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Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields

文献类型：期刊论文

作者Wang, Anhui1,2; Li, Guohui1; Zhang, Zhichao2
刊名JOURNAL OF PHYSICAL CHEMISTRY LETTERS
出版日期2018-12-20
卷号9期号:24页码:7110-7116
ISSN号1948-7185
DOI10.1021/acs.jpclett.8b03471
通讯作者Li, Guohui(ghli@dicp.ac.cn)
英文摘要The accuracy of molecular mechanics force fields is of vital importance in biomolecular simulations. However, the admittedly more accurate polarizable force fields were recently reported to be less able to reproduce the experimental properties in comparison to additive force fields in some cases. Here, we perform long-time-scale molecular dynamics simulations to systematically evaluate the effect of explicit electronic polarization in polarizable force fields. The results show that the inclusion of electrostatic polarization effect in polarizable force fields can improve their accuracies in protein structure refinement and generate conformational ensembles more approximate to experiments for intrinsically disordered proteins. In contrast, it is difficult for polarizable force fields to approach the native structure, let alone to predict the native state when it is unknown a priori in the real protein structure predictions. We speculate that these effects might be attributed to the preference of protein-water interactions in polarizable force fields.
WOS关键词MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY SIMULATIONS ; MODEL ; HYDRATION ; PEPTIDES ; PREDICTION
资助项目National Natural Science Foundation of China[31700647] ; National Natural Science Foundation of China[21625302] ; National Natural Science Foundation of China[21573217]
WOS研究方向Chemistry ; Science & Technology - Other Topics ; Materials Science ; Physics
语种英语
出版者AMER CHEMICAL SOC
WOS记录号WOS:000454752000029
资助机构National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China
源URL[http://cas-ir.dicp.ac.cn/handle/321008/166330]  
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
通讯作者Li, Guohui
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.Dalian Univ Technol, Sch Chem, State Key Lab Fine Chem, Dalian 116024, Peoples R China
推荐引用方式
GB/T 7714		 Wang, Anhui,Li, Guohui,Zhang, Zhichao. Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields[J]. JOURNAL OF PHYSICAL CHEMISTRY LETTERS,2018,9(24):7110-7116.
APA Wang, Anhui,Li, Guohui,&Zhang, Zhichao.(2018).Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields.JOURNAL OF PHYSICAL CHEMISTRY LETTERS,9(24),7110-7116.
MLA Wang, Anhui,et al."Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields".JOURNAL OF PHYSICAL CHEMISTRY LETTERS 9.24(2018):7110-7116.

入库方式： OAI收割

来源：大连化学物理研究所

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