The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method

Electrostatic energy
has a significant contribution to intermolecular
interaction energy, especially in biological systems. Unfortunately,
precise quantum mechanics calculations are not feasible for large
biological systems; hence, simpler calculation methods are required.
We propose a method called UBDB+EPMM (University at Buffalo Pseudoatom
DataBank + Exact Potential Multipole Moments), which shortens computational
time without losing accuracy. Here, we characterize electrostatic
interactions in selected complexes of IFIT proteins with RNA. IFIT
proteins are effectors of the innate immune system, and by binding
foreign RNA, they prevent the synthesis of viral proteins in human
host cells; hence, they block the propagation of viruses. We show
that by using the UBDB+EPMM method it is possible to describe protein-RNA
interactions not only qualitatively but also quantitatively. Looking
at the charge penetration contribution to electrostatic interactions,
we find all amino acid residues with strong local interactions. Moreover,
we confirm that electrostatic interaction of IFIT5 with pppRNA does
not depend on the sequence of the RNA.