Biol. 7 (2000) 611613
29. Cochran A.G., Skelton N.J., and Starovasnik M.A. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 55785583
30. Neidigh J.W., Fesinmeyer R.M., and Andersen N.H. Nat. Struct. Biol. 9 (2002) 425-430
31. Chowdhury S., Lee M.C., Xiong G.M., and Duan Y. J. Mol. Biol. 327 (2003) 711-717
32. Zhou R.H. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 13280-13285
33. Chowdhury S., Lee M.C., and Duan Y. J. Phys. Chem. B 108 (2004) 13855-13865
34. Juraszek J., and Bolhuis P.G. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 15859-15864
35. Qiu L.L., Pabit S.A., Roitberg A.E., and Hagen S.J. J. Am. Chem. Soc. 124 (2002) 12952-12953
36. Ahmed Z., Beta I.A., Mikhonin A.V., and Asher S.A. J. Am. Chem. Soc. 127 (2005) 10943-10950
37. Neuweiler H., Doose S., and Sauer M. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 16650-16655
38. Berendsen H.J.C., van der Spoel D., and van Drunen R. Comput. Phys. Commun. 91 (1995) 43-56
39. Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. J. Am. Chem. Soc. 118 (1996) 11225-11236
40. Ferrenberg A.M., and Swendsen R.H. Phys. Rev. Lett. 63 (1998) 1195-1198
41. Xu W.X., Wang J., and Wang W. Proteins 61 (2005) 777-794
42. Snow C.D., Qiu L., Du D., Gai F., Hagen S.J., and Pande V.S. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 4077-4082
43. Sanbonmatsu K.Y., and García A.E. Proteins 46 (2002) 225-234
44. Zhan L., Chen J., and Liu W.K. Proteins 66 (2007) 436
45. Dinner A.R., Lazaridis T., and Karplus M. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 9068-9073
46. García A.E., and Sanbonmatsu K.Y. Proteins 42 (2001) 345-354
47. Zagrovic B., Sorin E.J., and Pande V.S. J. Mol. Biol. 313 (2001) 151-169
48. Zhou R., Berne B.J., and Germain R. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 14931-14936
49. Zhou R., and Berne B.J. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 12777-12782
50. Nguyen P.H., Mu Y.G., and Stock G. Proteins 60 (2005) 485-494
51. Gruebele M. C. R. Biologies 328 (2005) 701-712
52. Pitera J.W., and Swope W. Proc. Natl. Acad. Sci. U. S. A 100 (2003) 7587-7592
53. Geney R., Layten M., Gomperts R., Hornak V., and Simmerling C. J. Chem. Theory Comput. 2 (2006) 115-127
54. Kim E., Jang S., and Pak Y. J. Chem. Phys. 127 (2007) 145104-145109
55. Linhananta A., Boer J., and Chem M.L.J. Phys. 122 (2005) 114901
56. Snow C.D., Zagrovic B., and Pande V.S. J. Am. Chem. Soc. 124 (2002) 14548-14549
57. Kabsch W., and Sander C. Biopolymers 22 (1983) 2577-2637
58. Mok K.H., Kuhn L.T., Goez M., Day I.J., Lin J.C., Andersen N.H., and Hore P.J. Nature 447 (2007) 106-109
59. Simmerling C., Strockbine B., and Roitberg A.E. J. Am. Chem. Soc. 124 (2002) 11258-11259
60. Carnevali P., Toth G., Toubassi G., and Meshkat S.N. J. Am. Chem. Soc. 125 (2003) 14244-14245
61. Ota M., Ikeguchi M., and Kidera A. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 17658-17663
62. Schug A., Herges T., and Wenzel W. Phys. Rev. Lett. 91 (2003) 158102
63. Schug A., and Wenzel W. Europhys. Lett. 67 (2004) 303-313
64. Schug A., and Wenzel W. J. Chem. Phys. 122 (2005) 194711
65. Schug A., Herges T., Verma A., Lee K.H., and Wenzel W. Chem. Phys. Chem. 6 (2005) 2640-2646
66. Steinbach P.J. Proteins 57 (2004) 665-677
67. Ding F., Buldyrev S.V., and Dkholyan N.V. Biophys. J. 88 (2005) 147-155
68. Irbäck A., and Mohanty S. Biophys. J. 88 (2005) 1560-1569
69. R. Koradi, M. Billeter, and K. Wuthrich. J. Mol. Graphics. 14(51-55) 66-93.