Source Code for Module Bio.SeqUtils.IsoelectricPoint

  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   
 30  # access this module through ProtParam.ProteinAnalysis class. 
 31  # first make a ProteinAnalysis object and then call its isoelectric_point method. 
 32 -class IsoelectricPoint(object): 
 33 -    def __init__(self, ProteinSequence, AminoAcidsContent): 
 34          self.sequence = ProteinSequence 
 35          self.charged_aas_content = self._select_charged(AminoAcidsContent) 
 36   
 37      # This function creates a dictionary with the contents of each charged aa, 
 38      # plus Cterm and Nterm. 
 39 -    def _select_charged(self, AminoAcidsContent): 
 40          charged = {} 
 41          for aa in charged_aas: 
 42              charged[aa] = float(AminoAcidsContent[aa]) 
 43          charged['Nterm'] = 1.0 
 44          charged['Cterm'] = 1.0 
 45          return charged 
 46   
 47      #This function calculates the total charge of the protein at a given pH. 
 48 -    def _chargeR(self, pH, pos_pKs, neg_pKs): 
 49          PositiveCharge = 0.0 
 50          for aa, pK in pos_pKs.iteritems(): 
 51              CR = 10**(pK-pH) 
 52              partial_charge = CR/(CR+1.0) 
 53              PositiveCharge += self.charged_aas_content[aa] * partial_charge 
 54   
 55          NegativeCharge = 0.0 
 56          for aa, pK in neg_pKs.iteritems(): 
 57              CR = 10**(pH-pK) 
 58              partial_charge = CR/(CR+1.0) 
 59              NegativeCharge += self.charged_aas_content[aa] * partial_charge 
 60   
 61          return PositiveCharge - NegativeCharge 
 62   
 63      # This is the action function, it tries different pH until the charge of the protein is 0 (or close). 
 64 -    def pi(self): 
 65          pos_pKs = dict(positive_pKs) 
 66          neg_pKs = dict(negative_pKs) 
 67          nterm = self.sequence[0] 
 68          cterm = self.sequence[-1] 
 69          if nterm in pKnterminal.keys(): 
 70              pos_pKs['Nterm'] = pKnterminal[nterm] 
 71          if cterm in pKcterminal.keys(): 
 72              neg_pKs['Cterm'] = pKcterminal[cterm] 
 73   
 74          # Bracket between pH1 and pH2 
 75          pH = 7.0 
 76          Charge = self._chargeR(pH, pos_pKs, neg_pKs) 
 77          if Charge > 0.0: 
 78              pH1 = pH 
 79              Charge1 = Charge 
 80              while Charge1 > 0.0: 
 81                  pH = pH1 + 1.0 
 82                  Charge = self._chargeR(pH, pos_pKs, neg_pKs) 
 83                  if Charge > 0.0: 
 84                      pH1 = pH 
 85                      Charge1 = Charge 
 86                  else: 
 87                      pH2 = pH 
 88                      Charge2 = Charge 
 89                      break 
 90          else: 
 91              pH2 = pH 
 92              Charge2 = Charge 
 93              while Charge2 < 0.0: 
 94                  pH = pH2 - 1.0 
 95                  Charge = self._chargeR(pH, pos_pKs, neg_pKs) 
 96                  if Charge < 0.0: 
 97                      pH2 = pH 
 98                      Charge2 = Charge 
 99                  else: 
100                      pH1 = pH 
101                      Charge1 = Charge 
102                      break 
103   
104          # Bisection 
105          while pH2 - pH1 > 0.0001 and Charge != 0.0: 
106              pH = (pH1 + pH2) / 2.0 
107              Charge = self._chargeR(pH, pos_pKs, neg_pKs) 
108              if Charge > 0.0: 
109                  pH1 = pH 
110                  Charge1 = Charge 
111              else: 
112                  pH2 = pH 
113                  Charge2 = Charge 
114   
115          return pH 
116