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学科主题: 物理化学
题名: Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials
作者: Shen, Hujun1;  Li, Yan1;  Ren, Pengyu2;  Zhang, Dinglin1;  Li, Guohui1
通讯作者: 李国辉
刊名: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
发表日期: 2014-02-01
DOI: 10.1021/ct400974z
卷: 10, 期:2, 页:731-750
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Physical ;  Physics, Atomic, Molecular & Chemical
研究领域[WOS]: Chemistry ;  Physics
英文摘要: Gay-Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10-200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.
关键词[WOS]: PACE FORCE-FIELD ;  MOLECULAR-DYNAMICS ;  STATISTICAL POTENTIALS ;  BIOMOLECULAR SIMULATIONS ;  STRUCTURE PREDICTION ;  FOLDING SIMULATIONS ;  MECHANICS ;  EXTENSION ;  PATHWAYS ;  BACKBONE
语种: 英语
WOS记录号: WOS:000331342400027
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/144020
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, Lab Mol Modeling & Design, Dalian 116023, Peoples R China
2.Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA

Recommended Citation:
Shen, Hujun,Li, Yan,Ren, Pengyu,et al. Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2014,10(2):731-750.
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