how to calculate the pI of a protein?

Answer 1

The isoelectric point of a protein is most often determined by experimentation. In order to calculate the pI, you would have to know the amino acid content of the protein in order to determine what amino acid side chains there are in the protein (denatured protein) and then use the theoretical values from a table showing the pKs of the side chains. The amino and acidic groups of the amino acids are used in the peptide bond and therefore do not contribute to the pI.

Even doing the calculation to get a theoretical answer does not give the same answer as experimentally determined.
(the answer given pI = 1/2 (pKa + pKb) applies only to an amino acid with non-ionizable side chains and the oligo ploypeptides that are made with these amino acids)

Answer 2

The above answers covered the difference between theoretical calculation and experimental determination and also how to calculate pI on your own.

If you have protein sequences and you want to calculate it fast you can use

http://www.embl-heidelberg.de/cgi/pi-wrapper.pl

It will give you not only the pI, but also the calculated net charge at different pH values.

Answer 3

pI = 1/2 (pKa1 + pKa2)

Amino acids usually have different pKas due to the presence of a basic and acidic group on the amino acid, so add them up and diivide by two. or add up and multiply by 1/2.