Ascertaining mesoscopic parameters for SARS-CoV-2 assembly from all atom and coarse-grained simulations of the associated membrane protein.

Abstract

The assembly of SARS-CoV-2 in the ER-Golgi intermediate compartment (ERGIC) is a result of the interplay between the virus' accumulated structural proteins. As the most abundant structural protein, the membrane (M) protein is thought to interact with the envelope (E), nucleocapsid (N), and spike (S) proteins such that sufficient curvature is produced for viral budding. Experimentally, it has been shown that M proteins phase separate with a combination of N proteins and RNA, possibly mediating the onset of budding. This phase separation can be demonstrated analytically by modeling the coupled evolution of M protein density and membrane shape, where proper parameterization requires a microscopic understanding of the interactions and dynamics of M proteins. Newly determined M protein structures show its similarities with the SARS-CoV-2 ORF3a protein and that it takes the form of a homodimer with two different conformations. However, neither the capability nor the process of forming higher order M protein oligomers is known. Importantly, it is also undetermined how M protein induces change in the nascent envelope membrane and whether binding to N protein, RNA, or other SARS-CoV-2 proteins plays a role. To help determine these mechanisms, we are taking a multiscale modeling approach. We have used mesoscale, continuum models of membrane-bound M protein dimers to determine how different properties of the protein will affect membrane curvature. Additionally, we are using all-atom simulations of M protein dimers, both free and bound in the membrane, to estimate parameters needed for our mesoscopic model. Our findings using coarse-grained molecular dynamics simulations of M protein dimers embedded in the membrane will also be reported. Combining the parameters determined with our mesoscopic model allows for improved understanding of the budding and assembly process for SARS-CoV-2.