binaries/src/globplot/biopython-1.50/Bio/SeqUtils/IsoelectricPoint.py

   1 # Copyright Yair Benita Y.Benita@pharm.uu.nl
   2 # Biopython (http://biopython.org) license applies
   3
   4 """Calculate isoelectric points of polypeptides using methods of Bjellqvist.
   5
   6 pK values and the methos are taken from:
   7
   8 * Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
   9 J.-Ch., Frutiger, S. & Hochstrasser, D.F.
  10 The focusing positions of polypeptides in immobilized pH gradients can be predicted
  11 from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
  12
  13 * Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
  14 Reference points for comparisons of two-dimensional maps of proteins from
  15 different human cell types defined in a pH scale where isoelectric points correlate
  16 with polypeptide compositions. Electrophoresis 1994, 15, 529-539.
  17
  18 I designed the algorithm according to a note by David L. Tabb, available at:
  19 http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf
  20
  21 """
  22
  23 positive_pKs = { 'Nterm': 7.5, 'K': 10.0, 'R': 12.0, 'H':5.98 }
  24 negative_pKs = { 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C':9.0, 'Y':10.0 }
  25 pKcterminal= {'D':4.55, 'E':4.75}
  26 pKnterminal = {'A':7.59, 'M':7.0, 'S':6.93, 'P':8.36, 'T':6.82, 'V':7.44, 'E':7.7}
  27 charged_aas = ('K', 'R', 'H', 'D', 'E', 'C', 'Y')
  28
  29 # access this module through ProtParam.ProteinAnalysis class.
  30 # first make a ProteinAnalysis object and then call its isoelectric_point method.
  31 class IsoelectricPoint:
  32     def __init__(self, ProteinSequence, AminoAcidsContent):
  33         self.sequence = ProteinSequence
  34         self.charged_aas_content = self._select_charged(AminoAcidsContent)
  35
  36     # This function creates a dictionary with the contents of each charged aa,
  37     # plus Cterm and Nterm.
  38     def _select_charged(self, AminoAcidsContent):
  39         charged = {}
  40         for aa in charged_aas:
  41             charged[aa] = float(AminoAcidsContent[aa])
  42         charged['Nterm'] = 1.0
  43         charged['Cterm'] = 1.0
  44         return charged
  45
  46         #This function calculates the total charge of the protein at a given pH.
  47     def _chargeR(self, pH, pos_pKs, neg_pKs):
  48         PositiveCharge = 0.0
  49         for aa, pK in pos_pKs.iteritems():
  50              CR = 10**(pK-pH)
  51              partial_charge = CR/(CR+1.0)
  52              PositiveCharge += self.charged_aas_content[aa] * partial_charge
  53
  54         NegativeCharge = 0.0
  55         for aa, pK in neg_pKs.iteritems():
  56              CR = 10**(pH-pK)
  57              partial_charge = CR/(CR+1.0)
  58              NegativeCharge += self.charged_aas_content[aa] * partial_charge
  59
  60         return PositiveCharge - NegativeCharge
  61
  62         # This is the action function, it tries different pH until the charge of the protein is 0 (or close).
  63     def pi(self):
  64         pos_pKs = dict(positive_pKs)
  65         neg_pKs = dict(negative_pKs)
  66         nterm = self.sequence[0]
  67         cterm = self.sequence[-1]
  68         if nterm in pKnterminal.keys():
  69             pos_pKs['Nterm'] = pKnterminal[nterm]
  70         if cterm in pKcterminal.keys():
  71             neg_pKs['Cterm'] = pKcterminal[cterm]
  72
  73         # Bracket between pH1 and pH2
  74         pH = 7.0
  75         Charge = self._chargeR(pH, pos_pKs, neg_pKs)
  76         if Charge > 0.0:
  77             pH1 = pH
  78             Charge1 = Charge
  79             while Charge1 > 0.0:
  80                 pH = pH1 + 1.0
  81                 Charge = self._chargeR(pH, pos_pKs, neg_pKs)
  82                 if Charge > 0.0:
  83                     pH1 = pH
  84                     Charge1 = Charge
  85                 else:
  86                     pH2 = pH
  87                     Charge2 = Charge
  88                     break
  89         else:
  90             pH2 = pH
  91             Charge2 = Charge
  92             while Charge2 < 0.0:
  93                 pH = pH2 - 1.0
  94                 Charge = self._chargeR(pH, pos_pKs, neg_pKs)
  95                 if Charge < 0.0:
  96                     pH2 = pH
  97                     Charge2 = Charge
  98                 else:
  99                     pH1 = pH
 100                     Charge1 = Charge
 101                     break
 102
 103         # Bisection
 104         while pH2 - pH1 > 0.0001 and Charge!=0.0:
 105             pH = (pH1 + pH2) / 2.0
 106             Charge = self._chargeR(pH, pos_pKs, neg_pKs)
 107             if Charge > 0.0:
 108                 pH1 = pH
 109                 Charge1 = Charge
 110             else:
 111                 pH2 = pH
 112                 Charge2 = Charge
 113
 114         return pH