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

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.