How to use theMEROPSdatabase and website to help understand peptidase specificity

TheMEROPSwebsite () and database was established in 1996 to present the classification and nomenclature of proteolytic enzymes. This was expanded to include a classification of protein inhibitors of proteolytic enzymes in 2004. Each peptidase or inhibitor is assigned to a distinct identifier, based on its biochemical and biological properties, and homologous sequences are assembled into a family. Families in which the proteins share similar tertiary structures are assembled into a clan. TheMEROPSclassification is thus a hierarchy with at least three levels (protein-species, family, and clan) showing the evolutionary relationship. Several other data collections have been assembled, which are accessed from all levels in the hierarchy. These include, sequence homologs, selective bibliographies, substrate cleavage sites, peptidase-inhibitor interactions, alignments, and phylogenetic trees. The substrate cleavage collection has been assembled from the literature and includes physiological, pathological, and nonphysiological cleavages in proteins, peptides, and synthetic substrates. In this article, we make recommendations about how best to analyze these data and show analyses to indicate peptidase binding site preferences and exclusions. We also identify peptidases where co-operative binding occurs between adjacent binding sites.

Automated summary

The MEROPS website and database classify proteolytic enzymes and protein inhibitors based on biochemical and biological properties, creating a hierarchy with levels such as protein species, family, and clan. Various data collections are accessible from all levels, including sequence homologs, bibliographies, substrate cleavage sites, and more. Data analysis can reveal peptidase binding site preferences and exclusions, as well as identify instances of cooperative binding between adjacent binding sites.