Protein Isoeletric point calculation

Keith Robison robison at lipid.harvard.edu
Thu Sep 15 17:59:22 EST 1994


Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands (sbtnfh at rulsfb.LeidenUniv.nl) wrote:
: In article <Pine.SUN.3.90.940912131219.3226A-100000 at snfma1.if.usp.br>, szeinfel at SNFMA1.IF.USP.BR (Rafael Iosef Najmanovich Szeinfeld {S) writes:
: >	Hi All,
: >	I read a recent message about Proteins Isoeletric point (PIP) and the 
: >replayer said something about a progam that calculates PIP's so I'll like 
: >someone to say something about the method used for such calculations...


: Hi Rafael,

: I don't want to disappoint you, but pI calculation is very diificult. You
: have to take into account which amino acids are on the protein surface,
: becauce their pK's are important for the charge of the protein. I've asked
: Gert Vriend and the biocomputing group at the EMBL in Heidelberg just the same
: question about a year ago. He said that at the time they were very busy with a
: whole team to come up with a suitable algorithm, but that it could take quite
: some time still. I don't know how far they are now, you'll have to ask him
: (Gert.Vriend at EMBL-Heidelberg.de) Still you would need the 3D coordinates of
: your protein. With other methods you'll end up with a pI, but it won't be very
: reliable.

It all depends on whether you want to calculate the native pI or
the denatured pI.  The latter is calculable by a number of programs
(you can get a speadsheet to do it if you are willing to count
the numbers of each residue) and useful for predicting the position
of a protein on a 2D gel.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 






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