Multiscale theory and computational method for biomolecule simulations

Li Wen-Fei; Zhang Jian; Wang Jun; Wang Wei

doi:10.7498/aps.64.098701

Abstract

Molecular simulation is one of the most important ways of studying biomolecules. In the last two decades, by combining the molecular simulations with experiments, a number of key features of structure and dynamics of biomolecules have been reflealed. Traditional molecular simulations often use the all-atom model or some coarse grained models. In practical applications, however, these all-atom models and coarse grained models encounter the bottlenecks in accuracy and efficiency, respectively, which hinder their applications to some extent. In reflent years, the multiscale models have attracted much attention in the field of biomolecule simulations. In the multiscale model, the atomistic models and coarse grained models are combined together based on the principle of statistical physics, and thus the bottlenecks encountered in the traditional models can be overcome. The currently available multiscale models can be classified into four categories according to the coupling ways between the all-atom model and coarse gained model. They are 1) hybrid resolution multiscale model, 2) parallel coupling multiscale model, 3) one-way coupling multiscale model, and 4) self-learning multiscale model. All these multiscale strategies have achieved great success in certain aspects in the field of biomolecule simulations, including protein folding, aggregation, and functional motions of many kinds of protein machineries. In this review, we briefly introduce the above-mentioned four multiscale strategies, and the examples of their applications. We also discuss the limitations and advantages, as well as the application scopes of these multiscale methods. The directions for future work on improving these multiscale models are also suggested. Finally, a summary and some prospects are preflented.

Keywords:

Authors and contacts

1.
National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China;
2.
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11174134, 11334004, 11274157, 11174133), and the Natural Science Foundation of Jiangsu Province (Grant No. BK2011546).

References

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[51]	Moritsugu K, Terada T, Kidera A 2010 J. Chem. Phys. 133 224105
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[53]	Li W F, Wang W, Takada S 2014 Proc. Natl. Acad. Sci. USA 111 10550
[54]	Li W F, Terakawa T, Wang W, Takada S 2012 Proc. Natl. Acad. Sci. USA 109 17789
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[59]	Hori N, Takada S 2012 J. Chem. Theory Comput. 8 3384
[60]	Gohlke H, Kiel C, Case D A 2003 J. Mol. Biol. 330 891
[61]	Li W F, Wang J, Zhang J, Wang W 2014 Curr. Opin. Struct. Biol. 30 25
[62]	Terakawa T, Takada S 2011 Biophys. J. 101 1450
[63]	Bryngelson J D, Onuchic J N, Socci N D, Wolynes P G 1995 Proteins 21 167
[64]	Pirchi M, Ziv G, Riven I, Cohen SS, Zohar N, Barak Y, Haran G 2011 Nat. Commun. 2 493
[65]	King N P, Jacobitz A W, Sawaya M R, Goldschmidt L, Yeates T O 2010 Proc. Natl. Acad. Sci. USA 107 20732
[66]	Kenzaki H, Koga N, Hori N, Kanada R, Li W, Okazaki K I, Yao X Q, Takada S 1992 J. Chem. Theory Comput. 7 1979
[67]	Kumar S, Bouzida D, Swendsen R H, Kollman P A, Rosenberg J M 2013 J. Comput. Chem. 13 1011
[68]	Heath A P, Kavraki L E, Clementi C 2007 Proteins 68 646
[69]	Gront D, Kmiecik S, Kolinski A 2007 J. Comput. Chem. 28 1593
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Cited By

