Pyteomics documentation v3.3.1

pyteomics.electrochem

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Source code for pyteomics.electrochem

"""
electrochem - electrochemical properties of polypeptides
========================================================

Summary
-------

This module is used to calculate the
electrochemical properties of polypeptide molecules.

The theory behind this module is based on the Henderson-Hasselbalch
equation and was thoroughly described in a number of sources [#Aronson]_,
[#Moore]_.

Briefly, the formula for the charge of a polypeptide in given pH is the following:

.. math::

   Q_{peptide} = \sum{\\frac{Q_i}{1+10^{Q_i(pH-pK_i)}}},

where the sum is taken over all ionizable groups of the polypeptide, and
:math:`Q_i` is -1 and +1 for acidic and basic functional groups,
respectively.

Main functions
--------------

  :py:func:`charge` - calculate the charge of a polypeptide

  :py:func:`pI` - calculate the isoelectric point of a polypeptide

Data
----

  :py:data:`pK_lehninger` - a set of pK from [#Lehninger]_.

  :py:data:`pK_sillero` - a set of pK from [#Sillero]_.

  :py:data:`pK_dawson` - a set of pK from [#Dawson]_, the pK values for NH2-
  and -OH are taken from [#Sillero]_.

  :py:data:`pK_rodwell` - a set of pK from [#Rodwell]_.

  :py:data:`pK_bjellqvist` - a set of pK from [#Bjellqvist]_.

  :py:data:`pK_nterm_bjellqvist` - a set of N-terminal pK from [#Bjellqvist]_.

  :py:data:`pK_cterm_bjellqvist` - a set of C-terminal pK from [#Bjellqvist]_.

References
----------

.. [#Aronson] Aronson, J. N. The Henderson-Hasselbalch equation
   revisited.  Biochemical Education, 1983, 11 (2), 68.
   `Link. <http://dx.doi.org/10.1016/0307-4412(83)90046-8>`_

.. [#Moore] Moore, D. S.. Amino acid and peptide net charges: A
   simple calculational procedure. Biochemical Education, 1986, 13 (1), 10-12.
   `Link. <http://dx.doi.org/10.1016/0307-4412(85)90114-1>`_

.. [#Lehninger] Nelson, D. L.; Cox, M. M. Lehninger Principles of
   Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100.

.. [#Sillero] Sillero, A.; Ribeiro, J. Isoelectric points of proteins:
   Theoretical determination. Analytical Biochemistry, 1989, 179 (2), 319-325.
   `Link. <http://dx.doi.org/10.1016/0003-2697(89)90136-X>`_

.. [#Dawson] Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M.
   Data for biochemical research. Oxford University Press, 1989; p. 592.

.. [#Rodwell] Rodwell, J. Heterogeneity of component bands in isoelectric
   focusing patterns. Analytical Biochemistry, 1982, 119 (2), 440-449.
   `Link. <http://dx.doi.org/10.1016/0003-2697(82)90611-X>`_

.. [#Bjellqvist] Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
    Reference points for comparisons of two-dimensional maps of proteins from
    different human cell types defined in a pH scale where isoelectric points
    correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539.
    `Link. <http://dx.doi.org/10.1002/elps.1150150171>`_

-------------------------------------------------------------------------------

"""

#   Copyright 2012 Anton Goloborodko, Lev Levitsky
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.

from . import parser
from .auxiliary import PyteomicsError
from collections import Iterable

