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A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent
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1.
1. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers 60, 96 (2001).
http://dx.doi.org/10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F
2.
2. J. Higo, J. Ikebe, N. Kamiya, and H. Nakamura, Biophys. Rev. 4, 27 (2012).
http://dx.doi.org/10.1007/s12551-011-0063-6
3.
3. G. H. Paine and H. A. Scheraga, Biopolymers 24, 1391 (1985).
http://dx.doi.org/10.1002/bip.360240802
4.
4. M. Mezei, J. Comput. Phys. 68, 237 (1987).
http://dx.doi.org/10.1016/0021-9991(87)90054-4
5.
5. U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
http://dx.doi.org/10.1016/0009-2614(96)00761-0
6.
6. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
http://dx.doi.org/10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I
7.
7. Y. Iba, G. Chikenji, and M. Kikuchi, J. Phys. Soc. Jpn. 67, 3327 (1998).
http://dx.doi.org/10.1143/JPSJ.67.3327
8.
8. F. Wang and D. P. Landau, Phys. Rev. E 64, 056101 (2001).
http://dx.doi.org/10.1103/PhysRevE.64.056101
9.
9. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002).
http://dx.doi.org/10.1063/1.1472510
10.
10. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
http://dx.doi.org/10.1073/pnas.202427399
11.
11. Y. Fukunishi, Y. Mikami, and H. Nakamura, J. Phys. Chem. B 107, 13201 (2003).
http://dx.doi.org/10.1021/jp035478e
12.
12. J. G. Kim, Y. Fukunishi, A. Kidera, and H. Nakamura, Phys. Rev. E 70, 057103 (2004).
http://dx.doi.org/10.1103/PhysRevE.70.057103
13.
13. H. Okumura and Y. Okamoto, Chem. Phys. Lett. 391, 248 (2004).
http://dx.doi.org/10.1016/j.cplett.2004.04.073
14.
14. L. Zheng, N. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008).
http://dx.doi.org/10.1073/pnas.0810631106
15.
15. J. Kim, T. Keyes, and J. E. Straub, J. Chem. Phys. 132, 224107 (2010).
http://dx.doi.org/10.1063/1.3432176
16.
16. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992).
http://dx.doi.org/10.1103/PhysRevLett.68.9
17.
17. U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 14, 1333 (1993).
http://dx.doi.org/10.1002/jcc.540141110
18.
18. A. Kidera, Proc. Natl. Acad. Sci. U.S.A. 92, 9886 (1995).
http://dx.doi.org/10.1073/pnas.92.21.9886
19.
19. N. Hori, G. Chikenji, R. Berry, and S. Takada, Proc. Natl. Acad. Sci. U.S.A. 106, 73 (2009).
http://dx.doi.org/10.1073/pnas.0811560106
20.
20. N. Nakajima, H. Nakamura, and A. Kidera, J. Phys. Chem. 101, 817 (1997).
http://dx.doi.org/10.1021/jp962142e
21.
21. J. Higo, O. V. Galzitskaya, S. Ono, and H. Nakamura, Chem. Phys. Lett. 337, 169 (2001).
http://dx.doi.org/10.1016/S0009-2614(01)00118-X
22.
22. J. Ikebe, N. Kamiya, H. Shindo, H. Nakamura, and J. Higo, Chem. Phys. Lett. 443, 364 (2007).
http://dx.doi.org/10.1016/j.cplett.2007.06.102
23.
23. J. Ikebe, D. M. Standley, H. Nakamura, and J. Higo, Protein Sci. 20, 187 (2011).
http://dx.doi.org/10.1002/pro.553
24.
24. J. Higo, N. Kamiya, T. Sugihara, Y. Yonezawa, and H. Nakamura, Chem. Phys. Lett. 473, 326 (2009).
http://dx.doi.org/10.1016/j.cplett.2009.03.077
25.
25. J. Ikebe, K. Umezawa, N. Kamiya, T. Sugihara, Y. Yonezawa, Y. Takano, H. Nakamura, and J. Higo, J. Comput. Chem. 32, 1286 (2011).
http://dx.doi.org/10.1002/jcc.21710
26.
26. J. Higo, Y. Nishimura, and H. Nakamura, J. Am. Chem. Soc. 133, 10448 (2011).
http://dx.doi.org/10.1021/ja110338e
27.
27. J. Higo and H. Nakamura, Biophysics 8, 139 (2012).
http://dx.doi.org/10.2142/biophysics.8.139
28.
28. M. Yanagisawa and T. Masaki, Trends Pharmacol. Sci. 10, 374 (1989).
http://dx.doi.org/10.1016/0165-6147(89)90011-4
29.
29. K. A. Hickey, G. B. Rubani, R. J. Paul, and R. F. Highsmith, Am. J. Physiol. 248, C550 (1985).
30.
30. M. N. Gillespie, J. O. Owasoyo, I. F. McMurtry, and R. F. O’Brien, J. Pharmacol. Exp. Ther. 236, 339 (1986).
31.
31. M. Yanagisawa, H. Kurihara, S. Kimura, Y. Tomobe, M. Kobayashi, Y. Mitsui, Y. Yazaki, K. Goto, and T. Masaki, Nature (London) 332, 411 (1988).
http://dx.doi.org/10.1038/332411a0
32.
32. K. A. Fagan, I. F. McMurtry, and D. M. Rodman, Respir. Res. 2, 90 (2001).
