Translocation of NS3 from Hepatitis C Virus on RNA: Insights from Atomistic Molecular Simulations

Helicases are motor proteins that unwind double stranded nucleic acids and are important parts of the genetic apparatus. A notable member of this family of enzymes is the nun-structural protein NS3 from Hepatitis C Virus. NS3 helicase unwinds nucleic acids by translocating along a single strand. Single molecule experiments and X-ray crystallography suggest that NS3 follows an inchworm-like motion during the translocation mechanism, consuming one ATP molecule per cycle. In spite of the available experimental data, the mechanistic and chemical details of the translocation process are still unclear. The aim of this study is to model at atomistic detail the NS3h-RNA complex at the different stages of the translocation. For this purpose, atomistic molecular dynamics simulations were performed in explicit solvent in the presence and in the absence of ATP and ADP. Simulations were initialized based on existing crystallographic structures. All the stages of translocation were considered, and their relative stabilities were analyzed by computing electrostatic interactions, relative enthalpies, and hydrogen-bond patterns. Additionally, well-tempered metadynamics and Hamiltonian replica exchange simulations were performed to characterize the free-energy landscape associated to translocation and to describe the conformational transitions.