[docs]def charge(sequence, pH, **kwargs): """Calculate the charge of a polypeptide in given pH or list of pHs using a given list of amino acid electrochemical properties. .. warning:: Be cafeful when supplying a list with a parsed sequence or a dict with amino acid composition as `sequence`. Such values must be obtained with enabled `show_unmodified_termini` option. .. warning:: If you provide `pK_nterm` or `pK_cterm` and provide `sequence` as a dict, it is assumed that it was obtained with ``term_aa=True`` (see :py:func:`pyteomics.parser.amino_acid_composition` for details). Parameters ---------- sequence : str or list or dict A string with a polypeptide sequence, a list with a parsed sequence or a dict of amino acid composition. pH : float or iterable of floats pH or iterable of pHs for which the charge is calculated. pK : dict {str: [(float, int), ...]}, optional A set of pK of amino acids' ionizable groups. It is a dict, where keys are amino acid labels and the values are lists of tuples (pK, charge_in_ionized_state), a tuple per ionizable group. The default value is `pK_lehninger`. pK_nterm : dict {str: [(float, int),]}, optional pK_cterm : dict {str: [(float, int),]}, optional Sets of pK of N-terminal and C-terminal (respectively) amino acids' ionizable groups. Dicts with the same structure as ``pK``. These values (if present) are used for N-terminal and C-terminal residues, respectively. If given, `sequence` must be a :py:class:`str` or a :py:class:`list`. The default value is an empty dict. Returns ------- out : float or list of floats A single value of charge or a list of charges. """ nterm = cterm = n_aa = c_aa = None pK = kwargs.get('pK', pK_lehninger).copy() pK_nterm = kwargs.get('pK_nterm', {}) pK_cterm = kwargs.get('pK_cterm', {}) if isinstance(sequence, dict): peptide_dict = sequence.copy() for k, v in sequence.items(): if k[-1] == '-': if v > 1 or nterm: raise PyteomicsError( 'More that one N-terminal group in {}'.format( sequence)) nterm = k if k[0] == '-': if v > 1 or cterm: raise PyteomicsError( 'More that one C-terminal group in {}'.format( sequence)) cterm = k if k[:5] == 'nterm': if v > 1 or n_aa: raise PyteomicsError( 'More that one N-terminal residue in {}'.format( sequence)) n_aa = k[5:] peptide_dict[n_aa] = peptide_dict.get(n_aa, 0) + 1 if k[:5] == 'cterm': if v > 1 or c_aa: raise PyteomicsError( 'More that one C-terminal residue in {}'.format( sequence)) c_aa = k[5:] peptide_dict[c_aa] = peptide_dict.get(c_aa, 0) + 1 if nterm is None or cterm is None: raise PyteomicsError('Peptide must have two explicit terminal groups') if (n_aa is None or c_aa is None) and (pK_nterm or pK_cterm): raise PyteomicsError('Two terminal residues must be present in ' 'peptide (designated as "ntermX" and "ctermX", where "X" is ' 'the one-letter residue label). Use ' '``term_aa=True`` when calling ' '`parser.amino_acid_composition`.') elif isinstance(sequence, (str, list)): if isinstance(sequence, str): parsed_sequence = parser.parse(sequence, show_unmodified_termini=True) elif isinstance(sequence, list): if sequence[0][-1] != '-' or sequence[-1][0] != '-': raise PyteomicsError('Parsed sequences must contain terminal ' 'groups at 0-th and last positions.') parsed_sequence = sequence n_aa = parsed_sequence[1] c_aa = parsed_sequence[-2] nterm = parsed_sequence[0] cterm = parsed_sequence[-1] peptide_dict = parser.amino_acid_composition(parsed_sequence) else: raise PyteomicsError('Unsupported type of sequence: %s' % type(sequence)) if nterm in pK_nterm: if n_aa in pK_nterm[nterm]: pK[nterm] = pK_nterm[nterm][n_aa] if cterm in pK_cterm: if c_aa in pK_cterm[cterm]: pK[cterm] = pK_cterm[cterm][c_aa] # Process the case when pH is a single float. pH_list = pH if isinstance(pH, Iterable) else [pH,] # Check if a sequence was parsed with `show_unmodified_termini` enabled. # Calculate the charge for each value of pH. charge_list = [] for pH_value in pH_list: charge = 0 for aa in peptide_dict: for ionizable_group in pK.get(aa, []): charge += peptide_dict[aa] * ionizable_group[1] * ( 1.0 / (1.0 + 10 ** (ionizable_group[1] * (pH_value - ionizable_group[0])))) charge_list.append(charge) return charge_list[0] if len(charge_list) == 1 else charge_list
