ArticlePLoS computational biology2018
Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Computational methods in physical virology: a critical perspective across lengths and timescales.FEMS microbiology reviews · 2026Review
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Probing the Internal pH and Permeability of a Carboxysome Shell.Biomacromolecules · 2022Article
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Molecular mechanism of capsid disassembly in hepatitis B virus.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.Viruses · 2021Article
- Rubisco proton production can drive the elevation of COProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural and dynamic asymmetry in icosahedrally symmetric virus capsids.Current opinion in virology · 2020Review
- On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2.Virus research · 2020Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Exploring the role of genome and structural ions in preventing viral capsid collapse during dehydration.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work, we assess a previously advanced hypothesis that predicts the existence of ion channels in the capsid of small and non-enveloped icosahedral viruses. With this purpose we examine Triatoma Virus (TrV) as a case study. This virus has a stable capsid under highly acidic conditions but disassembles and releases the genome in alkaline environments. Our calculations range from a subtle sub-atomic proton interchange to the dismantling of a large-scale system representing several million of atoms. Our results provide structure-based explanations for the three roles played by the capsid to enable genome release. First, we observe, for the first time, the formation of a hydrophobic gate in the cavity along the five-fold axis of the wild-type virus capsid, which can be disrupted by an ion located in the pore. Second, the channel enables protons to permeate the capsid through a unidirectional Grotthuss-like mechanism, which is the most likely process through which the capsid senses pH. Finally, assuming that the proton leak promotes a charge imbalance in the interior of the capsid, we model an internal pressure that forces shell cracking using coarse-grained simulations. Although qualitatively, this last step could represent the mechanism of capsid opening that allows RNA release. All of our calculations are in agreement with current experimental data obtained using TrV and describe a cascade of events that could explain the destabilization and disassembly of similar icosahedral viruses.
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