All-Atom Molecular Dynamics simulations of the interaction between viral capsid proteins and single-stranded RNA molecules.

We carried out All-Atom Molecular Dynamics (MD) simulations of the interaction between the positively charged tails of viral capsid proteins and negatively charged homopolymeric polyU and polyA RNA molecules. Recent experiments showed that the encapsidation of homopolymeric RNA by viral capsids is sensitively dependent on the nature of the RNA nucleotide (C.Beren, L.Dreesens, K.Liu, C.Knobler and W.Gelbart, Biophys.J. 2017, 339). We found that the degree of base-stacking and helical ordering strongly influences the strength of the electrostatic component of the protein-RNA interaction, and hence the ability of the capsid proteins to package single-stranded RNA molecules. We compare the Potential of Mean Force measured by the MD simulations with the predictions of Poisson-Boltzmann theory for electrostatic interactions.