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Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs

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Abstract
Using a targeted peptide-centric proteomics approach, we performed in vitro protease substrate profiling of the apoptotic serine protease granzyme B resulting in the delineation of more than 800 cleavage sites in 322 human and 282 mouse substrates, encompassing the known substrates Bid, caspase-7, lupus La protein, and fibrillarin. Triple SILAC (stable isotope labeling by amino acids in cell culture) further permitted intra-experimental evaluation of species-specific variations in substrate selection by the mouse or human granzyme B ortholog. For the first time granzyme B substrate specificities were directly mapped on a proteomic scale and revealed unknown cleavage specificities, uncharacterized extended specificity profiles, and macromolecular determinants in substrate selection that were confirmed by molecular modeling. We further tackled a substrate hunt in an in vivo setup of natural killer cell-mediated cell death confirming in vitro characterized granzyme B cleavages next to several other unique and hitherto unreported proteolytic events in target cells.
Keywords
CELL-DEATH, KEY MEDIATORS, AUTOANTIGEN B23, SEQUENCE ALIGNMENT, CASPASE ACTIVATION, CYTOLYTIC LYMPHOCYTES-T, DIAGONAL CHROMATOGRAPHY, APOPTOSIS, IDENTIFICATION, CLEAVAGE

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Chicago
Van Damme, Petra, Sebastian Maurer-Stroh, Kim Plasman, Joost Van Durme, Niklaas Colaert, Evy Timmerman, Pieter-Jan De Bock, et al. 2009. “Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs.” Molecular & Cellular Proteomics 8 (2): 258–272.
APA
Van Damme, Petra, Maurer-Stroh, S., Plasman, K., Van Durme, J., Colaert, N., Timmerman, E., De Bock, P.-J., et al. (2009). Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs. MOLECULAR & CELLULAR PROTEOMICS, 8(2), 258–272.
Vancouver
1.
Van Damme P, Maurer-Stroh S, Plasman K, Van Durme J, Colaert N, Timmerman E, et al. Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs. MOLECULAR & CELLULAR PROTEOMICS. BETHESDA, MD 20814-3996 USA: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC; 2009;8(2):258–72.
MLA
Van Damme, Petra, Sebastian Maurer-Stroh, Kim Plasman, et al. “Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs.” MOLECULAR & CELLULAR PROTEOMICS 8.2 (2009): 258–272. Print.
@article{537409,
  abstract     = {Using a targeted peptide-centric proteomics approach, we performed in vitro protease substrate profiling of the apoptotic serine protease granzyme B resulting in the delineation of more than 800 cleavage sites in 322 human and 282 mouse substrates, encompassing the known substrates Bid, caspase-7, lupus La protein, and fibrillarin. Triple SILAC (stable isotope labeling by amino acids in cell culture) further permitted intra-experimental evaluation of species-specific variations in substrate selection by the mouse or human granzyme B ortholog. For the first time granzyme B substrate specificities were directly mapped on a proteomic scale and revealed unknown cleavage specificities, uncharacterized extended specificity profiles, and macromolecular determinants in substrate selection that were confirmed by molecular modeling. We further tackled a substrate hunt in an in vivo setup of natural killer cell-mediated cell death confirming in vitro characterized granzyme B cleavages next to several other unique and hitherto unreported proteolytic events in target cells.},
  author       = {Van Damme, Petra and Maurer-Stroh, Sebastian and Plasman, Kim and Van Durme, Joost and Colaert, Niklaas and Timmerman, Evy and De Bock, Pieter-Jan and Goethals, Marc and Rousseau, Frederic and Schymkowitz, Joost and Vandekerckhove, Joël and Gevaert, Kris},
  issn         = {1535-9476},
  journal      = {MOLECULAR & CELLULAR PROTEOMICS},
  keywords     = {CELL-DEATH,KEY MEDIATORS,AUTOANTIGEN B23,SEQUENCE ALIGNMENT,CASPASE ACTIVATION,CYTOLYTIC LYMPHOCYTES-T,DIAGONAL CHROMATOGRAPHY,APOPTOSIS,IDENTIFICATION,CLEAVAGE},
  language     = {eng},
  number       = {2},
  pages        = {258--272},
  publisher    = {AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC},
  title        = {Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs},
  url          = {http://dx.doi.org/10.1074/mcp.M800060-MCP200},
  volume       = {8},
  year         = {2009},
}

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