摘要
| 原文 | 英語 |
|---|---|
| 文章編號 | 155104 |
| 期刊 | Journal of Chemical Physics |
| 卷 | 135 |
| 發行號 | 15 |
| DOIs | |
| 出版狀態 | 已發佈 - 十月 21 2011 |
| 對外發佈 | Yes |
指紋
ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry
引用此文
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. / Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu.
於: Journal of Chemical Physics, 卷 135, 編號 15, 155104, 21.10.2011.研究成果: 雜誌貢獻 › 文章
}
TY - JOUR
T1 - Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
AU - Wu, Johnny
AU - Zhen, Xia
AU - Shen, Hujun
AU - Li, Guohui
AU - Ren, Pengyu
PY - 2011/10/21
Y1 - 2011/10/21
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=80155157254&partnerID=8YFLogxK
U2 - 10.1063/1.3651626
DO - 10.1063/1.3651626
M3 - Article
C2 - 22029338
AN - SCOPUS:80155157254
VL - 135
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 15
M1 - 155104
ER -