The ATPase cycle of the RNA helicase protein NS3 from hepatitis C virus

Abstract

The hepatitis C virus (HCV) NS3 protein possesses both RNA helicase and serine protease activities that are vital to HCV replication in infected cells. NS3 is also a more effective RNA helicase with the protease domain intact. NS3 is a member of the DExD/H‐box RNA helicase family, which recognize and remodel short structured stretches of RNA during every stage of RNA metabolism from synthesis to degradation. However, NS3 plays an important role in unwinding the + and − strands of the HCV genome during viral replication. This role requires ATPase activity that is tightly coupled with rapid helicase translocation and high processivity in concert with the viral RNA polymerase. To characterize the coupling of ATPase with helicase translocation activity of NS3, we utilized equilibrium binding and kinetic biophysical methods. By comparing a series of RNA substrates, we show that maximal RNA stimulation of ATPase activity occurs with very long RNAs, which affect both KM,RNA and kcat. The rate of ATPase cycling and helicase translocation along the RNA may be partially limited by rebinding NS3 to RNA following dissociation from the nucleic acid lattice during the ATPase cycle. The intact protease domain affords more productive engagement with the RNA lattice, which increases the ATPase‐translocase coupling efficiency (ATP consumed per RNA nt/bp travelled). An NSF CAREER Award (MCB‐0546353 to E.D.L.C.) supports this research.