Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane

Abstract

During infection the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host. The viral spike (S) protein mediates both the initial contact with the host cell and the subsequent membrane fusion. Proteolytic cleavage of S at the S2′ site exposes its fusion peptide (FP) as the new N-terminus. By binding to the host membrane, the FP anchors the virus to the host cell. The reorganization of S2 between virus and host then pulls the two membranes together. Here we use molecular dynamics (MD) simulations to study the two core functions of the SARS-CoV-2 FP: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion. In eight 10 μs long MD simulations of FP in proximity to endosomal and plasma membranes, we find that FP binds spontaneously to the membranes and that binding proceeds predominantly by insertion of two short amphipathic helices into the membrane interface. Connected via a flexible linker, the two helices can bind the membrane independently, yet binding of one promotes the binding of the other by tethering it close to the target membrane. By simulating mechanical pulling forces acting on the C-terminus of the FP, we then show that the bound FP can bear forces up to 250 pN before detaching from the membrane. This detachment force is more than 10-fold higher than an estimate of the force required to pull host and viral membranes together for fusion. We identify a fully conserved disulfide bridge in the FP as a major factor for the high mechanical stability of the FP membrane anchor. We conclude, first, that the sequential binding of two short amphipathic helices allows the SARS-CoV-2 FP to insert quickly into the target membrane, before the virion is swept away after shedding the S1 domain connecting it to the host cell receptor. Second, we conclude that the double attachment and the conserved disulfide bridge establish the strong anchoring required for subsequent membrane fusion. Multiple distinct membrane-anchoring elements ensure high avidity and high mechanical strength of FP–membrane binding.

Different Binding Modes of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides to Cell Membranes: The Influence of Peptide Helix Length

“…All-atom molecular dynamics (MD) simulation performed by Banerjee et al 31 showed that the trimeric unit of SARS-CoV-2 FP (residues 816–855) could effectively trigger the initial stages of membrane fusion within hundreds of nanoseconds. Hummer and co-workers 32 used all-atom MD simulations to study the binding of the SARS-CoV-2 FP (residues 816–855) to cellular membranes, finding that two short amphipathic helices ensure high binding strength of the SARS-CoV-2 FP to the cell membrane. Gorgun et al 33 used the FP segment (residues 798–823) of SARS-CoV-1 S-protein as a template for modeling the membrane binding of SARS-CoV-2 FP (residues 816–841) to the human cellular membrane, revealing three major membrane-binding modes.…”

Sublytic gasdermin-D pores captured in atomistic molecular simulations

“…To simulate GSDMD NT in its native environment, we designed a plasma membrane mimetic with asymmetric lipid composition. Following our earlier work 54 and Lorent et al, 33 the outer leaflet of our membrane is rich in sphingolipids, phospholipids with PC headgroups and holds very few poly-unsaturated lipids. By contrast, the inner leaflet has a high content of lipids with PE headgroups and mostly polyunsaturated tails.…”

A mechanistic understanding of the modes of Ca ion binding to the SARS-CoV-1 fusion peptide and their role in the dynamics of host membrane penetration

“…A recent study from Koppisetti et al asserts that a Ca 2+ may be binding to D843/D849 in SARS-CoV-2 FP (corresponding to D825/D830 in SARS-CoV FP); however, as shown from the simulations in this study and Khelashvili et al , there is a high likelihood that second Ca 2+ ion will bind to D812/D821 (corresponding to the D830/D839 in SARS-CoV-2 FP) for the maximal membrane penetration [23, 25]. Recent NMR studies regarding the membrane interaction with the fusion peptide still have yet to be fully resolved as current models use bicelles [25] and micelles [33], which do not completely capture the composition of the bilayer as was done for the computational modeling shown here; though the model of membrane insertion proposed by Koppisetti et al [25] most aligns with our proposed CoV FP interaction with bilayer ( Fig 8 ). Thus, as shown in Figs 6 and 7 , mutations that creates a high propensity for the Ca 2+ binding mode involving the E821/D825 pair, stabilize peptide conformations that are non-productive for membrane penetration and are found here to inactivate the FP ( Fig 6 ).…”