Proteomic Identification of Protease Cleavage Sites Characterizes Prime and Non-prime Specificity of Cysteine Cathepsins B, L, and S.
26.10.2011
Biniossek ML, Nägler DK, Becker-Pauly C, Schilling O
J Proteome Res. 2011; 10(12):5363-73
Cysteine cathepsins mediate proteome homeostasis and have pivotal functions in diseases like cancer. To better understand substrate recognition by cathepsins B, L, and S, we applied "proteomic identification of protease cleavage sites (PICS)" for simultaneous profiling of prime- and non-prime specificity. PICS profiling of cathepsin B endopeptidase specificity highlights strong selectivity for glycine in P3' due to an occluding loop blocking access to the primed subsites. In P1', cathepsin B has a partial preference for phenylalanine which is not found for cathepsins L and S. Occurrence of P1' phenylalanine often coincides with aromatic residues in P2. For cathepsin L, PICS identifies 845 cleavage sites, representing the most comprehensive PICS profile to date. Cathepsin L specificity
is dominated by the canonical preference for aromatic residues in P2 with limited contribution of prime-site selectivity determinants. Profiling of cathepsins B and L with a shorter incubation time (4 h instead of 16 h) did not reveal timedependency of individual specificity determinants. Cathepsin S specificity was profiled at pH 6.0 and pH 7.5. The PICS profiles at both pH values display a high
degree of similarity. Cathepsin S specificity is primarily guided by aliphatic residues in P2 with limited importance of prime-site residues.
