Proteolytic profiling of the extracellular matrix degradome.

The profiling of protein function is one of the most challenging scientific tasks in the postgenomic age. Traditional protein expression methodologies have focused only on the quantification of proteins under varying conditions or pathologies. Determining the functional differences between protein populations allows for a more accurate view of the outcomes in normal vs diseased proteomes. Because the presence or absence of a protein's function can affect its complex surroundings (consisting of multiple other proteins and substrates), the study of proteome functionality yields information on protein-protein interactions, amplification cascades, signaling pathways, and posttranslational modifications. Of significant interest are proteinases, as proteolysis is responsible for tight regulation of various cellular and tissue processes. Proteinase activities, or lack there of, alter the proteome makeup by regulating other proteins or by generating cleavage products. This chapter describes current proteolytic profiling technologies using activity or target-based formats. In particular, the analysis of collagenolytic matrix metalloproteinase activity using fluorogenic triple-helical substrates is discussed.