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Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzymethat unwinds and translocates along nucleic acids with an ATP-dependentmechanism and has a key role in the replication of the viral RNA. Aninchworm-like mechanism for translocation has been proposed based on crystalstructures and single molecule experiments. We here perform atomistic moleculardynamics in explicit solvent on the microsecond time scale of the availableexperimental structures. We also construct and simulate putative intermediatesfor the translocation process, and we perform non-equilibrium targetedsimulations to estimate their relative stability. For each of the simulatedstructures we carefully characterize the available conformational space, theligand binding pocket, and the RNA binding cleft. The analysis of the hydrogenbond network and of the non-equilibrium trajectories indicates an ATP-dependentstabilization of one of the protein conformers. Additionally, enthalpycalculations suggest that entropic effects might be crucial for thestabilization of the experimentally observed structures.

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations