title: Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S.
abstract: Cysteine cathepsins mediate proteome homeostasis and have pivotal functions in diseases such as 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 time-dependency of individual specificity determinants. Cathepsin S specificity was profiled at pH 6.0 and 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.
authors.affiliation: Institute for Molecular Medicine and Cell Research, University of Freiburg, Germany.
authors.forename: Martin L
authors.initials: ML
authors.lastname: Biniossek
authors.forename: Dorit K
authors.initials: DK
authors.lastname: Nägler
authors.forename: Christoph
authors.initials: C
authors.lastname: Becker-Pauly
authors.forename: Oliver
authors.initials: O
authors.lastname: Schilling
mesh_terms: D020134:Catalytic Domain; D002401:Cathepsin B / Q000235:genetics / Q000378:metabolism*; D056668:Cathepsin L / Q000235:genetics / Q000378:metabolism*; D002403:Cathepsins / Q000235:genetics / Q000378:metabolism*; D057075:Enzyme Assays; D005998:Glycine / Q000378:metabolism; D057809:HEK293 Cells; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D010447:Peptide Hydrolases / Q000378:metabolism; D019151:Peptide Library; D010649:Phenylalanine / Q000378:metabolism; D010843:Pichia / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*; D013379:Substrate Specificity; D013997:Time Factors
chemical_list: D019151:Peptide Library; D010649:Phenylalanine; D002403:Cathepsins; D010447:Peptide Hydrolases; C533912:CTSB protein, human; D002401:Cathepsin B; C534281:CTSL protein, human; D056668:Cathepsin L; C028217:cathepsin S; D005998:Glycine