Subject: Calc. of pKa and total charge??

From: [email-masked]
Date: Tue, 25 Jul 2000 10:06:30 +0100

*** (Sorry for sending a second copy of this but this one has a correction
of my email adress.) ***

Hi,

I would like to calculate pKa of individual residues within a protein in
order to get the total charge as a function of pH. As far as I understand
the pKa is dependent to some extent on the local micro environment. I
wonder if there is a program that calculates pKa of individual residues in
a position specific manner.

With this information I think it´s possible to calculate charges of the
residues and the protein in total as a function of pH.

Perhaps someone knows a program that can do any of this or help me with a
description of how to proceed.

I have DelPhi available but any other program is of interest.

Thanks in advance!

/Mathias Norrman
[email-masked]
Amersham Pharmacia Biotech

---

From: "Gavin Shear" <[email-masked]>
Date: Tue, 25 Jul 2000 14:31:47 -0400

Dear Mathias,

You may be interested in ACD/pKa predictions, which will calculate
pKa in one of three selected modes.

The “apparent constant” of the pKa is a method of calculation which
mimics the experimental situation by “adding” protons to the molecule
in the order the molecule would normally be protonated in solution.

The “microconstants of current form” is a method of calculation which
accepts the input structure exactly as it is, and tries to remove a
proton from it.

The "single pKa" is a method intuitive to the way medicinal chemists view
pKa values.  If there are two acidic sites in the molecule, a chemist
desires to know the relative acid pKa values.  It could be done by
calculating the pKa for each ionization site while the rest of the
molecule is considered neutral.  This is not what actually happens
experimentally, if a di-acid is dissolved in strong base and titrated
with acid, but it does indicate the relative ease of ionization at each
center.

If you would like to trial these methods, please visit our online
interactive laboratory, www.acdlabs.com/ilab , or you may email
me a structure, and I can do a prediction for you.  You may also
contact one of our representatives at [email-masked] .

You may use our freeware ChemSketch 4.5 interface to connect
to the interactive lab, by downloading at www.acdlabs.com/download ,
or simply use the JAVA structure drawing applet at the ILAB web
site.

Best wishes,
Gavin Shear

-----Original Message-----
From: Computational Chemistry List [mailto:[email-masked]]On
Behalf Of [email-masked]
Sent: Tuesday, July 25, 2000 5:07 AM
To: [email-masked]
Subject: CCL:Calc. of pKa and total charge??

Hi,

Thanks in advance!

/Mathias Norrman

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