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Journal Articles Journal of Chemical Information and Modeling Year : 2022

Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis

Abstract

Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild-type and five variants that emerged in late 2020 focusing on the Spike RBD/ACE2 monomer complex and dynamics using existing X-Ray structures and Molecular Dynamics simulations. Dihedral angle PCA shows strong similarities inside the Spike RBD dynamics in the Alpha, Beta, Gamma and Delta variants in contrast with the WT and Epsilon. Dynamical perturbation networks shows that differences arise in interface dynamics between the Alpha, Beta and Gamma variant relative to the Delta variant but that those effects are not directly imputable to the L452R and T478K mutations. Finally contact principal component analysis shows how the L452R and T478K mutations acts synergistically on neighboring residues to provoke these drastic changes.
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Dates and versions

hal-03708020 , version 1 (07-11-2022)

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Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, et al.. Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. Journal of Chemical Information and Modeling, 2022, 62 (12), pp.3107-3122. ⟨10.1021/acs.jcim.2c00350⟩. ⟨hal-03708020⟩
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