Design, high-level expression, purification and characterization of soluble fragments of the hepatitis C virus NS3 RNA helicase suitable for NMR-based drug discovery methods and mechanistic studies

RNA helicases represent a family of enzymes that unwind double-stranded (ds ) RNA in a nucleoside triphosphate (NTP)-dependent fashion and which are re quired in all aspects of cellular RNA metabolism and processing. The hepati tis C virus (HCV) non-structural 3 (NS3) protein possesses a serine proteas e activity in the N-terminal one-third, whereas RNA-stimulated NTPase and h elicase activities reside in the C-terminal portion of the 631 amino acid r esidue bifunctional enzyme. The HCV NS3 RNA helicase is of key importance i n the life cycle of HCV, which makes it a target for the development of the rapeutics. However, neither the precise mechanism nor the substrate structu re has been defined for this enzyme. For nuclear magnetic resonance (NMR)-b ased drug discovery methods and for mechanistic studies we engineered, prep ared and characterized various truncated constructs of the 451-residue HCV NS3 RNA helicase. Our goal was to produce smaller fragments of the enzyme, which would be amenable to solution NMR techniques while retaining their na tive NTP and/or nucleic. acid binding sites. Solution conditions were optim ized to obtain high-quality heteronuclear NMR spectra of nitrogen-15 isotop e-labeled constructs, which are typical of well-folded monomeric proteins. Moreover, NMR binding studies and functional data directly support the corr ect folding of these fragments.