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Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation

文献类型：期刊论文

作者Wang, Jinan2; Peng, Cheng1,2; Yu, Yuqu2; Chen, Zhaoqiang2; Xu, Zhijian1,2; Cai, Tingting2; Shao, Qiang1,2; Shi, Jiye4; Zhu, Weiliang1,2,3
刊名BIOPHYSICAL JOURNAL
出版日期2020-03-10
卷号118期号:5页码:1009-1018
ISSN号0006-3495
DOI10.1016/j.bpj.2020.01.001
通讯作者Wang, Jinan(jawang@simm.ac.cn) ; Zhu, Weiliang(wlzhu@simm.ac.cn)
英文摘要Replica exchange molecular dynamics (REMD) simulation is a popular enhanced sampling method that is widely used for exploring the atomic mechanism of protein conformational change. However, the requirement of huge computational resources for REMD, especially with the explicit solvent model, largely limits its application. In this study, the availability and efficiency of a variant of velocity-scaling REMD (vsREMD) was assessed with adenylate kinase as an example. Although vsREMD achieved results consistent with those from conventional REMD and experimental studies, the number of replicas required for vsREMD (30) was much less than that for conventional REMD (80) to achieve a similar acceptance rate (similar to 0.2), demonstrating high efficiency of vsREMD to characterize the protein conformational change and associated free-energy profile. Thus, vsREMD is a highly efficient approach for studying the large-scale conformational change of protein systems.
WOS关键词IMPLICIT SOLVENT MODELS ; FREE-ENERGY ; SUBSTRATE-BINDING ; FOLDING PATHWAYS ; FORCE-FIELD ; TRANSITION ; EXPLICIT ; THERMODYNAMICS ; EFFICIENCY ; LANDSCAPE
资助项目National Key Research and Development Program[2016YFA0502301] ; National Science & Technology Major Project Key New Drug Creation and Manufacturing Program''[2018ZX09711002] ; National Natural Science Foundation of China[81573350] ; National Natural Science Foundation of China[81872797] ; National Natural Science Foundation of China[21403283] ; Special Program for Applied Research on Super Computation of the National Natural Science Foundation of China-Guangdong Joint Fund (the second phase)[U1501501]
WOS研究方向Biophysics
语种英语
WOS记录号WOS:000518857100005
出版者CELL PRESS
源URL[http://119.78.100.183/handle/2S10ELR8/281160]  
专题中国科学院上海药物研究所
通讯作者Wang, Jinan; Zhu, Weiliang
作者单位1.Univ Chinese Acad Sci, Beijing, Peoples R China
2.Chinese Acad Sci, Drug Discovery & Design Ctr, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Shanghai, Peoples R China
3.Qingdao Natl Lab Marine Sci & Technol, Open Studio Druggabil Res Marine Lead Cpds, Qingdao, Peoples R China
4.UCB Biopharma SPRL, Braine Lalleud, Belgium
推荐引用方式
GB/T 7714		 Wang, Jinan,Peng, Cheng,Yu, Yuqu,et al. Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation[J]. BIOPHYSICAL JOURNAL,2020,118(5):1009-1018.
APA Wang, Jinan.,Peng, Cheng.,Yu, Yuqu.,Chen, Zhaoqiang.,Xu, Zhijian.,...&Zhu, Weiliang.(2020).Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.BIOPHYSICAL JOURNAL,118(5),1009-1018.
MLA Wang, Jinan,et al."Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation".BIOPHYSICAL JOURNAL 118.5(2020):1009-1018.

入库方式： OAI收割

来源：上海药物研究所

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