Protein walking: cleavage islands in the HCV polyprotein.

Over 2660 peptides were cleaved by NS3/4A and by thrombin and furin (controls). The cleavage data of the peptide sequences (P4–P4′) which either overlap or are proximal to the NS3-NS4A (1654EVVT↓STWV1661), NS4A-NS4B (1708MEEC↓SQHL1715), NS5A↓NS5B (1969TTPC↓SGSW1976) and NS5A↓NS5B (2417VVCC↓SMSY2424) junction regions are shown here. Peptides which directly correspond to the known cleavage sites are both in bold and italicized. The asterisk marks the peptides overlapping a putative additional NS3/4A cleavage site (2431VTPC↓AAEE2438). Only the Z-score equal or above 3 are shown. Minus indicates Z-scores below 3. The peptide PCSGSWLR↓ was cleaved by a thrombin (TR) control while all of other peptides were resistant to both thrombin and furin controls. In addition, our set included multiple control cleavage peptides for furin, such as RKKR↓STSA (Z-score = 6.0) and RRKR↓YAIQ (Z-score = 7.2). These peptides were not cleaved by thrombin and NS3/4A. Our set also included multiple control cleavage peptides for thrombin such as VVPR↓GVNL (Z-score = 10) and IEPR↓SFSQ (Z-score = 13) which were not cleaved by furin and NS3/4A.