DNA-mediated anisotropic mechanical reinforcement of a virus

Abstract

In this work, we provide evidence of a mechanism to reinforce the strength of an icosahedral virus by using its genomic DNA as a structural element. The mechanical properties of individual empty capsids and DNA-containing virions of the minute virus of mice are investigated by using atomic force microscopy. The stiffness of the empty capsid is found to be isotropic. Remarkably, the presence of the DNA inside the virion leads to an anisotropic reinforcement of the virus stiffness by approximately 3%, 40%, and 140% along the fivefold, threefold, and twofold symmetry axes, respectively. A finite element model of the virus indicates that this anisotropic mechanical reinforcement is due to DNA stretches bound to 60 concavities of the capsid. These results, together with evidence of biologically relevant conformational rearrangements of the capsid around pores located at the fivefold symmetry axes, suggest that the bound DNA may reinforce the overall stiffness of the viral particle without canceling the conformational changes needed for its infectivity.

Fig. 1.

MVM particles as viewed along fivefold (a), threefold (b), and twofold (c) symmetry axes. (Left) Simplified cartoons. (Center) Molecular surface models derived from crystallographic data. The Protein Data Bank coordinates corresponding to the MVM virion (PDB ID code 1MVM; ref. 19) and the program Pymol (DeLano Scientific, San Carlos, CA) were used. (Right) Actual AFM images of individual MVM particles (image sizes: 60 × 60 nm). The MVM topographies appear laterally expanded because of the usual tip-sample dilation effects.

Fig. 2.

Comparison of the mechanical properties of MVM empty capsids (a) and virions (b). (Left) Shown are the crystallographic structures of the empty capsid (a) and DNA-filled virion (b) as space-filling models obtained by using the program RasMol (23). The models have been cut in half to show the particle interior. In the virion, the DNA stretches whose conformation was crystallographically solved are shown in green, coating in a periodic way 60 cavities of the capsid internal surface. (Right) The histograms obtained for empty capsids (a) and virions (b) are shown. They depict the stiffness (spring constant, k) values obtained for individual particles subjected to nano-indentation along fivefold (red), threefold (green), and twofold (blue) axes. (Insets) The k values from Gaussian fits obtained for empty capsids and virions along each symmetry axis. A Student t test for samples with an unequal variance reveals with >99% confidence that the three mean k values shown in b Inset do not overlap.

Fig. 3.

Space-filling representations of several symmetry-related MVM capsid subunits (in different colors) and crystallographically observed DNA stretches bound to those subunits (white). Views are from the particle interior and were obtained by using RasMol software (23). (a) Five protein subunits related by a fivefold symmetry axis. (b) Three subunits related by a threefold symmetry axis. (c) Six subunits related by a twofold symmetry axis. Distance measurements show that the center of gravity of each visible DNA stretch is located closer to the capsid twofold axis and further from the fivefold axis.

Fig. 4.

Finite element modeling. We used a rib size of 15 nm and a Young's modulus of 1.25 GPa. (a) The plot shows the calculated spring constant k along fivefold (red), threefold (green), and twofold (blue) symmetry axes as a function of the wall thickness t. (Inset) Homogeneous icosahedral model. (b) Five different reinforced icosahedral models with added circular patches of thickness t_c positioned at different sites. Only 1 of the 20 faces of the icosahedron is shown for each model. Models 1 and 2 (circular patches at the three- or fivefold axis, respectively) did not predict the observed behavior. Models 3, 4, and 5 (circular patches positioned close to the twofold axes where the capsid-bound DNA is located) predicted a small increase of k along the fivefold axis and the largest one along the twofold axes. (c) Plot of the calculated spring constant k along fivefold (red), threefold (green), and twofold (blue) symmetry axes as a function of the added wall thickness t_c in the circular regions depicted in gray in the reinforced icosahedral model used (Inset and model 4 in b), which are roughly coincident with the periodic locations where ordered DNA is bound to the capsid in the MVM virion.