Stability and dynamics of virus capsids described by coarse-grained modeling
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We report a study of the structural dynamics of viral capsids, simulated on a microsecond timescale, by employing a coarse-graining molecular dynamics method. The method was calibrated against an all-atom simulation of one complete virus. Among the studied capsids, some collapsed rapidly, while others were found to be stable. Interlocking between coat proteins is found to be a key factor determining the stability of the capsids.
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Traditional molecular modeling methods usually provide reliable simulation results but require heavy computational resources, limiting their applicability.
“The methods in the first category, such as coarse-grained molecular dynamics simulations [9, 10], usually provide reliable simulation results but require heavy computational resources, which limits their applicability [11].”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [10]
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- Authors
- Arkhipov, A., Freddolino, L., & Schulten, K.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Schulten, Klaus
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2006-12
- Volume
- 14
- Issue
- 12
- Pages
- 1767-1777
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W1984909504
- Cited by
- 262
- References
- 67
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 12 · 2023: 13 · 2022: 10 · 2021: 14 · 2020: 8 · 2019: 14 · 2018: 12 · 2017: 11 · 2016: 15 · 2015: 11 · 2014: 13 · 2013: 19 · 2012: 24
- FWCI
- 5.72
- 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, 2420 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)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Center for Research Resources (5P41 RR 05969, P41RR005969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- viral capsid, capsid stability, structural dynamics, coarse-grained molecular dynamics
- MeSH terms
- Biochemistry, Calibration, Capsid, Computer Simulation, Computers, Models, Molecular, Molecular Conformation, Protein Binding, Protein Conformation, Time Factors, User-Computer Interface, Viral Proteins, Models, Statistical, Computational Biology
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