AMBER Archive (2003)

Subject: Re: AMBER: modelling a Ca binding site

From: Karsten Suhre (Karsten.Suhre_at_igs.cnrs-mrs.fr)
Date: Fri Aug 15 2003 - 04:44:09 CDT

Bonjour Xavier,

thank you very much for your answer. I agree that it might be quite difficult
to realistically model the Ca binding.

However, my major problem at present is to introduce a Ca molecule at the
coding level into the Amber simulation. Do you have any example code of a
similar simulation (I am thinking in particular of the leap part).

Anyho, as I am trying to improve a homology model, i presume that even a crude
parameterization of the Ca as a positive charge sitting inside the protein
and pulling the side chains together would already be better much better than
just leaving it out.

Best regards, Karsten.

On Thursday 14 August 2003 19:07, Xavier Periole wrote:
> Hi Karsten,
>
> first of all simulations of calci-proteins is a subject in its own and
> lots of people have tried and stoped because the parametrization
> of the calcium interacting with the protein is kind of very sensitive.
> Some collegues (from Toulouse) have published a paper about the
> parvalbumin and determined free energy of changing a Ca in Mg
> in different sites of the protein (Allouche D. J Mol Biol. 1999;285(2):857)
> The results are quite good and done with CHARMM. Note that
> only the binding site was allowed to adjust to the modification. After
> I was develloping new potentials for calcium and others cations
> and we just got to the conclusion that we could have a better
> description of the structure of the binding site of the calcium/magnesium
> when compare to the crystal structures but the energetics was out of
> range. The reason is that calcium is extremely polarizable and so
> the two body description of its interactions is not accurate enough.
> Basically it is very delicate to try to study the specific effect of a
> cation
> on a protein.
>
> This work was done with a very high resolution x-ray structure. MD on
> homology model is also something very delicate to manage. It has been
> observed that with less than 50-60% identity it is almost impossible to
> rich the quality of a NMR structure compare to a x-ray structure. I
> guess that if you restrict your system on the binding site you could do
> some ab initio simulations. For the rest of the protein it is gonna to be
> difficult to differentiate between the effect of cation presence/absence
> and the fact that you have a model contructed by homology.
>
> Hope it'll help,
> XAvier

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