http://dx.doi.org/10.1186/rr44
33.
33. J. Pernow, A. Shemyakin, and F. Böhm, Life Sci. 91, 507 (2012).
http://dx.doi.org/10.1016/j.lfs.2012.03.029
34.
34. T. Sugiyama, S. Moriya, H. Oku, and I. Azuma, Surv. Ophthalmol. 39(Suppl. 1), S49 (1995).
http://dx.doi.org/10.1016/S0039-6257(05)80073-6
35.
35. M. Cellini, G. L. Possati, V. Profazio, M. Sbrocca, N. Caramazza, and R. Caramazza, Acta Ophthalmol. Scand. Suppl. 224, 11 (1997).
http://dx.doi.org/10.1111/j.1600-0420.1997.tb00448.x
36.
36. T. Yorio, R. Krishnamoorthy, and G. Prasanna, J. Glaucoma 11, 259 (2002).
http://dx.doi.org/10.1097/00061198-200206000-00016
37.
37. N. H. Andersen, C. Chen, T. M. Marschner, S. R. Krystek, Jr., and D. A. Bassolinoil, Biochemistry 31, 1280 (1992).
http://dx.doi.org/10.1021/bi00120a003
38.
38. H. Takashima, N. Mimura, T. Ohkubo, T. Yoshida, H. Tamaoki, and Y. Kobayashi, J. Am. Chem. Soc. 126, 4504 (2004).
http://dx.doi.org/10.1021/ja031637w
39.
39. S. Endo, H. Inooka, Y. Ishibashi, C. Kitada, E. Mizuta, and M. Fujino, FEBS Lett. 257, 149 (1989).
http://dx.doi.org/10.1016/0014-5793(89)81808-3
40.
40. R. W. Janes, D. H. Peapus, and B. A. Wallace, Nat. Struct. Biol. 1, 311 (1994).
http://dx.doi.org/10.1038/nsb0594-311
41.
41. Y. Kobayashi, H. Takashima, H. Tamaoki, Y. Kyogoku, P. Lambert, H. Kuroda, N. Chino, T. X. Watanabe, T. Kimura, S. Sakakibara, and L. Moroder, Biopolymers 31, 1213 (1991).
http://dx.doi.org/10.1002/bip.360311009
42.
42. H. Tamaoki, R. Miura, M. Kusunoki, Y. Kyogoku, Y. Kobayashi, and L. Moroder, Protein Eng. 11, 649 (1998).
http://dx.doi.org/10.1093/protein/11.8.649
43.
43. A. Aumelas, L. Chiche, S. Kubo, N. Chino, H. Tamaoki, and Y. Kobayashi, Biochemistry 34, 4546 (1995).
http://dx.doi.org/10.1021/bi00014a007
44.
44. F. Hoh, R. Cerdan, Q. Kaas, Y. Nishi, L. Chiche, S. Kubo, N. Chino, Y. Kobayashi, C. Dumas, and A. Aumelas, Biochemistry 43, 15154 (2004).
http://dx.doi.org/10.1021/bi049098a
45.
45. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
http://dx.doi.org/10.1016/S0009-2614(99)01123-9
46.
46. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 329, 261 (2000).
http://dx.doi.org/10.1016/S0009-2614(00)00999-4
47.
47. K. Morikami, T. Nakai, A. Kidera, M. Saito, and H. Nakamura, Comput. Chem. 16, 243 (1992).
http://dx.doi.org/10.1016/0097-8485(92)80010-W
48.
48. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
http://dx.doi.org/10.1016/0021-9991(77)90098-5
49.
49. H.-Q. Ding, N. Karasawa, and W. A. Goddard III, J. Chem. Phys. 97, 4309 (1992).
http://dx.doi.org/10.1063/1.463935
50.
50. D. J. Evans and G. P. Morriss, Phys. Lett. A 98, 433 (1983).
http://dx.doi.org/10.1016/0375-9601(83)90256-6
51.
51. N. Kamiya, Y. S. Watanabe, S. Ono, and J. Higo, Chem. Phys. Lett. 401, 312 (2005).
http://dx.doi.org/10.1016/j.cplett.2004.11.070
52.
52. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
http://dx.doi.org/10.1021/ja00124a002
53.
53. P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot, and A. Pohorille, in Computer Simulation of Biomolecular Systems, edited by W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson (Kluwer/ESCOM, Dordrecht, 1997), Vol. 3, p. 83.
54.
54. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
http://dx.doi.org/10.1063/1.445869
55.
55. T. Terada, Y. Matsuo, and A. Kidera, J. Chem. Phys. 118, 4306 (2003).
http://dx.doi.org/10.1063/1.1541613
56.
56. See supplementary material at http://dx.doi.org/10.1063/1.4803468 for testing the virtual-state coupling method introducing a simple model, presenting the free-energy landscape in different conformational spaces, and to report results of additional conventional McMD by using Emc obtained from V-McMD. [Supplementary Material]
57.
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/content/aip/journal/jcp/138/18/10.1063/1.4803468
2013-05-10
2014-07-28

Abstract

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

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Scitation: A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/18/10.1063/1.4803468
10.1063/1.4803468
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