ArticlePLoS computational biology2012
Virus capsid dissolution studied by microsecond molecular dynamics simulations.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 84 citations in OpenAlex.
- 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
- Computational methods in physical virology: a critical perspective across lengths and timescales.FEMS microbiology reviews · 2026Review
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Disassembly of Virus-Like Particles and the Stabilizing Role of the Nucleic Acid Cargo.The journal of physical chemistry. B · 2025Article
- Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?The journal of physical chemistry letters · 2024Article
- Survival of surface bacteriophages and their hosts inMicrobiology spectrum · 2024Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions.Journal of structural biology · 2023Article
- Applications of Charge Detection Mass Spectrometry in Molecular Biology and Biotechnology.Chemical reviews · 2022Review
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Molecular mechanism of capsid disassembly in hepatitis B virus.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Atomistic dynamics of a viral infection process: Release of membrane lytic peptides from a non-enveloped virus.Science advances · 2021Article
- Structural and dynamic asymmetry in icosahedrally symmetric virus capsids.Current opinion in virology · 2020Review
- Article
- Scaffolds as Structural Tools for Bone-Targeted Drug Delivery.Pharmaceutics · 2018Review
- All-atom virus simulations.Current opinion in virology · 2018Review
- Article
- All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.The journal of physical chemistry letters · 2017Article
- Ammonia as an In Situ Sanitizer: Influence of Virus Genome Type on Inactivation.Applied and environmental microbiology · 2016Article
- Computational virology: From the inside out.Biochimica et biophysica acta · 2016Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.