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PreprintCited by 13SARS-CoV-2 and COVID-19 ResearchLipid Membrane Structure and BehaviorProtein Structure and Dynamics

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Autophagy and evasion of immune system by SARS-CoV-2. Structural features of the Non-structural protein 6 from Wild Type and Omicron viral strains interacting with a model lipid bilayer. †

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Bignon, Emmanuelle, Marazzi, Marco, Grandemange, Stéphanie, Monari, Antonio·2022·Chemical Science
DOI 10.1101/2022.01.05.475107PMC PMC9132136

Preprint — published as 10.1039/d2sc00108j · Paper page

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Abstract

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 called 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 property of Nsp6 thanks to long-time scale molecular dynamic 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 anchoring the viral protein to the lipid bilayer interface. Electronic Supplementary Information (ESI) available: Analysis protein of the secondary structure and of the specific lipid/amino acid interactions. RMSF per amino acid. Distribution of the distance between the center of mass of the 89 to 99 α-helix and the center of the lipid bilayer. Analysis of the behavior of the 195 to 207 α-helix. See DOI: 10.1039/x0xx00000x

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Metadata

Authors
Bignon, E., Marazzi, M., Grandemange, S., & Monari, A.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Universidad de Alcalá (ES)
Corresponding author
  • Bignon, Emmanuelle
  • Marazzi, Marco
  • Monari, Antonio
ORCID
Venue
Chemical Science
Publisher
openRxiv
Published
2022-01-05
Volume
13
Issue
20
Pages
6098-6105
ISSN
2041-6520 (ISSN-L)
DOI
10.1101/2022.01.05.475107
PMC
PMC9132136
OpenAlex
W4282922850
Cited by
13
References
2
Citations by year
2025: 2 · 2024: 3 · 2023: 5 · 2022: 3
FWCI
1.59
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Chemical Science (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
Funders
  • Comunidad de Madrid
  • Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation
  • Laboratoire d'Excellence SEAM (ANR-11-IDEX-05-02, ANR-18-IDEX-0001, ANR-11-LABX-086)
  • European Commission
  • Agence Nationale de la Recherche (11 IDEX 05 02, 11 LABX 086, ANR 11 LABX 086, ANR 11 IDEX 05 02, ANR-11-IDEX-0502, ANR 11 LABX 086, ANR18, ANR 11, ANR-10-LABX-0096, ANR11-LABX, ANR-11-IDEX-0005, ANR-18-IDEX-0001)
  • Centre National de la Recherche Scientifique (#ANR-18-IDEX-0001)
  • Commissariat Général à l'Investissement
  • Universidad de Alcalá
  • Grand Équipement National De Calcul Intensif (ANR-18-IDEX-0001)
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
SARS-CoV-2, Omicron variant, NSP6, autophagy evasion, endoplasmic reticulum membrane, lipid bilayer interaction, protein-lipid interactions, viral immune evasion, long-timescale molecular dynamics

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