Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarsegrained molecular dynamics simulations  

作　　者：Dali Wang Jiaxuan Li Lei Wang Yipeng Cao Bo Kang Xiangfei Meng Sai Li Chen Song 

机构地区：[1]Center for Quantitative Biology,Academy for Advanced Interdisciplinary Studies,Peking University,Bejing,China [2]Peking-Tsinghua Center for Life Sciences,Beijing,China [3]Tianjin Medical University Cancer Institute and Hospital,National Clinical Research Center for Cancer,Tianjin,China [4]National Supercomputer Center in Tianjin,Tianjin,China [5]Bejing Frontier Research Center for Biological Structure,State Key Laboratory of Membrane Biology,School of Life Sciences,Tsinghua University,Beijing,China

出　　处：《Quantitative Biology》2023年第4期421-433,共13页定量生物学（英文版）

基　　金：National Key R&D Program of China,Grant/Award Number:2021YFE0108100;National Natural Science Foundation of China,Grant Award Numbers:32241031,32171195;Tsinghua University Spring Breeze Fund,Grant/Award Number:2021Z99CFZ004;Tsinghua University Dushi Fund,Grant/Award Number:2023Z11DSZ001。

摘　　要：The causative pathogen of coronavirus disease 2019(COVID-19),severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is an enveloped virus assembled by a lipid envelope and multiple structural proteins.In this study,by integrating experimental data,structural modeling,as well as coarse-grained and all-atom molecular dynamics simulations,we constructed multiscale models of SARS-CoV-2.Our 500-ns coarse-grained simulation of the intact virion allowed us to investigate the dynamic behavior of the membrane-embedded proteins and the surrounding lipid molecules in situ.Our results indicated that the membrane-embedded proteins are highly dynamic,and certain types of lipids exhibit various binding preferences to specific sites of the membrane-embedded proteins.The equilibrated virion model was transformed into atomic resolution,which provided a 3D structure for scientific demonstration and can serve as a framework forfuture exascale allatom molecular dynamics(MD)simulations.A short all-atom molecular dynamics simulation of 255 ps was conducted as a preliminary test for largescale simulationsofthis complexsystem.

关 键 词：enveloped virus molecular dynamics simulation multiscale modeling SARS-CoV-2 

分 类 号：R373[医药卫生—病原生物学]