ArticleThe journal of physical chemistry letters2017
All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.
Article in The journal of physical chemistry letters, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
- Lipid Architecture in the Zika Virus.ACS physical chemistry Au · 2026Article
- Tailoring virus-inspired nanoparticles for advanced drug and gene delivery.Materials today. Bio · 2026Review
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Atomic force microscopy at the forefront: unveiling foodborne viruses with biophysical tools.Npj viruses · 2025Review
- Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.Biophysical reviews · 2025Review
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities.ACS central science · 2022Article
- The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus.Vaccines · 2022Review
- Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.bioRxiv : the preprint server for biology · 2022Article
- Article
- Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly.Physical chemistry chemical physics : PCCP · 2021Article
- Atomistic dynamics of a viral infection process: Release of membrane lytic peptides from a non-enveloped virus.Science advances · 2021Article
- Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis.Frontiers in molecular biosciences · 2021Article
- Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity.Applied clay science · 2020Article
- Structural and dynamic asymmetry in icosahedrally symmetric virus capsids.Current opinion in virology · 2020Review
- Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions.Journal of mathematical biology · 2020Article
- Article
- Multi-resolution dimer models in heat baths with short-range and long-range interactions.Interface focus · 2019Article
- MS2 bacteriophage capsid studied using all-atom molecular dynamics.Interface focus · 2019Article
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Authors and funding
7 authors at 3 institutions in 4 countries.
Funding
Abstract
Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.
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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.