Bio.SeqUtils.IsoelectricPoint module

Calculate isoelectric points of polypeptides using methods of Bjellqvist.

pK values and the methods are taken from:

* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F.
The focusing positions of polypeptides in immobilized pH gradients can be
predicted from their amino acid sequences. Electrophoresis 1993, 14,
1023-1031.

* 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.

I designed the algorithm according to a note by David L. Tabb, available at: http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf

class Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint(protein_sequence, aa_content=None)

Bases: object

A class for calculating the IEP or charge at given pH of a protein.

Parameters
:protein_sequence: A ``Bio.Seq`` or string object containing a protein

sequence.

:aa_content: A dictionary with amino acid letters as keys and its

occurrences as integers, e.g. {"A": 3, "C": 0, ...}. Default: None. If None, the dic will be calculated from the given sequence.

Examples

The methods of this class can either be accessed from the class itself or from a ProtParam.ProteinAnalysis object (with partially different names):

>>> from Bio.SeqUtils.IsoelectricPoint import IsoelectricPoint as IP
>>> protein = IP("INGAR")
>>> print(f"IEP of peptide {protein.sequence} is {protein.pi():.2f}")
IEP of peptide INGAR is 9.75
>>> print(f"Its charge at pH 7 is {protein.charge_at_pH(7.0):.2f}")
Its charge at pH 7 is 0.76

>>> from Bio.SeqUtils.ProtParam import ProteinAnalysis as PA
>>> protein = PA("PETER")
>>> print(f"IEP of {protein.sequence}: {protein.isoelectric_point():.2f}")
IEP of PETER: 4.53
>>> print(f"Charge at pH 4.53: {protein.charge_at_pH(4.53):.2f}")
Charge at pH 4.53: 0.00

Methods

:charge_at_pH(pH): Calculates the charge of the protein for a given pH

:pi(): Calculates the isoelectric point
__init__(protein_sequence, aa_content=None)

Initialize the class.

charge_at_pH(pH)

Calculate the charge of a protein at given pH.

pi(pH=7.775, min_=4.05, max_=12)

Calculate and return the isoelectric point as float.

This is a recursive function that uses bisection method. Wiki on bisection: https://en.wikipedia.org/wiki/Bisection_method

Arguments:

  • pH: the pH at which the current charge of the protein is computed. This pH lies at the centre of the interval (mean of min_ and max_).

  • min_: the minimum of the interval. Initial value defaults to 4.05, which is below the theoretical minimum, when the protein is composed exclusively of aspartate.

  • max_: the maximum of the the interval. Initial value defaults to 12, which is above the theoretical maximum, when the protein is composed exclusively of arginine.