How to use the MEROPS database and website to help understand peptidase specificity
Autor: | Alex Bateman, Neil D. Rawlings |
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Rok vydání: | 2020 |
Předmět: |
substrate specificity
Computational biology Biology Biochemistry Homologous Sequences 03 medical and health sciences Biological property Protease Inhibitors Amino Acid Sequence enzyme classification Binding site Databases Protein Molecular Biology 030304 developmental biology 0303 health sciences Binding Sites Sequence Homology Amino Acid Tools for Protein Science Phylogenetic tree binding site 030302 biochemistry & molecular biology Proteolytic enzymes peptidase proteolytic enzyme Sequence Homologs Substrate specificity Peptide Hydrolases MEROPS |
Zdroj: | Protein Science : A Publication of the Protein Society |
ISSN: | 1469-896X 0961-8368 |
Popis: | The MEROPS website (https://www.ebi.ac.uk/merops) 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. The MEROPS classification 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. |
Databáze: | OpenAIRE |
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