Mechanical modeling of viral capsids

Abstract

As revealed by techniques of structural biology and single-molecule experimentation, the protein shells of viruses (capsids) are some of nature’s best examples of highly symmetric multiscale self-assembled structures, with impressive mechanical properties of strength and elasticity. Mechanical models of viral capsids built “from the bottom up,” i.e., from all-atom models in the context of molecular dynamics and normal mode analysis, have chiefly focused on unforced vibrational capsid dynamics. Due to the size of viral capsids, which can contain several hundred thousand atoms, the computer power needed for these types of methods has only recently reached the level required for all-atom simulations of entire viral capsids. Coarse-grained normal mode analysis has provided a simplified means of studying the unforced vibrational dynamics of viral capsids. Recent focus on “top-down” mechanical models of viral capsids based on two- and three-dimensional continuum elasticity have provided a theoretical complement to single molecule experiments such as atomic force microscopy, and have advanced the fundamental understanding of the forced mechanics. This review serves to assess the current state of modeling techniques for the study of the mechanics of viral capsids, and to highlight some of the key insights gained from such modeling. In particular, a theme is established of a link between shape—or geometry—and the global mechanical properties of these hierarchical multiscale biological structures.