Module IsoelectricPoint
source code
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
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positive_pKs = { ' H ' : 5.98, ' K ' : 10.0, ' Nterm ' : 7.5, ' R ' : 12.0}
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negative_pKs = { ' C ' : 9.0, ' Cterm ' : 3.55, ' D ' : 4.05, ' E ' : 4.45, ...
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pKcterminal = { ' D ' : 4.55, ' E ' : 4.75}
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pKnterminal = { ' A ' : 7.59, ' E ' : 7.7, ' M ' : 7.0, ' P ' : 8.36, ' S ' : ...
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charged_aas = ( ' K ' , ' R ' , ' H ' , ' D ' , ' E ' , ' C ' , ' Y ' )
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negative_pKs
- Value:
{ ' C ' : 9.0, ' Cterm ' : 3.55, ' D ' : 4.05, ' E ' : 4.45, ' Y ' : 10.0}
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pKnterminal
- Value:
{ ' A ' : 7.59,
' E ' : 7.7,
' M ' : 7.0,
' P ' : 8.36,
' S ' : 6.93,
' T ' : 6.82,
' V ' : 7.44}
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