Evolution of SARS-CoV-2 spike glycoprotein

Abstract

The spike glycoprotein (S) of SARS-CoV-2 mediates attachment of the virus to cell surface receptors and fusion between virus and cell membranes1. The receptor for SARS-CoV-2, like that for SARS-CoV, is the human cell-surface membrane protein ACE22–4. Membrane fusion activity, as for other class-1 fusion glycoproteins, requires S to be proteolytically cleaved into S1 and S2 that remain associated following cleavage4–7. SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host8,9. To better understand the transmission of SARS-CoV-2 we have determined the structure of its furin-cleaved S by cryoEM, which shows that cleavage at this polybasic amino-acid site increases the structural plasticity of the receptor binding region and facilitates the adoption of an open conformation that is required for it to bind to the ACE2 receptor. To investigate relationships between S proteins of SARS-CoV-2 and of the most closely related bat virus, RaTG138, we have determined and compared their structures and characterised biochemically their affinities for ACE2 and their relative stabilities. Whilst the overall structures are similar, there are key differences likely pertinent to virus infectivity. These include a more stable pre-cleavage form of human S, about 1000-fold tighter binding of SARS-CoV-2 to human receptor, and a higher proportion of S in the conformation required for binding ACE2 upon protease cleavage.

Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2

“…While the structural integrality of the spikes has a significant effect on the bioassay of the ACE2 binding affinity, the mechanism of this effect is unknown. Several structures with different RBD up states of CoV-2-S are available in the Protein Data Bank (PDB), ,− but there is no criterion defined to judge whether a conformation is accessible or inaccessible to human ACE2. It is unknown how easily the spike undergoes conformational change from ACE2 inaccessible to accessible.…”

Molecular biology of the SARs‐CoV‐2 spike protein: A review of current knowledge

“…55 "Priming" occurs at S1/S2 boundary providing the SARS-CoV-2 S protein with the structural flexibility required for separating S1 and S2. 56 And a subsequent "activation" cleavage at S2´site generates the exposure of FP and its insertion into the membrane. 57 A variety of proteases including, but are not limited to, Furin, TMPSS2, and cathepsin B/L, have been shown to mediate SARS-CoV-2 for priming and activation, [58][59][60] indicating a relatively high degree of flexibility in cleavage mechanisms.…”

“…for RBD-hACE2 binding. 56 A Furin cleavage motif insertion at the S1/ S2 junction of SARS-CoV enhances spike-driven cell to cell fusion. 66 However blockade of the Furin cleavage motif in SARS-CoV-2 affected its entry into the TMPRSS2 + human lung cell line Calu-3.…”

Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites

“…Our previous simulations have shown that binding of LAin the FA site helps to stabilize a locked conformation (9) which appears more condensed than the LA-free closed form) and that the carboxylate head group of the FA makes consistent salt-bridge interactions with the R408, occasional interactions with K417 and persistent H-bonding interactions with Q409, across the locked subunit interfaces (10). Fatty acids have since been retrospectively discovered in the FA sites of spike proteins from SARS viruses that infect other species (11,12). The S1 domain of the spike protein is responsible for attaching the SARS-CoV-2 virus to the host cell by means of interaction with host cell receptors.…”