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