CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties

Abstract

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.