Dynamics of SARS-CoV-2 Spike Proteins in Cell Entry: Control Elements in the Amino-Terminal Domains

Abstract

Adaptive changes that increase SARS-CoV-2 transmissibility may expand and prolong the coronavirus disease 2019 (COVID-19) pandemic. Transmission requires metastable and dynamic spike proteins that bind viruses to cells and catalyze virus-cell membrane fusion.

S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity

“…We next investigated whether S-acylation of spike influences its lipid environment in the context of two minimal viral particle assembly systems: an HIV-derived lentivector-based system to generate spike harboring pseudo particles (PPs) ( Fenwick et al., 2021 ) ( Figure S5 A) and a SARS-CoV-based system to generate viral-like particles (VLPs) ( Kumar et al., 2021 ; Qing et al., 2020 , 2021 ). In both systems, the particles produced include a built-in luminescence-based reporter system, which allows for evaluation of particle production and subsequent infectivity.…”

“…We next analyzed the importance of spike acylation for the infectivity of SARS-CoV VLPs. We used a recently described split reporter system engineered into the N genes of the CoV VLPs ( Kumar et al., 2021 ; Qing et al., 2021 ). Fusion dynamics were monitored by measuring bioluminescence as a function of time, using either TMPRSS2-expressing target cells or a cell-free system based on ACE-2-containing extracellular vesicles, both harboring the complementary reporter fragment tagged to ACE2.…”

Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity

“…The SARS-CoV-2 spike glycoprotein (S) is a 1273 amino acid, type I membrane protein that binds to the ACE2 receptor on the host cell surface to initiate infection, virus uptake, and cell–cell fusion [ 1 , 2 ]. The unprocessed S protein precursor consists of an N-terminal signal sequence for endoplasmic reticulum (ER) insertion and a large ectodomain (ER luminal-virion exterior) composed of glycosylation sites, a receptor binding domain (RBD), a trimerization domain, and two proteolytic cleavage sites (S1/S2 and S2′) that are required for the conformational changes that present a fusion peptide domain for membrane insertion [ 3 , 4 ]. On the cytosolic side of the single membrane spanning domain is a short endodomain that contains a cysteine-rich domain (CRD) that undergoes S-acylation/palmitoylation, the functional significance of which is under active investigation [ 5 , 6 , 7 , 8 , 9 ].…”

Structural Dynamics and Molecular Evolution of the SARS-CoV-2 Spike Protein

“…However, binding to ACE2 stabilizes Spike in the 3 RBD open conformation, causing R815 to become much more exposed ( 49 ) and therefore accessible to proteases. Moreover, D614G synergizes with N-terminal domain (NTD) loop deletions to enable ACE2-independent S2′ cleavage ( 51 ). Therefore, S1/S2 cleavage, RBD opening, S2′ processing, and the postfusion conformational transition are not steps that must occur in fixed linear order.…”