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.