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 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 . Crossing results in a drop in the force and irreversible damage. Across the 35 capsids studied, both 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 , defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with , where 6 is the minimum coordination for elastic stability in three dimensions.
Highlights
Simple globular viruses protect their strands of RNA or DNA with remarkable self-assembled proteinic shells known as capsids
In this paper we use a coarse-grained structure-based model to explore the types of mechanical response that capsids may exhibit and their relation to capsid geometry and protein bonds
A pseudo-T = 3 virus has the symmetry of a T = 3 virus, but in which either the number of subunits in a capsomere is larger than in the standard classification, or the subunits are not sequentially identical
Summary
Simple globular viruses protect their strands of RNA or DNA with remarkable self-assembled proteinic shells known as capsids. There is little basic understanding of how mechanical strength varies between viruses, how it affects function, and how it is related to virus structure. The capsids of simple globular viruses are typically of icosahedral symmetry and they are assembled from one or several kinds of proteins. The proteins cluster into n-meric capsomeres that form morphological units of capsids (so the proteins act as subunits). The structure of capsids has been explained by Caspar and Klug [4] as resulting from a regular triangulation of a sphere and is governed by the triangulation number T such that the number of subunits is equal to 60T. The size of capsids tends to grow with T but the actual size depends on the size of the subunits. One question will be whether mechanical properties depend on T or on the nature of connectivity in the network of interactions between amino acids
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