SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid

Abstract

The SARS-CoV-2 spike protein contains a fatty acid binding site, also found in some other coronaviruses (e.g. SARS-CoV), which binds linoleic acid and is functionally important. When occupied by linoleic acid, it reduces infectivity, by ‘locking’ the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the response of spike variants to linoleic acid removal. These simulations show that the fatty acid site is coupled to functional regions of the protein, some of them far from the site (e.g. in the receptor-binding motif, N-terminal domain, the furin cleavage site located in position 679-685 and the fusion peptide-surrounding regions) and identify the allosteric networks involved in these connections. Comparison of the response of the original (‘Wuhan’) spike with four variants: Alpha, Delta, Delta plus and Omicron BA.1 show that the variants differ significantly in their response to linoleic acid removal. The allosteric connections to the fatty acid site on Alpha are generally similar to the original protein, except for the receptor-binding motif and S71-R78 region which show a weaker link to the FA site. In contrast, Omicron is the most affected variant exhibiting significant differences in the receptor-binding motif, N-terminal domain, V622-L629 and the furin cleavage site. These differences in allosteric modulation may be of functional relevance, e.g. in differences in transmissibility and virulence. Experimental comparison of the effects of linoleic acid on different variants is warranted.

Dynamical nonequilibrium molecular dynamics simulations identify allosteric sites and positions associated with drug resistance in the SARS-CoV-2 main protease

“…D-NEMD simulations are emerging as a useful tool to probe signal propagation and allosteric effects, 38 e.g., they have identified a general mechanism of signal propagation in nicotinic acetylcholine receptors; 39,40 communication pathways between allosteric and active sites in clinically relevant β-lactamases; 30 and modulation of SARS-CoV-2 spike protein behaviour by pH 41 and ligand occupancy in the fatty acid binding site. [42][43][44] Notably in this context, the pathways identified in the β-lactamases contain positions that differ between enzymes with different spectrums of antibiotic breakdown activity. 30 In the D-NEMD approach, the system is sampled first by equilibrium molecular dynamics (MD) simulations.…”

Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike

“…Surface plasmon resonance experiments and cryo-EM structures show that the FA site is 3 conserved in the spike proteins of highly pathogenic β-coronaviruses, such as SARS-CoV, MERS-CoV, SARS-CoV-2, but not in the spikes of common, mild disease-causing β-coronaviruses (24). Simulations using the dynamical-nonequilibrium molecular dynamics (D-NEMD) approach showed that the FA site allosterically modulates the behaviour of functional motifs in both the ancestral (also known as wild type, 'early 2020', or original) spike and in several variants (25)(26)(27). These D-NEMD simulations showed that the FA site is allosterically connected to the RBM, N-terminal domain (NTD), furin cleavage site, and the region sourrounding the fusion peptide (FP) (25)(26)(27).…”

“…Here, we use D-NEMD simulations (38,39) to characterise the response to LA removal of the fully glycosylated SARS-CoV-2 ancestral spike to investigate allosteric modulation by the FA site and the effects of glycans on allosteric behaviour. D-NEMD simulations (38,39) have proved to be an effective approach to investigate responses of receptors (40)(41)(42), identify allosteric effects (25)(26)(27)(43)(44)(45)(46) and study effects of pH changes (47) in biomolecular systems, including SARS-CoV-2 targets (25-27, 45, 47). LA complex model was built using the cryo-EM structure 7JJI as a reference (23).…”

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

“…All glycosylation sites in the Original spike sequence as described by Zhao et al, (21) are retained in these variants. These equilibrium simulation data also provide the basis for dynamical non-equilibrium molecular dynamics simulations to map the allosteric pathways arising from the ligand annihilation from the fatty acid binding site in our accompanying paper (22).…”