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Chin. Phys. B, 2017, Vol. 26(5): 050202    DOI: 10.1088/1674-1056/26/5/050202
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Smoothing potential energy surface of proteins by hybrid coarse grained approach

Yukun Lu(卢禹锟)1,2, Xin Zhou(周昕)2, ZhongCan OuYang(欧阳钟灿)1
1 Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China;
2 School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
Abstract  

Coarse-grained (CG) simulations can more efficiently study large conformational changes of biological polymers but usually lose accuracies in the details. Lots of different hybrid models involving multiple different resolutions have been developed to overcome the difficulty. Here we propose a novel effective hybrid CG (hyCG) approach which mixes the fine-grained interaction and its average in CG space to form a more smoothing potential energy surface. The hyCG approximately reproduces the potential of mean force in the CG space, and multiple mixed potentials can be further combined together to form a single effective force field for achieving both high efficiency and high accuracy. We illustrate the hyCG method in Trp-cage and Villin headpiece proteins to exhibit the folding of proteins. The topology of the folding landscape and thus the folding paths are preserved, while the folding is boosted nearly one order of magnitude faster. It indicates that the hyCG approach could be applied as an efficient force field in proteins.

Keywords:  coarse-grained      hybrid force field      enhanced sampling      protein folding  
Received:  10 January 2017      Revised:  13 February 2017      Accepted manuscript online: 
PACS:  02.50.-r (Probability theory, stochastic processes, and statistics)  
  87.10.Tf (Molecular dynamics simulation)  
  87.14.E- (Proteins)  
Fund: 

Project supported by the National Basic Research Program of China (Grant No. 2013CB932803), the National Natural Science Foundation of China (Grant No. 11574310), and the Joint NSFC-ISF Research Program, jointly funded by the National Natural Science Foundation of China and the Israel Science Foundation (Grant No. 51561145002).

Corresponding Authors:  Xin Zhou     E-mail:  xzhou@ucas.ac.cn

Cite this article: 

Yukun Lu(卢禹锟), Xin Zhou(周昕), ZhongCan OuYang(欧阳钟灿) Smoothing potential energy surface of proteins by hybrid coarse grained approach 2017 Chin. Phys. B 26 050202

[1] Lindorff-Larsen K, Piana S, Dror R O and Shaw D E 2011 Science 334 517
[2] Akkermans R L and Briels W 2001 J. Chem. Phys. 114 1020
[3] Clark A J, McCarty J, Lyubimov I Y and Guenza M G 2012 Phys. Rev. Lett. 109 168301
[4] Izvekov S and Voth G A 2005 J. Phys. Chem. B 109 2469
[5] Liwo A, Lee J, Ripoll D R, Pillardy J and Scheraga H A 1999 Proc. Natl. Acad. Sci. USA 96 5482
[6] Marrink S J, Risselada H J, Yefimov S, Tieleman D P and De Vries A H 2007 J. Phys. Chem. B 111 7812
[7] Shell M S 2008 J. Chem. Phys. 129 144108
[8] Soper A 1996 Chemical Physics 202 295
[9] Tóth G 2007 J. Phys.: Condens. Matter 19 335222
[10] Villa A, van der Vegt N F and Peter C 2009 Physical Chemistry Chemical Physics 11 2068
[11] Villa A, Peter C and van der Vegt N F 2010 Journal of Chemical Theory and Computation 6 2434
[12] Liwo A, Arlukowicz P, Czaplewski C, Oldziej S, Pillardy J and Scheraga H A 2002 Proc. Natl. Acad. Sci. USA 99 1937
[13] Oldziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila J, Khalili M, Arnautova Y, Jagielska A and Makowski M 2005 Proc. Natl. Acad. Sci. USA 102 7547
[14] Zhou X, Jiang Y, Rasmussen S and Ziock H 2008 J. Chem. Phys. 128 174107
[15] Lu S and Zhou X 2015 Communications in Theoretical Physics 63 10
[16] Noid W 2013 J. Chem. Phys. 139 090901
[17] Tozzini V 2005 Current Opinion in Structural Biology 15 144
[18] Clementi C 2008 Current Opinion in Structural Biology 18 10
[19] Rzepiela A J, Louhivuori M, Peter C and Marrink S J 2011 Physical Chemistry Chemical Physics 13 10437
[20] Ensing B, Nielsen S O, Moore P B, Klein M L and Parrinello M 2007 Journal of Chemical Theory and Computation 3 1100
[21] Heyden A and Truhlar D G 2008 Journal of Chemical Theory and Computation 4 217
[22] Praprotnik M, Delle Site L and Kremer K 2005 J. Chem. Phys. 123 224106
[23] Christen M and van Gunsteren W F 2006 J. Chem. Phys. 124 154106
[24] Liu P and Voth G A 2007 J. Chem. Phys. 126 045106
[25] Shen L and Hu H 2014 Journal of Chemical Theory and Computation 10 2528
[26] Sugita Y and Okamoto Y 1999 Chemical Physics Letters 314 141
[27] Gao Y Q 2008 J. Chem. Phys. 128 064105
[28] Mori T, Hamers R J, Pedersen J A and Cui Q 2014 J. Phys. Chem. B 118 8210
[29] Monticelli L, Kandasamy S K, Periole X, Larson R G, Tieleman D P and Marrink S J 2008 Journal of Chemical Theory and Computation 4 819
[30] de Jong D H, Singh G, BennettWD, Arnarez C, Wassenaar T A, Schafer L V, Periole X, Tieleman D P and Marrink S J 2013 Journal of Chemical Theory and Computation 9 687
[31] Onufriev A, Bashford D and Case D A 2000 J. Phys. Chem. B 104 3712
[32] Onufriev A, Bashford D and Case D A 2004 Proteins: Structure, Function, and Bioinformatics 55 383
[33] Chen J, Im W and Brooks C L 2006 Journal of the American Chemical Society 128 3728
[34] MacKerell A D, Feig M and Brooks C L 2004 Journal of Computational Chemistry 25 1400
[35] Yang L and Gao Y Q 2009 J. Chem. Phys. 131 214109
[36] Voter A F 1998 Phys. Rev. B 57 R13985
[37] Zhou X, Jiang Y, Kremer K, Ziock H and Rasmussen S 2006 Phys. Rev. E 74 R035701
[38] Lane T J, Shukla D, Beauchamp K A and Pande V S 2013 Current Opinion in Structural Biology 23 58-65
[39] Rao F and Caflisch A 2004 Journal of Molecular Biology 342 299
[40] Noé F and Fischer S 2008 Current Opinion in Structural Biology 18 154
[41] Noé F, Schütte C, Vanden-Eijnden E, Reich L and Weikl T R 2009 Proc. Natl. Acad. Sci. USA 106 19011
[42] Bowman G R, Huang X and Pande V S 2009 Methods 49 197
[43] Gong L and Zhou X 2010 J. Phys. Chem. B 114 10266
[44] Gong L, Zhou X and OuYang Z 2015 Plos One 10 e0125932
[45] Watanabe M and Karplus M 1993 J. Chem. Phys. 99 8063-8074
[46] Humphrey W, Dalke A and Schulten K 1996 Journal of Molecular Graphics 14 33
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