Journal
CHEMICAL SCIENCE
Volume 13, Issue 20, Pages 6098-6105Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/d2sc00108j
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Funding
- French Higher Education research and Innovation Ministry (MESRI)
- CNRS through the GAVO project
- ANR (Agence Nationale de la Recherche)
- IdEx Universite Paris 2019 [ANR-18-IDEX-0001]
- Universidad de Alcala, Comunidad de Madrid
- European Union
- CGI (Commissariat a l'Investissement d'Avenir) [ANR 11 LABX 086, ANR 11 IDEX 05 02]
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This study investigates the structural properties of the non-structural protein 6 (Nsp6) of SARS-CoV-2 using long-timescale molecular dynamics simulations and machine learning analysis. The findings reveal the interaction patterns of Nsp6 with the lipid membrane and suggest that the mutation brought by the Omicron variant may alter specific interactions, particularly aiding in anchoring the viral protein to the lipid bilayer interface.
The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms. Among the complex pathways induced by the viral infection, autophagy is particularly crucial and is strongly influenced by the action of the non-structural protein 6 (Nsp6) interacting with the endoplasmic reticulum membrane. Importantly, differently from other non-structural proteins, Nsp6 is mutated in the recently emerged Omicron variant, suggesting a possible different role of autophagy. In this contribution we explore, for the first time, the structural properties of Nsp6 thanks to long-timescale molecular dynamics simulations and machine learning analysis, identifying the interaction patterns with the lipid membrane. We also show how the mutation brought by the Omicron variant may indeed modify some of the specific interactions, and more particularly help anchor the viral protein to the lipid bilayer interface.
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