Abstract
Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures.
Highlights
Non-structural protein 3 (NS3) is a molecular motor encoded by Hepatitis C virus (HCV) consisting of a Nterminal region with a serine protease domain and a Cterminal superfamily 2 (SF2) helicase that unwinds and translocates on nucleic acids
We describe atomistic molecular dynamics (MD) simulations in explicit solvent of NS3-single-stranded ribonucleic acid (ssRNA) complex in the absence and presence of ATP/ADP
To the best of our knowledge, only a few MD simulations have been performed on the microsecond timescale for RNA-protein complexes of comparable or larger size [30,31,32], and our results provide a valuable benchmark for state-of-the-art molecular dynamics of these systems
Summary
Non-structural protein 3 (NS3) is a molecular motor encoded by Hepatitis C virus (HCV) consisting of a Nterminal region with a serine protease domain and a Cterminal superfamily 2 (SF2) helicase that unwinds and translocates on nucleic acids. A few intermediate snapshots have been reported so far related to NS3h translocation on RNA [20,24,25], and conformational differences between these snapshots have been interpreted using elastic network models [26,27] In this context, molecular dynamics simulations [28] with accurate force fields could add dynamical information to the available crystal structures providing a new perspective on the mechanism of action of this important molecular motor. To the best of our knowledge, only a few MD simulations have been performed on the microsecond timescale for RNA-protein complexes of comparable or larger size [30,31,32], and our results provide a valuable benchmark for state-of-the-art molecular dynamics of these systems
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