[docs]def pI(sequence, pI_range=(0.0, 14.0), precision_pI=0.0001, **kwargs): """Calculate the isoelectric point of a polypeptide using a given set of amino acids' electrochemical properties. .. warning:: Be cafeful when supplying a list with a parsed sequence or a dict with amino acid composition as `sequence`. Such values must be obtained with enabled `show_unmodified_termini` option. Parameters ---------- sequence : str or list or dict A string with a polypeptide sequence, a list with a parsed sequence or a dict of amino acid composition. pI_range : tuple (float, float) The range of allowable pI values. Default is (0.0, 14.0). precision_pI : float The precision of the calculated pI. Default is 0.01. pK : dict {str: [(float, int), ...]}, optional A set of pK of amino acids' ionizable groups. It is a dict, where keys are amino acid labels and the values are lists of tuples (pK, charge_in_ionized_state), a tuple per ionizable group. The default value is `pK_lehninger`. pK_nterm : dict {str: [(float, int),]}, optional pK_cterm : dict {str: [(float, int),]}, optional Sets of pK of N-terminal and C-terminal (respectively) amino acids' ionizable groups. Dicts with the same structure as ``pK``. These values (if present) are used for N-terminal and C-terminal residues, respectively. If given, `sequence` must be a :py:class:`str` or a :py:class:`list`. The default value is an empty dict. Returns ------- out : float """ pK = kwargs.get('pK', pK_lehninger.copy()) pK_nterm = {} pK_cterm = {} if isinstance(sequence, str) or isinstance(sequence, list): pK_nterm = kwargs.get('pK_nterm', {}) pK_cterm = kwargs.get('pK_cterm', {}) elif isinstance(sequence,dict) and (("pK_nterm" in kwargs) or ("pK_cterm" in kwargs)): raise PyteomicsError('Can not use terminal features for %s' % type(sequence)) # The algorithm is based on the fact that charge(pH) is a monotonic function. left_x, right_x = pI_range left_y = charge(sequence, left_x, pK=pK, pK_cterm=pK_cterm, pK_nterm=pK_nterm) right_y = charge(sequence, right_x, pK=pK, pK_cterm=pK_cterm, pK_nterm=pK_nterm) while (right_x - left_x) > precision_pI: if left_y * right_y > 0: return left_x if abs(left_y) < abs(right_y) else right_x middle_x = (left_x + right_x) / 2.0 middle_y = charge(sequence, middle_x, pK=pK, pK_cterm=pK_cterm, pK_nterm=pK_nterm) if middle_y * left_y < 0: right_x = middle_x right_y = middle_y else: left_x = middle_x left_y = middle_y return (left_x + right_x) / 2.0
pK_lehninger = { 'E': [(4.25, -1)], 'R': [(12.48, 1)], 'Y': [(10.07, -1)], 'D': [(3.65, -1)], 'H': [(6.00, +1)], 'K': [(10.53, +1)], 'C': [(8.18, -1)], 'H-': [(9.69, +1)], '-OH': [(2.34, -1)], } """A set of pK from Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100. """ pK_sillero = { 'E': [(4.5, -1)], 'R': [(12.0, +1)], 'Y': [(10.0, -1)], 'D': [(4.0, -1)], 'H': [(6.4, +1)], 'K': [(10.4, +1)], 'C': [(9.0, -1)], 'H-': [(8.2, +1)], '-OH': [(3.2, -1)], } """A set of pK from Sillero, A.; Ribeiro, J. Isoelectric points of proteins: Theoretical determination. Analytical Biochemistry, vol. 179 (2), pp. 319-325, 1989. """ pK_dawson = { 'E': [(4.3, -1)], 'R': [(12.0, +1)], 'Y': [(10.1, -1)], 'D': [(3.9, -1)], 'H': [(6.0, +1)], 'K': [(10.5, +1)], 'C': [(8.3, -1)], 'H-': [(8.2, +1)], '-OH': [(3.2, -1)], } """A set of pK from Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M. Data for biochemical research. Oxford University Press, 1989; p. 592. pKs for NH2- and -OH are taken from `pK_sillero`. """ pK_rodwell = { 'E': [(4.25, -1)], 'R': [(11.5, +1)], 'Y': [(10.7, -1)], 'D': [(3.86, -1)], 'H': [(6.0, +1)], 'K': [(11.5, +1)], 'C': [(8.33, -1)], 'H-': [(8.0, +1)], '-OH': [(3.1, -1)], } """A set of pK from Rodwell, J. Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, vol. 119 (2), pp. 440-449, 1982. """ pK_bjellqvist = { 'E': [(4.45, -1)], 'R': [(12.0, +1)], 'Y': [(10.0, -1)], 'D': [(4.05, -1)], 'H': [(5.98, +1)], 'K': [(10.0, +1)], 'C': [(9.0, -1)], 'H-': [(7.5, +1)], '-OH': [(3.55, -1)], } """ A set of pK from Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. """ pK_nterm_bjellqvist = { 'H-': { 'A': [(7.59, +1)], 'M': [(7.0, +1)], 'S': [(6.93, +1)], 'P': [(8.36, +1)], 'T': [(6.82, +1)], 'V': [(7.44, +1)], 'E': [(7.7, +1)] } } """ A set of N-terminal pK from Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. """ pK_cterm_bjellqvist = { '-OH': { 'D': [(4.55, -1)], 'E': [(4.75, -1)] } } """ A set of C-terminal pK from Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. """ if __name__ == "__main__": import doctest doctest.testmod()

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