| Bio::Protease |
use Bio::Protease;
my $protease = Bio::Protease->new(specificity => 'trypsin');
my $protein = 'MRAERVIKP'; # Could also be a Bio::Seq object.
# Perform a full digestion
my @products = $protease->digest($protein);
# products: ( 'MR', 'AER', 'VIKP' )
# Get all the siscile bonds.
my @sites = $protease->cleavage_sites($protein);
# sites: ( 2, 5 )
# Try to cut at a specific position.
@products = $protease->cut($protein, 2);
# products: ( 'MR', 'AERVIKP' )
This module is still in its infancy, and I might change its interface in the future (although I'm not planning to). Use at your own discretion (but please do, and send feedback!).
This module models the hydrolitic behaviour of a proteolytic enzyme. Its main purpose is to predict the outcome of hydrolitic cleavage of a peptidic substrate.
The enzyme specificity is currently modeled for 32 enzymes/reagents. This models are somewhat simplistic as they are largely regex-based, and do not take into account subtleties such as kinetic/temperature effects, accessible solvent area, secondary or tertiary structure elements. However, the module is flexible enough to allow the inclusion of any of these effects by subclassing from the module's interface, Bio::ProteaseI.
Set the enzyme's specificity. Required. Could be either of:
my $enzyme = Bio::Protease->new(specificity => 'enterokinase');
There are currently definitions for 36 enzymes/reagents. See
Specificities.
my $motif = ['MN[ED]K[^P].{3}'],
my $enzyme = Bio::Protease->new(specificity => $motif);
The motif should always describe an 8-character long peptide. When a an octapeptide matches the regex, its 4th peptidic bond (ie, between the 4th and 5th letter) will be marked for cleaving or reporting.
For example, the peptide AMQRNLAW is recognized as follows:
.----..----.----..----. .-----.-----.-----.-----.
| A || M | Q || R |*| N | L | A | W |
|----||----|----||----|^|-----|-----|-----|-----|
| P4 || P3 | P2 || P1 ||| P1' | P2' | P3' | P4' |
'----''----'----''----'|'-----'-----'-----'-----'
cleavage site
Some specificity rules can only be described with more than one regular expression (See the case for trypsin, for example). To account for those cases, the array reference could contain an arbitrary number of regexes, all of which should match the given octapeptide.
In the case your particular specificity rule requires an "or" clause, you can use the "|" separator in a single regex.
digest($substrate)Performs a complete digestion of the peptide argument, returning a list
with possible products. It does not do partial digests (see method
cut for that).
my @products = $enzyme->digest($protein);
Attempt to cleave $substrate at the C-terminal end of the $i-th residue (ie, at the right). If the bond is indeed cleavable (determined by the enzyme's specificity), then a list with the two products of the hydrolysis will be returned. Otherwise, returns false.
my @products = $enzyme->cut($peptide, $position);
cleavage_sites($protein)Returns a list with siscile bonds (bonds susceptible to be cleaved as determined by the enzyme's specificity). Bonds are numbered starting from 1, from N to C-terminal.
A hash reference with all the available regexep-based specificities. The keys are the specificity names, the value is an arrayref with the regular expressions that define it.
my @protease_pool = do {
Bio::Protease->new(specificity => $_)
for keys %{Bio::Protease->Specificities};
}
As a rule, all specificity names are lower case. Currently, they include:
For a complete description of their specificities, you can check out http://www.expasy.ch/tools/peptidecutter/peptidecutter_enzymes.html, or look at the regular expressions of their definitions in this same file.
PeptideCutter This module's idea is largely based on Expasy's PeptideCutter(http://www.expasy.ch/tools/peptidecutter/). For more information on the experimental evidence that supports both the algorithm and the specificity definitions, check their page.
| Bio::Protease |