ArticleJournal of structural biology2023
Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions.
Article in Journal of structural biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 5 citations in OpenAlex.
- Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of infection-critical peptide externalization.Biophysical journal · 2026Article
- Role of viral protein ratio in the structure and separation of empty and full adeno-associated virus capsids: A molecular dynamics study.Molecular therapy. Advances · 2026Article
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Flock House virus (FHV) is an animal virus and considered a model system for non-enveloped viruses. It has a small, icosahedral capsid (T=3) and a bipartite positive-sense RNA genome. We present an extensive study of the FHV capsid dynamics from all-atom molecular dynamics simulations of the complete capsid. The simulations explore different biologically relevant conditions (neutral/low pH, with/without RNA in the capsid) using the CHARMM force field. The results show that low pH destabilizes the capsid, causing radial expansion, and RNA stabilizes the capsid. The finding of low pH destabilization is biologically relevant because the capsid is exposed to low pH in the endosome, where conformational changes occur leading to genome release. We also observe structural changes at the fivefold and twofold symmetry axes that likely relate to the externalization of membrane active γ peptides through the fivefold vertex and extrusion of RNA at the twofold axis. Simulations using the Amber force field at neutral pH are also performed and display similar characteristics to the CHARMM simulations.
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Registered trials
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