Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo. [Display omitted] •SARS-CoV-2 envelope includes three structural proteins: spike, membrane, and envelope•Integrative multi-scale approach modeled envelope structure with near atomistic detail•We found that M dimers agglomerated into large, filament-like, molecular assemblies Pezeshkian et al. modeled the structure of SARS-CoV-2 envelope with near atomistic detail using an integrative multi-scale computational approach, highlighting the dynamic nature and molecular interactions of abundant but understudied M protein. Molecular dynamic simulations revealed а previously unknown property of M dimers: they agglomerated into large, filament-like, macromolecular assemblies.