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:
where the sum is taken over all ionizable groups of the polypeptide, and
is -1 and +1 for acidic and basic functional groups,
respectively.
Charge and pI functions¶
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. |
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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
(seepyteomics.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 astr
or alist
. 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
¶ 105-132 (1982).
Type: A set of hydropathicity indexes obtained from Kyte J., Doolittle F. J. Mol. Biol. 157
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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 astr
or alist
. The default value is an empty dict.
Returns: out
Return type:
-
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.
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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
¶ Theoretical determination. Analytical Biochemistry, vol. 179 (2), pp. 319-325, 1989.
Type: A set of pK from Sillero, A.; Ribeiro, J. Isoelectric points of proteins