scholarly journals How to use the MEROPS database and website to help understand peptidase specificity

2020 ◽  
Vol 30 (1) ◽  
pp. 83-92 ◽  
Author(s):  
Neil D. Rawlings ◽  
Alex Bateman
Keyword(s):  
Merops Database

The MEROPS Database as a Protease Information System

2001 ◽  
Vol 134 (2-3) ◽  
pp. 95-102 ◽  
Author(s):  
Alan J Barrett ◽  
Neil D Rawlings ◽  
Emmet A O'Brien
Keyword(s):  
Information System ◽  
Merops Database

An Introduction to Peptidases and the Merops Database

2007 ◽  
pp. 161-179 ◽  
Author(s):  
Neil D. Rawlings ◽  
Fraser R. Morton ◽  
Alan J. Barrett
Keyword(s):  
Merops Database

scholarly journals The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

2017 ◽  
Vol 46 (D1) ◽  
pp. D624-D632 ◽  
Author(s):  
Neil D Rawlings ◽  
Alan J Barrett ◽  
Paul D Thomas ◽  
Xiaosong Huang ◽  
Alex Bateman ◽  
...  
Keyword(s):  
Proteolytic Enzymes ◽  
Merops Database

scholarly journals Modelling Proteolytic Enzymes With Support Vector Machines

2011 ◽  
Vol 8 (3) ◽  
pp. 1-15
Author(s):  
Lionel Morgado ◽  
Carlos Pereira ◽  
Paula Veríssimo ◽  
António Dourado
Keyword(s):  
State Of The Art ◽  
Proteolytic Enzymes ◽  
Support Vector ◽  
Computational Techniques ◽  
Strong Activity ◽  
Discriminative Models ◽  
Vector Machines ◽  
Merops Database ◽  
Enzyme Detection ◽  
Silver Bullet

Summary The strong activity felt in proteomics during the last decade created huge amounts of data, for which the knowledge is limited. Retrieving information from these proteins is the next step. For that, computational techniques are indispensable. Although there is not yet a silver bullet approach to solve the problem of enzyme detection and classification, machine learning formulations such as the state-of-the-art Support Vector Machine (SVM) appear among the most reliable options. A SVM based framework for peptidase analysis, that recognizes the hierarchies demarked in the MEROPS database is presented. Feature selection with SVM-RFE is used to improve the discriminative models and build classifiers computationally more efficient than alignment based techniques.

scholarly journals A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

2013 ◽  
Vol 288 (29) ◽  
pp. 21279-21294 ◽  
Author(s):  
Mar López-Pelegrín ◽  
Núria Cerdà-Costa ◽  
Francisco Martínez-Jiménez ◽  
Anna Cintas-Pedrola ◽  
Albert Canals ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Structural Similarity ◽  
Rational Drug Design ◽  
Sequence Comparisons ◽  
Catalytic Domains ◽  
Rational Drug ◽  
Leukotriene A4 Hydrolase ◽  
Merops Database ◽  
Leukotriene A4 ◽  
Related Proteins

In the search for structural models of integral-membrane metallopeptidases (MPs), we discovered three related proteins from thermophilic prokaryotes, which we grouped into a novel family called “minigluzincins.” We determined the crystal structures of the zymogens of two of these (Pyrococcus abyssi proabylysin and Methanocaldococcus jannaschii projannalysin), which are soluble and, with ∼100 residues, constitute the shortest structurally characterized MPs to date. Despite relevant sequence and structural similarity, the structures revealed two unique mechanisms of latency maintenance through the C-terminal segments previously unseen in MPs as follows: intramolecular, through an extended tail, in proabylysin, and crosswise intermolecular, through a helix swap, in projannalysin. In addition, structural and sequence comparisons revealed large similarity with MPs of the gluzincin tribe such as thermolysin, leukotriene A4 hydrolase relatives, and cowrins. Noteworthy, gluzincins mostly contain a glutamate as third characteristic zinc ligand, whereas minigluzincins have a histidine. Sequence and structural similarity further allowed us to ascertain that minigluzincins are very similar to the catalytic domains of integral membrane MPs of the MEROPS database families M48 and M56, such as FACE1, HtpX, Oma1, and BlaR1/MecR1, which are provided with trans-membrane helices flanking or inserted into a minigluzincin-like catalytic domain. In a time where structural biochemistry of integral-membrane proteins in general still faces formidable challenges, the minigluzincin soluble minimal scaffold may contribute to our understanding of the working mechanisms of these membrane MPs and to the design of novel inhibitors through structure-aided rational drug design approaches.

Proteases: a primer

2002 ◽  
Vol 38 ◽  
pp. 1-8 ◽  
Author(s):  
Nigel M Hooper
Keyword(s):  
Active Site ◽  
Serine Proteases ◽  
Cysteine Proteases ◽  
Aspartic Proteases ◽  
Peptide Bonds ◽  
Endogenous Inhibitors ◽  
Merops Database ◽  
Internal Peptide ◽  
Synthesis And Degradation

A protease can be defined as an enzyme that hydrolyses peptide bonds. Proteases can be divided into endopeptidases, which cleave internal peptide bonds in substrates, and exopeptidases, which cleave the terminal peptide bonds. Exopeptidases can be further subdivided into aminopeptidases and carboxypeptidases. The Schechter and Berger nomenclature provides a model for describing the interactions between the peptide substrate and the active site of a protease. Proteases can also be classified as aspartic proteases, cysteine proteases, metalloproteases, serine proteases and threonine proteases, depending on the nature of the active site. Different inhibitors can be used experimentally to distinguish between these classes of protease. The MEROPs database groups proteases into families on the basis of similarities in sequence and structure. Protease activity can be regulated in vivo by endogenous inhibitors, by the activation of zymogens and by altering the rate of their synthesis and degradation.

scholarly journals Recombinant metalloprotease as a perspective enzyme for meat tenderization

10.5219/1087 ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 628-633
Author(s):  
Mikhail Minaev ◽  
Anzhelika Aleksandrovna Makhova
Keyword(s):  
Shear Force ◽  
Specific Effect ◽  
Peptide Bond ◽  
Aeromonas Salmonicida ◽  
Test Evaluation ◽  
Heat Treated ◽  
Maximum Shear Force ◽  
Substrate Peptide ◽  
Merops Database ◽  
Meat Tenderization

Peptidase family M9 (MEROPS database) is true collagenases and contains bacterial collagenases from Vibrio and Clostridium. One of the producers of M9A subfamily peptidase is Aeromonas salmonicida (locus - ASA_3723). The aim of the study was production of recombinant metallopeptidase Aeromonas salmonicida by transformation Pichia pastoris for further meat tenderization. Laboratory amounts of recombinant peptidase were obtained and test evaluation of enzyme activity was performed. Recombinant peptidase broke the peptide bond «Pro-Leu-Gly-Met-Trp-Ser-Arg» (one of the collagen chains, (Mw = 846.06)). The concentration of the substrate (peptide) after 180 min was 2 – fold decrease as compared with control. The maximum shear force of heat-treated samples had a 1.27 – fold decrease as compared with the control. As a result of histological studies of beef shank samples, the specific effect of the supernatant on the structure of connective tissue was established. Muscle fibers have not changed. The recombinant enzyme could be used for the meat tenderization.

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