ArticlePloS one2013
Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure.
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 24 papers.
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24 citing papers in PubMed, 71 citations in OpenAlex.
- Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of infection-critical peptide externalization.Biophysical journal · 2026Article
- Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions.Journal of structural biology · 2023Article
- Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles.International journal of molecular sciences · 2022Article
- Structural and dynamic properties of eutectic mixtures based on menthol and fatty acids derived from coconut oil: a MD simulation study.Scientific reports · 2022Article
- Minimal Design Principles for Icosahedral Virus Capsids.ACS nano · 2021Article
- Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.Viruses · 2021Article
- Biomechanical Features of Graphene-Augmented Inorganic Nanofibrous Scaffolds and Their Physical Interaction with Viruses.Materials (Basel, Switzerland) · 2020Article
- Structural and dynamic asymmetry in icosahedrally symmetric virus capsids.Current opinion in virology · 2020Review
- Single-particle virology.Biophysical reviews · 2020Review
- Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2020Article
- Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank.Frontiers in molecular biosciences · 2020Article
- Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes.Analytical chemistry · 2019Article
- Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids.Analytical chemistry · 2019Review
- Mechanical and thermodynamic properties of AβBeilstein journal of nanotechnology · 2019Article
- Effect of dsDNA on the Assembly Pathway and Mechanical Strength of SV40 VP1 Virus-like Particles.Biophysical journal · 2018Article
- Temperature-Dependent Nanomechanics and Topography of Bacteriophage T7.Journal of virology · 2018Article
- Viral nanomechanics with a virtual atomic force microscope.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages.Journal of biological physics · 2018Article
- TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- Self-assembly of model proteins into virus capsids.Journal of physics. Condensed matter : an Institute of Physics journal · 2017Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C[Formula: see text] atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV - satellite panicum mosaic virus) and 135 780 (for NBV - nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic region which extends to a characteristic force [Formula: see text]. Crossing [Formula: see text] results in a drop in the force and irreversible damage. Across the 35 capsids studied, both [Formula: see text] and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number [Formula: see text], defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with [Formula: see text], where 6 is the minimum coordination for elastic stability in three dimensions.
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