title: ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
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.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Pérez-Villa
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Darvas
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy bussi@sissa.it.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussi
mesh_terms: D000244:Adenosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D020365:RNA Helicases / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000737:chemistry* / Q000378:metabolism; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D012313:RNA; D020365:RNA Helicases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases