The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike (Toelzer et al. Science 2020). The presence of linoleic acid at this site modulates binding of the spike to the human ACE2 receptor, stabilizing a locked conformation of the protein. Here, dynamical-nonequilibrium molecular dynamics simulations reveal that this fatty acid site is coupled to functionally relevant regions of the spike, some of them far from the fatty acid binding pocket. Removal of a ligand from the fatty acid binding site significantly affects the dynamics of distant, functionally important regions of the spike, including the receptor-binding motif, furin cleavage site and fusion-peptide-adjacent regions. The results also show significant differences in behaviour between clinical variants of the spike: e.g. the D614G mutation shows a significantly different conformational response for some structural motifs relevant for binding and fusion. The simulations identify structural networks through which changes at the fatty acid binding site are transmitted within the protein. These communication networks significantly involve positions that are prone to mutation, indicating that observed genetic variation in the spike may alter its response to linoleate binding and associated allosteric communication.

QM/MM Study of the Reactivity of Zeolite Bound Methoxy and Carbene Groups

<div>The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C₂₊ species, rather than inter-framework migration and that the role of carbenes in the formation of the first –C bond will be via a concerted type of mechanism rather than stepwise. </div>

QM/MM Study of the Reactivity of Zeolite Bound Methoxy and Carbene Groups

<div>The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C₂₊ species, rather than inter-framework migration and that the role of carbenes in the formation of the first –C bond will be via a concerted type of mechanism rather than stepwise. </div>