Charge and pI¶
Electrochemical properties of polypeptides can be assessed via the
pyteomics.electrochem module. For now, it allows to calculate:
the charge of a polypeptide molecule at given pH;
the isoelectric point.
The pyteomics.electrochem module is based on the Henderson-Hasselbalch
equation.
Examples¶
Both functions in the module accept input in the form of a modX sequence, a parsed sequence or a dict with amino acid composition.
>>> from pyteomics import electrochem
>>> electrochem.charge('PEPTIDE', 7)
-2.9980189709606284
>>> from pyteomics import parser
>>> parsed_seq = parser.parse('PEPTIDE', show_unmodified_termini=True)
>>> electrochem.charge(parsed_seq, 7)
-2.9980189709606284
>>> aa_composition = parser.amino_acid_composition('PEPTIDE', show_unmodified_termini=True)
>>> electrochem.charge(aa_composition, 7)
-2.9980189709606284
>>> electrochem.pI('PEPTIDE')
2.87451171875
>>> electrochem.pI('PEPTIDE', precision_pI=0.0001)
2.876354217529297
(Source code, png, hires.png, pdf)
Customization¶
The pKas of individual amino acids are stored in dicts in the
following format: {modX label : (pKa, charge)}. The module contains
several datasets published in scientific journals:
pyteomics.electrochem.pK_lehninger (used by default),
pyteomics.electrochem.pK_sillero,
pyteomics.electrochem.pK_dawson,
pyteomics.electrochem.pK_rodwell.