Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
文献类型：期刊论文
| 作者 | Wu, Johnny2; Zhen, Xia2; Shen, Hujun1; Li, Guohui1; Ren, Pengyu2 |
| 刊名 | journal of chemical physics
 |
| 出版日期 | 2011-10-21 |
| 卷号 | 135期号:15 |
| 关键词 | biochemistry intermolecular forces macromolecules molecular biophysics molecular configurations molecular dynamics method polymer solutions solvation solvent effects |
| 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] |
| WOS标题词 | science & technology ; physical sciences |
| 类目[WOS] | physics, atomic, molecular & chemical |
| 研究领域[WOS] | physics |
| 关键词[WOS] | force-field ; molecular-mechanics ; born radii ; in-vacuo ; model ; dynamics ; polyalanine ; continuum ; helices ; simulations |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000296516800051 |
| 公开日期 | 2015-11-17 |
| 源URL | [http://159.226.238.44/handle/321008/142592]  |
| 专题 | 大连化学物理研究所_中国科学院大连化学物理研究所 |
| 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 |
| 推荐引用方式 GB/T 7714 | 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). |
| APA | Wu, Johnny,Zhen, Xia,Shen, Hujun,Li, Guohui,&Ren, Pengyu.(2011).Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.journal of chemical physics,135(15). |
| MLA | Wu, Johnny,et al."Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent".journal of chemical physics 135.15(2011). |
入库方式： OAI收割
来源：大连化学物理研究所
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