Elucidating the Mechanism of Membrane Destabilization by the Preferred Modes of Insertion of the Sars-Cov2 Fusion Peptide

Abstract

Cell penetration of the SARS-Cov2 virus after recognition by the ACE2 receptor requires the fusion of the viral envelope membrane with cellular membranes. The Spike protein (S) of the virus harbors a region identified as the “fusion peptide” (FP) which is liberated at its N-terminal site by a specific cleavage occurring in concert with the interaction of the receptor binding domain of the Spike. Studies have shown that the SARS-Cov2-FP binds Ca2+ ions and perturbs membranes in a calcium-dependent fashion. But the mechanisms of membrane insertion and destabilization remained unclear. We have identified the preferred modes of SARS-Cov2-FP insertion and the role of Ca2+ ions in mediating peptide-membrane interactions from extensive atomistic molecular dynamics (MD) simulations and trajectory analyses. Multiple Ca2+ binding modes in which the ion engaged with different pairs of acidic residues on the FP were observed. A systematic sampling of the interactions of these Ca2+-bound peptide models with lipid membranes showed that SARS-Cov2-FP penetrated the bilayer only in two modes involving different structural domains. In the first mode the hydrophobic residues F833/I834 from the middle region of the peptide are inserted. The second, and more prevalent mode of penetration involves residues L822/F823 in the freed N-terminus of the peptide. The latter insertion was related to the specific mode of Ca2+ association with the peptide in which one Ca2+ is bound to the D830/D839 pair and another to E819/D820. These findings explain the mechanistic role of the necessary cleavage (termed S2’) that frees the N-terminus of the peptide to effectuate the cell-entry of SARS-Cov2. Computational resources provided by the COVID-19 HPC Consortium are gratefully acknowledged.