Sequential receptor binding primes the SARS-CoV-2 S glycoprotein for membrane fusion

Abstract

SARS-CoV-2 infection is initiated by virus binding to ACE2 cell surface receptors, followed by fusion of virus and cell membranes to release the virus genome into the cell. Both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein, S. As with other class I membrane fusion proteins, S is post-translationally cleaved, in this case by furin, into S1 and S2 components that remain associated following cleavage. Fusion activation following receptor binding is proposed to involve the exposure of a second proteolytic site (S2’), cleavage of which is required for the fusion peptide release. We have investigated the binding of ACE2 to the furin-cleaved form of SARS-CoV-2 S by cryoEM. We classify ten different molecular species including the unbound, closed spike trimer, the fully open ACE2-bound trimer, and dissociated monomeric S1 bound to ACE2. The ten structures describe sequential ACE2 binding events which destabilise the spike trimer, progressively opening up, and out, the individual S1 components. The opening process reduces S1 contacts with each other and un-shields the trimeric S2 core, priming fusion activation and dissociation of ACE2-bound S1 monomers. The structures also reveal refolding of one of the S1 subdomains, following ACE2 binding, that disrupts interactions with S2, notably involving Asp614, leading to destabilisation of the structure of S2 proximal to the secondary (S2’) cleavage site.

Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses

“…Although the S-protein existing on the virus surface basically forms a trimer structure 13 , each RBD of S-protein trimer in the case of an open structure does not retain intramolecular interactions between another monomer of S-protein 67 . Since the trimer is almost observed as the open structure when it binds to ACE2 or an antibody, the monomer model will be appropriate to analyze molecular recognition between the Sprotein and the ACE2/antibody.…”

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

“…Figure 4 illustrates the different up or down conformations of spike protein complexed with ACE2 receptors. In the early phase of the pandemic, the D614G substitution adjacent to the NTD subdomain leads to a more open and thus receptor-accessible conformations of the spike compared with the wild-type (Benton et al, 2021;Gobeil et al, 2021;Mansbach et al, 2021;Zhang et al, 2021a). The D614G substitution confers the virus an adaptation advantage and higher transmissibility, facilitating the acquisition of further mutations and forming the variants of concern (Korber et al, 2020;Zhang et al, 2020;Plante et al, 2021).…”

Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection

“…An interesting structural consideration is that the SARS-CoV-2 Spike protein quaternary structure is a trimer with three receptor binding domains; all of which may be bound to ACE2 at the same time. 49,50 Exploring how various potential modes of avidity and molecular rearrangement with the viral and vesicle membranes contribute to the efficacy of decoy vesicles is an exciting avenue for future research.…”