[1]	Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P 2007 Molecular Biology of the Cell (1st Ed.) (New York: Garland Science, Taylor & Francis Group)
[2]	Abrahams J P, Leslie A G W, Lutter R, Walker J E 1994 Nature 370 621
[3]	Sun B, Wei K J, Zhang B, Zhang X H, Dou S X, Li M, Xi X G 2008 Embo. J. 27 3279
[4]	Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT 2009 Cell 139 744
[5]	Stigler J, Ziegler F, Gieseke A, Gebhardt J C, Rief M 2011 Science 334 512
[6]	Lv C, Gao X, Li W, Xue B, Qin M, Burtnick L D, Zhou H, Cao Y, Robinson R C, Wang W 2014 Nat. Commun. 5 4623
[7]	Lindorff-Larsen K, Piana S, Dror RO, Shaw D E 2011 Science 334 517
[8]	Zhang J, Li W F, Wang J, Qin M, Wu L, Yan Z Q, Xu W X, Zuo G H, Wang W 2009 Iubmb Life 61 627
[9]	Levitt M, Warshel A 1975 Nature 253 694
[10]	Li W F, Zhang J, Wang J, Wang W 2008 J. Am. Chem. Soc. 130 892
[11]	Duan Y, Kollman P A 1998 Science 282 740
[12]	Zhao G P, Perilla J R, Yufenyuy E L, Meng X, Chen B, Ning J Y, Ahn J, Gronenborn A M, Schulten K, Aiken C 2013 Nature 497 643
[13]	Guo C, Luo Y, Zhou R H, Wei G H 2012 ACS Nano 6 3907
[14]	Xie L G, Luo Y, Lin D D, Xi W H, Yang X J, Wei G H 2014 Nanoscale 6 9752
[15]	He J B, Zhang Z Y, Shi Y Y, Liu H Y 2013 J. Chem. Phys. 119 4005
[16]	Li W F, Zhang J, Su Y, Wang J, Qin M, Wang W 2007 J. Phys. Chem. B 111 13814
[17]	Bian Y, Tan C, Wang J, Sheng Y, Zhang J, Wang W 2014 PLoS Comput. Biol. 10 e1003562
[18]	Inanami T, Terada T P, Sasai M 2014 Proc. Natl. Acad. Sci. USA. 111 15969
[19]	Huang Y D, Shuai J W 2013 J. Phys. Chem. B 7 11
[20]	Takada S 2012 Curr. Opin. Struct. Biol. 22 130
[21]	Vendruscolo M, Dobson CM 2011 Current Biology 21 R68
[22]	Tozzini V 2010 Q. Rev. Biophys. 43 333
[23]	Tozzini V 2005 Curr. Opin. Struc. Biol. 15 144
[24]	Xu W X, Lai Z Z, Oliveira R J, Leite V B P, Wang J 2012 J. Phys. Chem. B 116 5152
[25]	Yao X Q, Kenzaki H, Murakami S, Takada S 2010 Nature Commun. 1 1116
[26]	Moritsugu K, Smith J C 2007 Biophys. J. 93 3460
[27]	Marrink S J, Risselada H J, Yefimov S, Tieleman D P, de Vries A H 2007 J. Phys. Chem. B 111 7812
[28]	Zuo G H, Wang J, Wang W 2006 Proteins 63 165
[29]	Koga N, Takada S 2001 J. Mol. Biol. 313 171
[30]	Clementi C, Nymeyer H, Onuchic J N 2000 J. Mol. Biol. 298 937
[31]	Onuchic J N, Luthey-Schulten Z, Wolynes P G 1997 Annu. Rev. Phys. Chem. 48 545
[32]	Go N 1983 Annu. Rev. Biophys. Bioeng. 12 183
[33]	Zhou H X 2014 Curr. Opin. Struct. Biol. 25 67
[34]	Li W F, Yoshii H, Hori N, Kameda T, Takada S 2010 Methods 52 106
[35]	Li W F, Takada S 2010 Biophys. J. 99 3029
[36]	Li WF, Takada S 2009 J. Chem. Phys. 130 214108
[37]	Praprotnik M, Delle Site L, Krefler K 2008 Annu. Rev Phys. Chem. 59 545
[38]	Liu P, Shi Q, Lyman E, Voth G A 2008 J. Chem. Phys. 129 114103
[39]	Liu P, Voth G A 2007 J. Chem. Phys. 126 045106
[40]	Chu J W, Ayton G S, Izvekov S, Voth G 2007 Mol. Phys. 105 167
[41]	Lyman E, Zuckerman D M 2006 J. Chem. Theory Comput. 2 656
[42]	Lyman E, Ytreflerg F M, Zuckerman D M 2006 Phys. Rev. Lett. 96 028105
[43]	Christen M, van Gunsteren W F 2006 J. Chem. Phys. 124 154106
[44]	Neri M, Anselmi C, Cascella M, Maritan A, Carloni P 2005 Phys. Rev. Lett. 95 218102
[45]	Lwin T Z, Luo R 2005 J. Chem. Phys. 123 194904
[46]	Izvekov S, Voth G A 2005 J. Phys. Chem. B 109 2469
[47]	Reith D, Putz M, Muller-Plathe F 2003 J. Comput. Chem. 24 1624
[48]	Peter C, Krefler K 2010 Faraday Discuss 144 9
[49]	Peter C, Krefler K 2009 Soft Matter 5 4357
[50]	Praprotnik M, Delle Site L, Krefler K J. Chem. Phys. 123 224106
[51]	Moritsugu K, Terada T, Kidera A 2010 J. Chem. Phys. 133 224105
[52]	Moritsugu K, Terada T, Kidera A 2012 J. Am. Chem. Soc. 134 7094
[53]	Li W F, Wang W, Takada S 2014 Proc. Natl. Acad. Sci. USA 111 10550
[54]	Li W F, Terakawa T, Wang W, Takada S 2012 Proc. Natl. Acad. Sci. USA 109 17789
[55]	Li W F, Wolynes P G, Takada S 2011 Proc. Natl. Acad. Sci. USA 108 3504
[56]	Warshel A, Levitt M 1976 J. Mol. Biol. 103 23
[57]	Thorpe I F, Zhou J, Voth G A 2008 J. Phys. Chem. B 112 13079
[58]	Trylska J, Tozzini V, McCammon J A 2005 Biophys. J. 89 1455
[59]	Hori N, Takada S 2012 J. Chem. Theory Comput. 8 3384
[60]	Gohlke H, Kiel C, Case D A 2003 J. Mol. Biol. 330 891
[61]	Li W F, Wang J, Zhang J, Wang W 2014 Curr. Opin. Struct. Biol. 30 25
[62]	Terakawa T, Takada S 2011 Biophys. J. 101 1450
[63]	Bryngelson J D, Onuchic J N, Socci N D, Wolynes P G 1995 Proteins 21 167
[64]	Pirchi M, Ziv G, Riven I, Cohen SS, Zohar N, Barak Y, Haran G 2011 Nat. Commun. 2 493
[65]	King N P, Jacobitz A W, Sawaya M R, Goldschmidt L, Yeates T O 2010 Proc. Natl. Acad. Sci. USA 107 20732
[66]	Kenzaki H, Koga N, Hori N, Kanada R, Li W, Okazaki K I, Yao X Q, Takada S 1992 J. Chem. Theory Comput. 7 1979
[67]	Kumar S, Bouzida D, Swendsen R H, Kollman P A, Rosenberg J M 2013 J. Comput. Chem. 13 1011
[68]	Heath A P, Kavraki L E, Clementi C 2007 Proteins 68 646
[69]	Gront D, Kmiecik S, Kolinski A 2007 J. Comput. Chem. 28 1593
[70]	Canutescu A A, Shelenkov A A, Dunbrack R L 2003 Protein Sci. 12 2001

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Vol. 64, Issue 9 - 2015-05-05

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