ArticlePloS one2013
Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 53 citations in OpenAlex.
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- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
- Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery.Scientific reports · 2025Article
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- Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.Scientific reports · 2022Article
- Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling.Frontiers in chemistry · 2022Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Simulating and analysing configurational landscapes of protein-protein contact formation.Interface focus · 2019Article
- Multiconfigurational Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers.PLoS computational biology · 2018Article
- TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
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- Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.Journal of molecular modeling · 2016Article
- Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.The Journal of membrane biology · 2015Article
- The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2014Article
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.The Journal of chemical physics · 2014Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable.
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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.