Subject: protein ionization

From: "Victor Anisimov" <[email-masked]>
Date: Tue, 29 May 2001 12:07:59 +0200

Dear CCLers,

Christian Pilger wrote:

From: "Christian Pilger" <[email-masked]>
Subject: CCL:titratable amino acids and counter ions

> while preparing a protein structure as input for MD simulations, I
> encountered the following  points, which I would like to ask your advice:
>
> - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ?
>   Are all of them simply taken in their ionized forms ?

I'm also very confused in general what to do with these residues, running QM
calculation. The issue of the initially correct model definition is highly important for
a quantum-chemical calculation of proteins. Certainly the ionization of these residues
should depend on the environment the protein is placed in. Does someone know
any MM or QM computational research papers modeling protein ionization as a
response on the environment.

I would greatly appreciate any hints.

With kind regards,
Victor.

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Victor Anisimov, PhD,
Senior Software Researcher - Computational Chemist
FQS Poland, a Fujitsu company
ul. Starowislna 13-15, 31-038 Krakow, Poland
Email: [email-masked]
Tel.(+48 12) 429-4345  Fax(+48 12) 429-6124
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