Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The fundamental functions of the capsid are to protect and transport the viral genome and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids (CapsidMesh) based on the atomic positions of their constituents. Material properties of the capsid proteins can be set on every mesh element individually. Hence, we have control over all levels of protein structure (atoms, amino acids, subunits, oligomers, and capsid). The CapsidMesh models are suitable for numerical simulations and analysis of a physical process using a third-party package. In particular, we used our methodology to generate a CapsidMesh of several capsids previously characterized by atomic force microscopy experiments and then simulated the mechanical nanoindentation through the finite element method. By fitting to the experimental linear elastic response, we estimated the elastic modulus and mechanical stresses produced on the capsids. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.
SUMMARYViruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The capsid has the fundamental functions to protect and transport the viral genome, and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation, but little is known about the physical properties of the capsid. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids, or CapsidMesh, based on their atomic information. The CapsidMesh models are suitable for numerical simulations and analysis, keeping control over all levels of protein structure (atoms, amino acids, chains, oligomers, capsid). Material properties of the capsid subunits can be set at every mesh element and then run a simulation of a physical process using a third-party package. Analysis can be made by extracting the information of interest. We validated our methodology by generating a CapsidMesh and simulating the nanoindentation through Finite Element analysis of several capsids previously characterized by Atomic Force Microscopy experiments. We estimated the elastic modulus consistently by reproducing the experimental linear elastic response. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle. Supplementary Information available.
The cover image, by José Luis Alonzo‐Velázquez et al., is based on the Research Article CapsidMesh: Atomic‐detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties, https://doi.org/10.1002/cnm.2991.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.