Pyteomics documentation v4.3.3dev1

electrochem - electrochemical properties of polypeptides

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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

[1]Aronson, J. N. The Henderson-Hasselbalch equation revisited. Biochemical Education, 1983, 11 (2), 68. Link.
[2]Moore, D. S.. Amino acid and peptide net charges: A simple calculational procedure. Biochemical Education, 1986, 13 (1), 10-12. Link.
[3]Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100.
[4](1, 2) Sillero, A.; Ribeiro, J. Isoelectric points of proteins: Theoretical determination. Analytical Biochemistry, 1989, 179 (2), 319-325. Link.
[5]Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M. Data for biochemical research. Oxford University Press, 1989; p. 592.
[6]Rodwell, J. Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, 1982, 119 (2), 440-449. Link.
[7](1, 2, 3) 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.
[8]Kyte, J.; Doolittle, R. F.. A simple method for displaying the hydropathic character of a protein. Journal of molecular biology 1982, 157 (1), 105-32. Link.

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 : float or list of floats

A single value of charge or a list of charges.

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 set of hydropathicity indexes obtained from Kyte J., Doolittle F. J. Mol. Biol. 157:105-132 (1982).

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 : float
pyteomics.electrochem.pK_bjellqvist

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

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

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_nterm_bjellqvist

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

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.

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