Figure 9.

Multiple alignment of NS3 protease sequences for different HCV genotypes. UniProtKB accession numbers are given in Table S1 in Additional data file 1. The aligned sequences contain amino acids 16 to 176 according to the PDB entry 1DY8 (UniProtKB accession number P26662). The DSSP secondary structure assignment for 1DY8 is illustrated at the top of the alignment with curled lines for α-helices and arrows for β-strands. The catalytic triad consisting of H57, D81 and S139 and a zinc finger formed by C97, C99 and C145 is indicated at the bottom of the alignment by orange and yellow squares, respectively. The binding cavity for the cyclopropyl group of the VX-950 compound and CPX ligand is marked by purple squares. Text labels annotate different sites of drug resistance mutations (V36, T54, R155, A156) for VX-950. Amino acids are shaded in different grey levels according to their physicochemical properties: aliphatic (A/C/G/I/L/M/N/Q/V), black (white letters); aromatic (F/W/Y), white (black letters); cyclic (P), light grey (white letters); basic (H/K/R), grey (white letters); acidic (D/E), dark grey (white letters). Amino acids with conformational changes described in the paper are framed by green boxes.