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 clef

SUBMITTER: Perez-Villa A 

PROVIDER: S-EPMC4605317 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature