Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure

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.