Impact of Membrane Thinning and Curvature in SARS-CoV-2 Membrane Protein Aggregation and Viral Budding

Assembly and budding for SARS-CoV-2 occurs in the ER-Golgi intermediate compartment (ERGIC) and is thought to be driven by the membrane (M) protein through its interactions with other viral structural proteins and the ERGIC membrane. Studies of SARS-CoV virions suggest the existence of a thinner membrane and induced curvature around the M protein. We performed all atom molecular dynamics (MD) simulations of the M protein in a lipid membrane and quantitatively measured both the thinning of the membrane and the induced deformation. These results are compared to atomic force microscopy (AFM) of the SARS-CoV-2 M protein embedded in an ERGIC-like membrane, where we obtain very good agreement, confirming this membrane thinning. Next, we developed a continuum model of M-protein aggregation that incorporates the line tension induced by thinning and the spontaneous curvature of the proteins. Through comparison with AFM measurements of protein cluster size, we were able to constrain the M-M interaction energy and make predictions for the onset of assembly and budding under physiological conditions. Our work provides a better understanding of how the dynamics and interactions of M protein leads to viral assembly and budding, which may provide insights into alternative methods for preventing viral replication.