The Proteolysis MAP (
PMAP) is an integrated
web resource focused on
proteases.
[1]
Rationale
PMAP is to aid the protease researchers in reasoning about
proteolytic networks and
metabolic pathways.
History and funding
PMAP was originally created at the
Burnham Institute for Medical Research, La Jolla, California. In 2004 the
National Institutes of Health (NIH) selected a team led by
Jeffrey W. Smith,
to establish the Center on Proteolytic Pathways (CPP). As part of the
NIH Roadmap for Biomedical research, the center develops technology to
study the behavior of proteins and to disburse that knowledge to the
scientific community at large.
Focal point
Proteases are a class of
enzymes that regulate much of what happens in the
human body, both inside the
cell and out, by cleaving
peptide bonds in
proteins. Through this activity, they govern the four essential cell functions:
differentiation,
motility, division and
cell death — and activate important
extracellular episodes, such as the
biochemical cascade effect in
blood clotting.
Simply stated, life could not exist without them. Extensive on-line
classification system for proteases (also referred as peptidases) is
deposited in the
MEROPS database.
The goal
Proteolytic pathways, or proteolysis, are the series of events
controlled by proteases that occur in response to specific stimuli. In
addition to the clotting of blood, the production of
insulin
can be viewed as a proteolytic pathway, as the activation, regulation
and inhibition of that protein is the result of proteases reacting to
changing
glucose levels and triggering other proteases downstream.
Database content
PMAP integrates five databases. ProteaseDB and SubstrateDB, are
driven by an automated annotation pipeline that generates dynamic
‘Molecule Pages’, rich in molecular information. CutDB
[2] has information on more than 6,600 proteolytic events, and ProfileDB is dedicated to information of the
substrate recognition specificity of proteases. PathwayDB, just begun accumulation of
metabolic pathways
whose function can be dynamically modeled in a rule-based manner.
Hypothetical networks are inferred by semi-automated culling from the
literature. Additionally, protease software tools are available for the
analysis of individual proteases and
proteome-wide data sets.
Usage
Popular destinations in PMAP are Protease Molecule Pages and
Substrate Molecule Pages. Protease Molecule Pages show recent news in
PubMed literature of the protease, known
proteolytic events,
protein domain location and
protein structure view, as well as a cross annotation in other
bioinformatic
databases section. Substrate Molecule Pages display protein domains and
experimentally derived protease cut-sites for a given protein target of
interest.
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