Using Peptide Libraries to Identify Optimal Cleavage Motifs for Proteolytic Enzymes

Methods. 2004 Apr;32(4):398-405. doi: 10.1016/j.ymeth.2003.10.003.


Proteases and peptidases are involved in a vast array of fundamental cellular processes, including cell growth, survival, motility, death, and differentiation, and can be important players in multicellular systems such as angiogenesis, inflammation, and immunity. Though long considered to be essentially digestive enzymes that mediate complete degradation of their substrates, many proteases are now known to be highly site specific. Knowledge of the cleavage site motif for a protease or peptidase can be useful in the design of substrates and inhibitors for the enzyme, and can also provide insight into its biological function through the identification and characterization of its protein substrates. Here, we describe in detail methodology that allows for the rapid and general determination of optimal recognition sequences for proteolytic enzymes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acetylation
  • Avidin / chemistry
  • Binding Sites / genetics
  • Biotinylation
  • Fluorescent Dyes / chemistry
  • Peptide Hydrolases / chemistry
  • Peptide Hydrolases / genetics
  • Peptide Hydrolases / metabolism*
  • Peptide Library*
  • Peptides / chemical synthesis
  • Peptides / genetics
  • Peptides / metabolism
  • Protease Inhibitors / chemical synthesis
  • Protease Inhibitors / chemistry
  • Sepharose / chemistry
  • Sequence Analysis, Protein
  • Substrate Specificity


  • Fluorescent Dyes
  • Peptide Library
  • Peptides
  • Protease Inhibitors
  • avidin-agarose
  • Avidin
  • Sepharose
  • Peptide Hydrolases