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Structural Analysis of the Spike Protein of SARS‐CoV‐2 Variants and Other Betacoronaviruses Using Molecular Dynamics

Von Wiley-VCH zur Verfügung gestellt

A structural analysis of twelve spike proteins from betacoronaviruses SARS-CoV, MERS-CoV, SARS-CoV-2 (wild-type, alpha, beta, gamma, delta, mu and omicron variants) and betacoronaviruses detected in bats (RaTG13) and pangolins (Pangolin-CoVs) is presented.


Abstract

A structural analysis over various spike proteins from three highly pathogenic Betacoronavirus was done to understand their structural differences. The proteins were modeled using crystal structures from SARS-CoV, MERS-CoV, and other Betacoronavirus that infect bats and pangolins. The group was split in two sets; the first set corresponds to the non-mutated spike proteins, while the second set corresponds to mutated spike variants alpha, beta, gamma, delta, omicron and mu; five of them classified as variants of concern and the last one as variant of interest. A conformational space exploration was carried out for every protein by using molecular dynamic simulations. Root mean square fluctuations, principal component and cross-correlation analysis were carried out over the dynamics to analyze the flexibility and rigidity of every protein in comparison to the wild type Spike protein from the SARS-CoV-2. The obtained results indicate that the proteins, which are not spread among humans, have smooth movements compared to those of SARS-CoV-2 and its variants. In addition, a relationship between the speed of the virulence and the movement of the protein can explain the behavior of delta and omicron variants.

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