OMICS Publishing Group | Full text | Proteolytic Enzymes Database

Proteolytic enzymes also referred to as proteases and proteinases, degrade proteins by hydrolyzing the peptide bond, proteases can either break specific peptide bonds called limited proteolysis, or break down a complete polypeptide chain to amino acid residues known as unlimited proteolysis. Earlier proteases were classified according to their molecular size, charge or substrate specificity. A more rational system is now based on a comparison of active site, mechanism of action and three-dimensional structure. Four mechanistic classes are recognized by the International Union of Biochemistry .The best characterized protease family is that of mammalian serine proteinases e.g. pancreatic trypsin, chymotrypsin, and elastase. The important features of their active sites are the catalytic triad of Asp102, His57, and Ser195. The catalytic reaction proceeds via a tetrahedral transition state intermediate during both the acylation and deacylation steps of catalysis. The same type of mechanism underlies the action of all other serine proteinases. The conformation of the pancreatic serine proteinases is essentially the same: two similarly folded domains with two-fold axis of symmetry. The P1 amino acid of primary substrate binding site of enzyme defines the substrate specificity.

The cysteine proteinase family is also well characterized. It includes several mammalian lysosomal cathepsins; the cytosolic calcium activated proteases and plant protease papain. Papain is the best-studied member of the cysteine protease family. The catalytic cysteine 25 acts like serine 195 of chymotrypsin. Catalysis reaction proceeds via thiol ester intermediate and is facilitated by the side chains of adjacent histidine 159 and aspartic acid 158. The aspartic proteinase family consists of pepsin, renin and many other proteases. The active site residues of aspartic proteinase are aspartic acids 33 and 213. These aspartic acid residues are in close geometric proximity to each other. In the pH range 2.0-3.0, one of the Asp is ionized and the other is unionized. A potent inhibitor of aspartic proteinase is pepstatin. The metallo-proteinases family include carboxypeptidase A and B. Their active site comprise of zinc, with its three ligands two glutamic acids and one histidine. Another glutamic acid side chain 270, acts as the nucleophile, directly or with the participation of a water molecule.

The proteolytic enzymes also play regulatory roles in a great variety of physiological processes. These include from the processing and molecular assembly of nascent polypeptide chain, processing of protein hormone and enzyme precursors to the development and fertilization (Neurath, 1957; Neurath, 1975; Davie and Fujikawa, 1975; Muller-Eberhard, 1975; Steiner et.al., 1975; Zanefeld et.al., 1975; Cabib and Farkas, 1971; Bornstein, 1974). Proteases also play a key role in cellular processes like separation of chromosome during mitosis, cell cycle and apoptosis. They have also been widely used as an analytical reagent for sequencing the protein and in the identification and isolation of domain of the more complex multifunctional proteins. Deregulation of proteolytic enzymes lead to human pathologies including arthritis, stroke, dementia, metabolic disorder, blood coagulation defects and cardiomyopathy. Preparations of proteolytic enzymes have been shown to be useful in cancer therapy, digestion, hardening of arteries, inflammation and many other chronic diseases.

There is a vast literature on proteolytic enzymes. Therefore, in the present study an attempt has been made in constructing datatabase containing bibliographical information and physicochemical properties of proteolytic enzymes.

Construction and Contents of Database
Proteolytic enzymes database was developed using Microsoft Access. The web based interface with the aim of helping users to search for specific information. This user interface has been built with ASP Server Side Scripts on an Microsoft Windows-based Web Server. Figure 1 shows first page of Proteolytic Enzymes Database. The database can be regularly updated. The bibliographic data for the database was collected from Pubmed [http://www.ncbi.nlm.nih.gov/].The database contains the bibliographic data from 1989 to 2007 .The data for physico-chemical properties on proteolytic enzymes were collected from Expasy Proteomic Server (http://www.expasy.org).

The database can be accessed through web site http://www.proteolyticenzymes.com/. There are 5144 records in the database. The database contains bibliographic informations and informations on physico-chemical properties of a total 30 proteolytic enzymes. The database can be searched by Keywords (in which user can type enzyme name ) and by simultaneously selecting “Search Type” option . Alternatively, the database can be searched by selecting enzyme ( shown in tabulated form ) alongwith by selecting “Search Type”. In “Search Type” menu option, if “Bibliography of Proteolytic Enzyme” is selected then the database will display the following information on enzyme: Enzyme, First Author, Year, Bibliography Type and Bibliography. Similarly, “About Proteolytic Enzyme” is selected then the database will display these information on enzyme : Enzyme, Class, Source, EC, Molecular Weight, N-Terminal, C-Terminal, Thiols, Activators, Inhibitors, Bond Specificity and Comments.

Utility to the Biological Community
Since proteolytic enzymes hydrolyze food proteins and play a regulatory role in a great variety of physiological processes. Therefore , database of proteolytic enzymes has the potential of becoming major hub of resource for the biological community. This database provides bibliography and Information on physicochemical properties of proteolytic enzymes to the researchers and students working in this area.