ArticleThe journal of physical chemistry. B2010
All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 63 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 biophysical characterization of a superradiant virus-like particle in its ground state.bioRxiv : the preprint server for biology · 2025Article
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses.Sub-cellular biochemistry · 2024Review
- An Observation of a Very High Swelling of Bromovirus Members at Specific Ionic Strengths and pH.Viruses · 2023Article
- Fast viral dynamics revealed by microsecond time-resolved cryo-EM.Nature communications · 2023Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- The Plant Viruses and Molecular Farming: How Beneficial They Might Be for Human and Animal Health?International journal of molecular sciences · 2023Review
- Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities.ACS central science · 2022Article
- Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.bioRxiv : the preprint server for biology · 2022Article
- Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles.The journal of physical chemistry. B · 2021Article
- Electrostatics-Driven Inflation of Elastic Icosahedral Shells as a Model for Swelling of Viruses.Biophysical journal · 2018Article
- 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
- Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.Journal of chemical theory and computation · 2015Article
- Swelling and softening of the cowpea chlorotic mottle virus in response to pH shifts.Biophysical journal · 2015Article
- Molecular dynamics simulations of large macromolecular complexes.Current opinion in structural biology · 2015Review
- Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision.Journal of chemical theory and computation · 2014Article
- Hierarchical Multiscale Modeling of Macromolecules and their Assemblies.Soft matter · 2013Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
An all-atom multiscale computational modeling approach, molecular dynamics/order parameter extrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is approximately 0.25 nm/ns (npn) during the early stage of the simulation, and propagation of the structural transition across the capsid is roughly 0.6 npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed.
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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.