Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal

Abstract

The mechanical properties of viral shells are crucial determinates for the pathway and mechanism by which the genetic material leaves the capsid during infection and have therefore been studied by atomic force microscopy as well as by atomistic simulations. The mechanical response to forces from inside the capsid are found to be relevant, especially after ion removal from the shell structure, which is generally assumed to be essential during viral infection; however, atomic force microscopy measurements are restricted to probing the capsids from outside, and the primary effect of ion removal is still inaccessible. To bridge this gap, we performed atomistic force-probe molecular dynamics simulations of the complete solvated icosahedral shell of Southern Bean Mosaic Virus and compared the distribution of elastic constants and yielding forces on the icosahedral shell for probing from inside with the distribution of outside mechanical properties obtained previously. Further, the primary effect of calcium removal on the mechanical properties on both sides, as well as on their spatial distribution, is quantified. Marked differences are seen particularly at the pentamer centers, although only small structural changes occur on the short timescales of the simulation. This unexpected primary effect, hence, precedes subsequent effects due to capsid swelling. In particular, assuming that genome release is preceded by an opening of capsomers instead of a complete capsid bursting, our observed weakening along the fivefold symmetry axes let us suggest pentamers as possible exit ports for RNA release.

Figure 1

Force-probe simulations of southern bean mosaic virus (SBMV) capsid. (a) SBMV is built up from 60 subunits, each of which is composed of protein A (red), protein B (blue), and protein C (green). Black symbols mark the five-, three- and twofold symmetry axes referred to in the text. The black triangle depicts one of the 60 subunits. The approaching tip-sphere (red sphere) was initially located close to the surface and attached to a virtual spring that pushed the tip-sphere toward the viral shell. (b) Nineteen equally distributed positions (black circles) were chosen on the surface of one of the 60 subunits. During each of the 152 force-probe simulation runs, the tip-sphere was pushed with constant velocity against one of these grid points, and the force exerted by the tip-sphere onto the capsid surface is recorded. From the obtained force-distance curves, respective elastic constants and yielding forces were derived.

Figure 2

Distribution of elastic constants on a viral subunit. Color-coded distribution of elastic constants on the surface of subunit 12 of the SBMV capsid (soft, blue; stiff, red). The viral shell was indented from the outside (a) with and (b) without calcium ions in the structure and (c and d) from the inside.

Figure 3

Distribution of yielding forces on a viral subunit. Color-coded distribution of yielding forces on the surface of subunit 12 of the SBMV capsid (low stability, blue; high stability, red). The viral shell was indented from the outside (a) with and (b) without calcium ions in the structure and (c and d) from the inside.

Figure 4

Changes of yielding forces after Ca²⁺ removal, mapped onto the complete capsid. Major differences are seen at the pentamer centers. Here, yielding forces dropped by 0.92 nN from 2.96 nN to 2.04 nN (red). (White) Unaffected regions. (Green) Regions with increased stability.