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Proteomic Identification of Protease Cleavage Sites Characterizes Prime and Non-prime Specificity of Cysteine Cathepsins B, L, and S

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† Institute for Molecular Medicine and Cell Research, University of Freiburg, Germany
‡ Division of Clinical Chemistry and Clinical Biochemistry, Department of Surgery, Ludwig-Maximilians-University, Munich, Germany
§ Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Mainz, Germany
Tel: +49 761 203 9615. E-mail: [email protected]
Cite this: J. Proteome Res. 2011, 10, 12, 5363–5373
Publication Date (Web):October 3, 2011
https://doi.org/10.1021/pr200621z
Copyright © 2011 American Chemical Society
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    Abstract

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    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.

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    The LC-MS/MS data associated with this manuscript may be downloaded from ProteomeCommons.org Tranche using the following hash:9vW9vw2eBchoa+zJvgpvBnFDRZuoYWUh+lMm/+tuQuF8olpOFNP/RLSgqem0fUO2fFuk/1CZv4zwuVQVpr2et9N2XpQAAAAAAAACvg== and zBwzs1VugEbcFXq5Iroi1ghudu7v2Hmb0jTfSpP/2sdudlhO8xHwHWEUv8XkvtoksNWMey9/4q62BlJxHLV079MvzuQAAAAAAAABqA==. The hash may be used to prove exactly what files were published as part of this manuscript′s data set, and the hash may also be used to check that the data has not changed since publication.

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