Toward an atomistic model of SARS-CoV-2 (preprint)

ABSTRACT

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, a positive-sense single-stranded RNA, and four structural proteins the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. Extensive experimental and computational studies have been carried out to reveal the architecture of the virus, but an intact and high-resolution structure of the virus is still desired. In this work, we construct atomistic models of the intact SARS-CoV-2 (without complete RNA) by fully employing the latest cryo-ET data, in combination with the available experimentally resolved protein structures, structure prediction and modeling methods, as well as coarse-grained molecular dynamics (MD) simulations. The atomistic model will not only provide a 3D structure for scientific demonstration and education, but also offer a framework for future exascale all-atom MD simulations to understand the dynamics of the intact virus and its mutations.