File Coverage

blib/lib/Bio/Protease.pm

Criterion	Covered	Total	%
statement	14	14	100.0
branch			n/a
condition			n/a
subroutine	5	5	100.0
pod			n/a
total	19	19	100.0

package Bio::Protease;
{
  $Bio::Protease::VERSION = '1.112900'; # TRIAL
}

# ABSTRACT: Digest your protein substrates with customizable specificity

use Moose 1.23;
use MooseX::ClassAttribute;
use Bio::Protease::Types qw(ProteaseRegex ProteaseName);
use namespace::autoclean;

with qw(
    Bio::ProteaseI
    Bio::Protease::Role::Specificity::Regex
    Bio::Protease::Role::WithCache
);

has '+regex' => ( init_arg => 'specificity' );

has specificity => (
    is  => 'ro',
    isa => ProteaseName,
    required => 1,
    coerce   => 1
);

class_has Specificities => (
    is         => 'ro',
    lazy_build => 1,
);

sub _build_Specificities {

    my %specificity_of = (
        'alcalase'                   => [ '.{3}[MYFLIVW].{4}'],
        'arg-c_proteinase'           => [ '.{3}R.{4}' ],
        'asp-n_endopeptidase'        => [ '.{4}D.{3}' ],
        'asp-n_endopeptidase_glu'    => [ '.{4}[DE].{3}' ],
        'bnps_skatole'               => [ '.{3}W.{4}' ],
        'caspase_1'                  => [ '[FWYL].[HAT]D[^PEDQKR].{3}' ],
        'caspase_2'                  => [ 'DVAD[^PEDQKR].{3}' ],
        'caspase_3'                  => [ 'DMQD[^PEDQKR].{3}' ],
        'caspase_4'                  => [ 'LEVD[^PEDQKR].{3}' ],
        'caspase_5'                  => [ '[LW]EHD.{4}' ],
        'caspase_6'                  => [ 'VE[HI]D[^PEDQKR].{3}' ],
        'caspase_7'                  => [ 'DEVD[^PEDQKR].{3}' ],
        'caspase_8'                  => [ '[IL]ETD[^PEDQKR].{3}' ],
        'caspase_9'                  => [ 'LEHD.{4}' ],
        'caspase_10'                 => [ 'IEAD.{4}' ],
        'chymotrypsin'               => [ '.{3}[FY][^P].{3}|.{3}W[^MP].{3}' ],
        'chymotrypsin_low'           => [ '.{3}[FLY][^P].{3}|.{3}W[^MP].{3}|.{3}M[^PY].{3}|.{3}H[^DMPW].{3}' ],
        'clostripain'                => [ '.{3}R.{4}' ],
        'cnbr'                       => [ '.{3}M.{4}' ],
        'enterokinase'               => [ '[DN][DN][DN]K.{4}' ],
        'factor_xa'                  => [ '[AFGILTVM][DE]GR.{4}' ],
        'formic_acid'                => [ '.{3}D.{4}' ],
        'glutamyl_endopeptidase'     => [ '.{3}E.{4}' ],
        'granzymeb'                  => [ 'IEPD.{4}' ],
        'hydroxylamine'              => [ '.{3}NG.{3}' ],
        'hcl'                        => [ '.{8}' ],
        'iodosobenzoic_acid'         => [ '.{3}W.{4}' ],
        'lysc'                       => [ '.{3}K.{4}' ],
        'lysn'                       => [ '.{4}K.{3}' ],
        'ntcb'                       => [ '.{4}C.{3}' ],
        'pepsin_ph1.3'               => [ '.[^HKR][^P][^R][FLWY][^P].{2}|.[^HKR][^P][FLWY].[^P].{2}' ],
        'pepsin'                     => [ '.[^HKR][^P][^R][FL][^P].{2}|.[^HKR][^P][FL].[^P].{2}' ],
        'proline_endopeptidase'      => [ '.{2}[HKR]P[^P].{3}' ],
        'proteinase_k'               => [ '.{3}[AFILTVWY].{4}' ],
        'staphylococcal_peptidase_i' => [ '.{2}[^E]E.{4}' ],
        'thermolysin'                => [ '.{3}[^XDE][AFILMV][^P].{2}' ],
        'thrombin'                   => [ '.{2}GRG.{3}|[AFGILTVM][AFGILTVWA]PR[^DE][^DE].{2}' ],
        'trypsin'                    => [ '.{2}(?!CKD).{6}', '.{2}(?!DKD).{6}', '.{2}(?!CKH).{6}', '.{2}(?!CKY).{6}', '.{2}(?!RRH).{6}', '.{2}(?!RRR).{6}', '.{2}(?!CRK).{6}',
                                        '.{3}[KR][^P].{3}|.{2}WKP.{3}|.{2}MRP.{3}' ]
    );

    return \%specificity_of;
}

__PACKAGE__->meta->make_immutable;








__END__
=pod

=head1 NAME

Bio::Protease - Digest your protein substrates with customizable specificity

=head1 VERSION

version 1.112900

=head1 SYNOPSIS

    use Bio::Protease;
    my $protease = Bio::Protease->new(specificity => 'trypsin');

    my $protein = 'MRAERVIKP';

