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 [1], [2].

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

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

Main functions¶

charge() - calculate the charge of a polypeptide

pI() - calculate the isoelectric point 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].

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.

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 list of floats pH or list 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.

Returns :

out : float or list of floats or None A single value of charge or a list of charges. Returns None if sequence is not of supported type.

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.

Returns :

out : float

pyteomics.electrochem.pK_dawson¶

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¶

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_rodwell¶

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¶

A set of pK from Sillero, A.; Ribeiro, J. Isoelectric points of proteins: Theoretical determination. Analytical Biochemistry, vol. 179 (2), pp. 319-325, 1989.