Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs

Mol Cell Proteomics. 2009 Feb;8(2):258-72. doi: 10.1074/mcp.M800060-MCP200. Epub 2008 Oct 3.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Apoptosis
  • Cell Death
  • Cell Line
  • Granzymes / chemistry
  • Granzymes / metabolism*
  • Humans
  • Killer Cells, Natural / cytology
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Peptides / chemistry
  • Phylogeny
  • Protein Processing, Post-Translational*
  • Proteome / chemistry
  • Proteomics / methods*
  • Reproducibility of Results
  • Sequence Homology, Amino Acid*
  • Species Specificity
  • Substrate Specificity


  • Peptides
  • Proteome
  • Granzymes