Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling
Open accessPublished version of a preprint
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.
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- Authors
- Pezeshkian, W., Grünewald, F., Narykov, O., Lu, S., Arkhipova, V., Solodovnikov, A., Wassenaar, T. A., Marrink, S. J., & Korkin, D.
- Affiliations
- University of Copenhagen (DK)
- University of Groningen (NL)
- Worcester Polytechnic Institute (US)
- Corresponding author
- Marrink, Siewert J.
- Korkin, Dmitry
- ORCID
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2023-04
- Volume
- 31
- Issue
- 4
- Pages
- 492-503.e7
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W4323038710
- Cited by
- 60
- References
- 5
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 18 · 2023: 17 · 2022: 7
- FWCI
- 4.71
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 371 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Structure (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion, cc-by-nc-nd)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Funders
- University of Texas at Austin
- Novo Nordisk (NNF18SA0035142)
- Novo Nordisk Fonden (NNF18SA0035142)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- SARS-CoV-2, viral envelope, membrane proteins, integrative modeling, multiscale modeling, protein aggregation, betacoronaviruses
- MeSH terms
- COVID-19, SARS-CoV-2, Humans, Molecular Dynamics Simulation
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