After binding to the ACE2 receptor through the specialized Receptor Binding Domain (RBD) of the trimeric Spike protein, the SARS-Cov2 virus is ready to enter the host cell by penetrating its membrane. This step starts with a “tectonic rearrangement” of the Spike into a "spear" aimed at the cell membrane. Its "spearhead" is the trimer of “fusion peptides” (FPs) each contributed by one Spike monomer. To reach this position, each FP must be liberated at the time of the conformational change to the spear from its embedded position in the Spike. This involves a specific enzymatic cleavage (S2') at its N-terminal end during form. The liberated FPs are thus repositioned to the far end of the protein, poised for membrane insertion. Experimental structure determinations of the Spike were unable to resolve this essential spearhead domain, leaving unclear the molecular mechanism of membrane insertion. From extensive atomistic molecular dynamics (MD) simulations and systematic sampling we have identified (1)-Ca²⁺ binding modes to each FP revealing the preferred mode of SARS-Cov2-FP insertion; (2)-the role of Ca²⁺ ions in mediating peptide-membrane interactions; and (3)-the modes interactions of these Ca²⁺-bound FP peptides with lipid membranes. The results reveal for the first time the preferred mode in which SARS-Cov2-FP penetrates the bilayer, using a mechanism that leverages the specific properties of the loaded Ca²⁺ binding sites, and a specific hydrophobic motif that is highly conserved in corona viruses. We show (A)-how the dynamics of the spearhead penetration into the cell membrane explain the mechanistic role of the necessary cleavage (termed S2’) that frees the N-terminus of the peptide to effectuate the cell-entry of the virus; (B)-the role of the Ca²⁺ binding in facilitating the insertion of the FP spearhead; and (C)-the type of membrane perturbation that is likely involved in the fusion of the viral membrane with host cell membranes to enable release of viral genetic material for replication in the host cell.

Professor Harel Weinstein

Professor and Chairman, Weill Cornell Medical College of Cornell University

Appearances