FIG. 9.

Structure of the NS3/4A serine protease/helicase enzyme complex derived from the genotype 1b BK strain of HCV (Protein Database 1CU1) (27), with the locations of adaptive mutations highlighted. (A) Wire diagram of structure showing the NS3 helicase domain in green and the protease domain in magenta. The NS4A cofactor polypeptide is shown in blue in space-filling view, with the NS3 protease active-site residues shown in yellow in space-filling view. Adaptive mutations identified in this study (red arrows) cluster near the protease active site or at sites involved in substrate recognition, including the mutations in the NS3 protease domain at Gln-1067, Gly-1188 (shown in space-filling view as red) and near the carboxyl terminus of NS3 in the helicase domain at Val-1655 (light green). The NS4A adaptive mutation at Lys-1691 (light blue) is just beyond the surface of the protease, at the site of exit of the NS4A strand. Adaptive mutations within the NS3 helicase domain that were identified in other studies, Ser-1222, Ala-1226, and Pro-1496 (4, 11), are shown in copper in space-filling view and are not close to the protease active site. (B) Space-filling view of the structure shown in panel A, in which the adaptive mutations and active site have similar color coding as in panel A. The helicase domain appears in green, and the protease domain is shown in grey. The NS3/4A adaptive mutations identified in this study (Q1067R, G1188R, V1655I, and K1691R) all occur at solvent accessible residues on this side of the molecule. (C) Flip-view of the structure shown in panel B, rotated approximately 180°. The helicase adaptive mutations identified in previous studies are located on the surface of the helicase, distant from the protease active site. (Note that in the HCV-BK sequence, Pro-1496 is Arg, and Lys-1691 is Ser.)