Isoelectric Point calculations

[T. Chyau Liang]

In article <4hok83$315 at net.bio.net>, Eugene A Kapp
<100277.2367 at CompuServe.COM> wrote:

> I have found that the predicted pI calculations from two WWW 
> sites differ by approximately 0.4 for a given protein sequence. 
> Expasy (http://expasy.hcuge.ch/ch2d/pi_tool.html) and the genome 
> sequencing site at (http://genome1.bio.bnl.gov/bbq.html) are 
> therefore using slightly different pKR values.
> 
> Could someone suggest the correct pKR values or add some light to 
> the situation.
> 
> Many thanks.

Here is my 2 cents:

(1) You are probably right that they do use different values in their
calculations.
(2) The exact pKa of individual amino acid side chain depends on its
microenvironment. Any prediction will just be that (PREDICTION).
Therefore, I don't think one can take the predicted value literally. So,
0.4 unit difference may not mean much.

Hope this helps.

T. Chyau Liang
U. Texas-Houston