Proteolytic Enzymes: Significance for Proteomics

Abstract

Proteolytic enzymes (peptidases) are important tools for proteomic research. This article reviews their application to digestion of proteins, which commonly precedes the mass spectrometry analysis of proteins. In the opening part, mechanism of proteolysis is described together with a detailed introduction to classification and nomenclature of enzymes. The following part brings an overview of proteolytic enzymes that are currently used in expression and functional proteomics including their properties and specificity. The review continues with reports on assays of proteolytic activity and computer prediction of peptide cleavage. The methodology of in-solution and in-gel digestion of samples and the use of peptidases for cleavage of proteins on membrane surfaces is also mentioned. Furthermore, chemical modifications of peptidases for improving their stability to autolysis and thermal inactivation are documented. Peptidase treatment of hydrophobic proteins in solutions containing organic solvents are also mentioned. Finally, new perspectives of proteolysis in shotgun proteomics are outlined.