Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Weria Pezeshkian, Fabian Grünewald, Oleksandr Narykov, Senbao Lu, Valeria Arkhipova, Alexey Solodovnikov, Tsjerk A Wassenaar, Siewert J Marrink, Dmitry Korkin

    Research output: Contribution to journalArticleAcademicpeer-review

    Abstract

    Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.

    Original languageEnglish
    Pages (from-to)492-503
    JournalStructure (London, England : 1993)
    Volume31
    Issue number4
    DOIs
    Publication statusPublished - 6 Apr 2023

    Keywords

    • humans
    • SARS-CoV-2
    • COVID-19
    • molecular dynamics simulation

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