+++ /dev/null
-# Copyright Yair Benita Y.Benita@pharm.uu.nl
-# Biopython (http://biopython.org) license applies
-
-"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
-
-pK values and the methos 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
-
-"""
-
-positive_pKs = { 'Nterm': 7.5, 'K': 10.0, 'R': 12.0, 'H':5.98 }
-negative_pKs = { 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C':9.0, 'Y':10.0 }
-pKcterminal= {'D':4.55, 'E':4.75}
-pKnterminal = {'A':7.59, 'M':7.0, 'S':6.93, 'P':8.36, 'T':6.82, 'V':7.44, 'E':7.7}
-charged_aas = ('K', 'R', 'H', 'D', 'E', 'C', 'Y')
-
-# access this module through ProtParam.ProteinAnalysis class.
-# first make a ProteinAnalysis object and then call its isoelectric_point method.
-class IsoelectricPoint:
- def __init__(self, ProteinSequence, AminoAcidsContent):
- self.sequence = ProteinSequence
- self.charged_aas_content = self._select_charged(AminoAcidsContent)
-
- # This function creates a dictionary with the contents of each charged aa,
- # plus Cterm and Nterm.
- def _select_charged(self, AminoAcidsContent):
- charged = {}
- for aa in charged_aas:
- charged[aa] = float(AminoAcidsContent[aa])
- charged['Nterm'] = 1.0
- charged['Cterm'] = 1.0
- return charged
-
- #This function calculates the total charge of the protein at a given pH.
- def _chargeR(self, pH, pos_pKs, neg_pKs):
- PositiveCharge = 0.0
- for aa, pK in pos_pKs.iteritems():
- CR = 10**(pK-pH)
- partial_charge = CR/(CR+1.0)
- PositiveCharge += self.charged_aas_content[aa] * partial_charge
-
- NegativeCharge = 0.0
- for aa, pK in neg_pKs.iteritems():
- CR = 10**(pH-pK)
- partial_charge = CR/(CR+1.0)
- NegativeCharge += self.charged_aas_content[aa] * partial_charge
-
- return PositiveCharge - NegativeCharge
-
- # This is the action function, it tries different pH until the charge of the protein is 0 (or close).
- def pi(self):
- pos_pKs = dict(positive_pKs)
- neg_pKs = dict(negative_pKs)
- nterm = self.sequence[0]
- cterm = self.sequence[-1]
- if nterm in pKnterminal.keys():
- pos_pKs['Nterm'] = pKnterminal[nterm]
- if cterm in pKcterminal.keys():
- neg_pKs['Cterm'] = pKcterminal[cterm]
-
- # Bracket between pH1 and pH2
- pH = 7.0
- Charge = self._chargeR(pH, pos_pKs, neg_pKs)
- if Charge > 0.0:
- pH1 = pH
- Charge1 = Charge
- while Charge1 > 0.0:
- pH = pH1 + 1.0
- Charge = self._chargeR(pH, pos_pKs, neg_pKs)
- if Charge > 0.0:
- pH1 = pH
- Charge1 = Charge
- else:
- pH2 = pH
- Charge2 = Charge
- break
- else:
- pH2 = pH
- Charge2 = Charge
- while Charge2 < 0.0:
- pH = pH2 - 1.0
- Charge = self._chargeR(pH, pos_pKs, neg_pKs)
- if Charge < 0.0:
- pH2 = pH
- Charge2 = Charge
- else:
- pH1 = pH
- Charge1 = Charge
- break
-
- # Bisection
- while pH2 - pH1 > 0.0001 and Charge!=0.0:
- pH = (pH1 + pH2) / 2.0
- Charge = self._chargeR(pH, pos_pKs, neg_pKs)
- if Charge > 0.0:
- pH1 = pH
- Charge1 = Charge
- else:
- pH2 = pH
- Charge2 = Charge
-
- return pH