NS3 has protease, helicase and NTPase activities. NS3 protease assays have been developed using full-length NS3 or its serine protease domain (residues 1–181) (Section 2.4). Polypeptides made by in vitro translation (Bouffard et al., 1995; Hahm et al., 1995; Lin & Rice, 1995), and expressed in E. coli (Yamada et al., 1998), mammalian (Bartenschlager et al., 1993; Eckart et al., 1993; Grakoui et al., 1993b) or insect cells (Hirowatari et al., 1993; Overton et al., 1995) have been shown to be active. For the in vitro assays, translated NS3 was mixed with radiolabeled synthetic peptide containing the desired cleavage site, and the products assayed by sodium dodecyl sulfate polyacrylamide gel electrophoresis or reversed phase high pressure liquid chromatography. For some cleavage reactions, in vitro translated NS4A cofactor and commercially available microsomal membranes were added along with the synthetic substrate. Purified protease from E. coli has also been tested against radiolabeled substrates made by solid-phase peptide synthesis or by in vitro translation (Bianchi et al., 1996; Shimizu et al., 1996; Sudo et al., 1996). In some studies, recombinant NS3 contained a hexahistadine tag, which permitted easy purification by affinity chromatography using a nickel (Ni2+) column that tightly bound the tag sequence (D'Souza et al., 1995; Kakiuchi et al., 1995).