Fig. 6.

Model for NS3 helicase interaction with the substrate RNA during active unwinding. The helicase (E) binds to dsRNA (DS) to form the complex E·DS. After this complex formation, the helicase destabilizes the duplex ahead of the opening fork. Depending on the strength of the barrier ahead, success in destabilization leads to the formation of helicase–substrate complex E′·DS*. In single-molecule experiments, this transition from E·DS to E′·DS* corresponds to pause of NS3 in front of a barrier. During the pause, strand separation has not yet occurred at the fork. Failure of the helicase to cross the barrier between E·DS and E′·DS* leads to detachment from RNA. The complex E′·DS* can proceed to form the NS3–product complex (E″·SS), which occurs through NS3 substeps (4). This strand-separation process is less dependent on barriers than the pause. After substeps, the helicase resets to E·DS and starts the next cycle of pausing and stepping. The various states of the helicase and the substrate RNA are schematically depicted in the cartoons below the free energy diagram.