    # 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' )

=head1 DESCRIPTION

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 37 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 consuming the module's interface, L<Bio::ProteaseI>.
Alternatively, if your desired specificity can be correctly described by
a regular expression, you can pass it to the specificity attribute at
construction time. See L<specificity> below.

=head1 ATTRIBUTES

=head2 specificity

Set the enzyme's specificity. Required. Could be either of:

=over 4

=item * an enzyme name: e.g. 'enterokinase'

    my $enzyme = Bio::Protease->new(specificity => 'enterokinase');

There are currently definitions for 37 enzymes/reagents. See
L<Specificities>.

=item * a regular expression:

    my $motif = qr/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, you can also pass an array reference of regular expressions; all
of which should match the given octapeptide:

    my $rule = [$rule1, $rule2, $rule3];

    my $enzyme = Bio::Protease->new( specificity => $rule );

In the case your particular specificity rule requires an "or" clause,
you can use the "|" separator in a single regex.

=back

=head2 Specificities

This B<class attribute> contains 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 them.

    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:

=over 2

=item * alcalase

=item * arg-cproteinase

=item * asp-n_endopeptidase

=item * asp-n_endopeptidase_glu

=item * bnps_skatole

=item * caspase_1

=item * caspase_2

=item * caspase_3

=item * caspase_4

=item * caspase_5

=item * caspase_6

=item * caspase_7

=item * caspase_8

=item * caspase_9

=item * caspase_10

=item * chymotrypsin

=item * chymotrypsin_low

=item * clostripain

=item * cnbr

=item * enterokinase

=item * factor_xa

=item * formic_acid

=item * glutamyl_endopeptidase

=item * granzymeb

=item * hydroxylamine

=item * iodosobenzoic_acid

=item * lysc

=item * lysn

=item * ntcb

=item * pepsin_ph1.3

=item * pepsin

=item * proline_endopeptidase

=item * proteinase_k

=item * staphylococcal_peptidase i

=item * thermolysin

=item * thrombin

=item * trypsin

=back

For a complete description of their specificities, you can check out
L<http://www.expasy.ch/tools/peptidecutter/peptidecutter_enzymes.html>,
or look at the regular expressions of their definitions in this same
file.

=head2 use_cache

Turn caching on, trading memory for speed. Defaults to 0 (no caching).
Useful when any method is being called several times with the same
argument.

    my $p = Bio::Protease->new( specificity => 'trypsin', use_cache => 0 );
    my $c = Bio::Protease->new( specificity => 'trypsin', use_cache => 1 );

    my $substrate = 'MAAEELRKVIKPR' x 10;

    $p->digest( $substrate ) for (1..1000); # time: 5.11s
    $c->digest( $substrate ) for (1..1000); # time: 0.12s

=head2 cache

The cache object, which has to do the L<Cache::Ref::Role::API> role.
Uses L<Cache::Ref::LRU> by default with a cache size of 5000, but you
can set this to your liking at construction time:

    my $p = Bio::Protease->new(
        use_cache   => 1,
        cache       => Cache::Ref::Random->new( size => 50 ),
        specificity => 'trypsin'
    );

=head1 METHODS

=head2 digest

Performs a complete digestion of the peptide argument, returning a list
with possible products. It does not do partial digests (see method
C<cut> for that).

    my @products = $enzyme->digest($protein);

=head2 cut

Attempt to cleave C<$peptide> at the C-terminal end of the C<$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, $i);

=head2 cleavage_sites

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. Takes a string with the protein sequence
as an argument:

    my @sites = $enzyme->cleavage_sites($peptide);

=head2 is_substrate

Returns true or false whether the peptide argument is a substrate or
not. Esentially, it's equivalent to calling C<cleavage_sites> in boolean
context, but with the difference that this method short-circuits when it
finds its first cleavable site. Thus, it's useful for CPU-intensive
tasks where the only information required is whether a polypeptide is a
substrate of a particular enzyme or not

=head1 SEE ALSO

=over

=item * PeptideCutter

This module's idea is largely based on Expasy's
PeptideCutter (L<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.

=back

=head1 AUTHOR

Bruno Vecchi <vecchi.b gmail.com>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Bruno Vecchi.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut