Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations.

RNA-dependent RNA polymerases (RdRps) are enzymes catalyzing RNA replication from a RNA template. Active-site closure in RdRps, normally induced by correct nucleotide triphosphate (NTP) binding, is a prerequisite for the cycle of nucleotide incorporation. So, a complete understanding of polymerase function (in particular polymerase fidelity) of a RdRp requires more complete knowledge of active-site closure in the RdRp. In this work, based on solved crystal structures, we have built different models for the RNA-dependent RNA polymerase from poliovirus (termed PV 3D(pol)). Through MD simulations and free energy calculations of these PV 3D(pol) models, we have revealed the dynamic correlation between motif A and motif D and between motif A and incoming NTP, have deepened our understanding of polymerase fidelity from dynamic aspects, and have provided an explanation to the puzzle that arises from different observations based on kinetic studies and structural data.