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题名: Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
作者: Wu, Johnny2;  Zhen, Xia2;  Shen, Hujun1;  Li, Guohui1;  Ren, Pengyu2
关键词: biochemistry ;  intermolecular forces ;  macromolecules ;  molecular biophysics ;  molecular configurations ;  molecular dynamics method ;  polymer solutions ;  solvation ;  solvent effects
刊名: JOURNAL OF CHEMICAL PHYSICS
发表日期: 2011-10-21
DOI: 10.1063/1.3651626
卷: 135, 期:15
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Physics, Atomic, Molecular & Chemical
研究领域[WOS]: Physics
英文摘要: A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3651626]
关键词[WOS]: FORCE-FIELD ;  MOLECULAR-MECHANICS ;  BORN RADII ;  IN-VACUO ;  MODEL ;  DYNAMICS ;  POLYALANINE ;  CONTINUUM ;  HELICES ;  SIMULATIONS
语种: 英语
WOS记录号: WOS:000296516800051
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/142592
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
2.Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA

Recommended Citation:
Wu, Johnny,Zhen, Xia,Shen, Hujun,et al. Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent[J]. JOURNAL OF CHEMICAL PHYSICS,2011,135(15).
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