electrochem - electrochemical properties of polypeptides¶

Summary¶

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

The theory behind most of this module is based on the Henderson-Hasselbalch equation and was thoroughly described in a number of sources [1], [2].

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

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

where the sum is taken over all ionizable groups of the polypeptide, and \(Q_i\) is -1 and +1 for acidic and basic functional groups, respectively.

Charge and pI functions¶

charge() - calculate the charge of a polypeptide

pI() - calculate the isoelectric point of a polypeptide

GRand AVerage of hYdropathicity (GRAVY)¶

gravy() - calculate the GRAVY index of a polypeptide

Data¶

pK_lehninger - a set of pK from [3].

pK_sillero - a set of pK from [4].

pK_dawson - a set of pK from [5], the pK values for NH2- and -OH are taken from [4].

pK_rodwell - a set of pK from [6].

pK_bjellqvist - a set of pK from [7].

pK_nterm_bjellqvist - a set of N-terminal pK from [7].

pK_cterm_bjellqvist - a set of C-terminal pK from [7].

hydropathicity_KD - a set of hydropathicity indexes from [8].

References

pyteomics.electrochem.charge(sequence, pH, **kwargs)[source]¶

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 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 str or a list. The default value is an empty dict.

Returns:

out – A single value of charge or a list of charges.

Return type:

float or list of floats

pyteomics.electrochem.gravy(sequence, hydropathicity={'A': 1.8, 'C': 2.5, 'D': -3.5, 'E': -3.5, 'F': 2.8, 'G': -0.4, 'H': -3.2, 'I': 4.5, 'K': -3.9, 'L': 3.8, 'M': 1.9, 'N': -3.5, 'P': -1.6, 'Q': -3.5, 'R': -4.5, 'S': -0.8, 'T': -0.7, 'V': 4.2, 'W': -0.9, 'Y': -1.3})[source]¶

Calculate GRand AVerage of hYdropathicity (GRAVY) index for amino acid sequence.

Parameters:

sequence (str) – Polypeptide sequence in one-letter format.
hydropathicity (dict, optional) – Hydropathicity indexes of amino acids. Default is hydropathicity_KD.

Returns:

out (float) – GRand AVerage of hYdropathicity (GRAVY) index.
Examples
>>> gravy(‘PEPTIDE’)
-1.4375

pyteomics.electrochem.hydropathicity_KD = {'A': 1.8, 'C': 2.5, 'D': -3.5, 'E': -3.5, 'F': 2.8, 'G': -0.4, 'H': -3.2, 'I': 4.5, 'K': -3.9, 'L': 3.8, 'M': 1.9, 'N': -3.5, 'P': -1.6, 'Q': -3.5, 'R': -4.5, 'S': -0.8, 'T': -0.7, 'V': 4.2, 'W': -0.9, 'Y': -1.3}¶

105-132 (1982).

Type:: A set of hydropathicity indexes obtained from Kyte J., Doolittle F. J. Mol. Biol. 157

pyteomics.electrochem.pI(sequence, pI_range=(0.0, 14.0), precision_pI=0.01, **kwargs)[source]¶

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 str or a list. The default value is an empty dict.

Returns:

out

Return type:

float

pyteomics.electrochem.pK_bjellqvist = {'-OH': [(3.55, -1)], 'C': [(9.0, -1)], 'D': [(4.05, -1)], 'E': [(4.45, -1)], 'H': [(5.98, 1)], 'H-': [(7.5, 1)], 'K': [(10.0, 1)], 'R': [(12.0, 1)], 'Y': [(10.0, -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.

pyteomics.electrochem.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.

pyteomics.electrochem.pK_dawson = {'-OH': [(3.2, -1)], 'C': [(8.3, -1)], 'D': [(3.9, -1)], 'E': [(4.3, -1)], 'H': [(6.0, 1)], 'H-': [(8.2, 1)], 'K': [(10.5, 1)], 'R': [(12.0, 1)], 'Y': [(10.1, -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.

pyteomics.electrochem.pK_lehninger = {'-OH': [(2.34, -1)], 'C': [(8.18, -1)], 'D': [(3.65, -1)], 'E': [(4.25, -1)], 'H': [(6.0, 1)], 'H-': [(9.69, 1)], 'K': [(10.53, 1)], 'R': [(12.48, 1)], 'Y': [(10.07, -1)]}¶: A set of pK from Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100.

pyteomics.electrochem.pK_nterm_bjellqvist = {'H-': {'A': [(7.59, 1)], 'E': [(7.7, 1)], 'M': [(7.0, 1)], 'P': [(8.36, 1)], 'S': [(6.93, 1)], 'T': [(6.82, 1)], 'V': [(7.44, 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.

pyteomics.electrochem.pK_rodwell = {'-OH': [(3.1, -1)], 'C': [(8.33, -1)], 'D': [(3.86, -1)], 'E': [(4.25, -1)], 'H': [(6.0, 1)], 'H-': [(8.0, 1)], 'K': [(11.5, 1)], 'R': [(11.5, 1)], 'Y': [(10.7, -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.

pyteomics.electrochem.pK_sillero = {'-OH': [(3.2, -1)], 'C': [(9.0, -1)], 'D': [(4.0, -1)], 'E': [(4.5, -1)], 'H': [(6.4, 1)], 'H-': [(8.2, 1)], 'K': [(10.4, 1)], 'R': [(12.0, 1)], 'Y': [(10.0, -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.

Pyteomics documentation v5.0rc2