Re: [AMBER] System preparation for

Date: Wed, 4 Nov 2020 11:19:38 +0530


I am talking about the systems where Zn is pre-coordinated to one of the
protein systems (so, P-Zn + P -> complex case).

In one system, the water ligand bound to the zinc ion is not quite replaced
by some atom of a protein. From literature what we know is there are three
amino acids bound to zinc (two from the zinc bound protein (P-Zn) and one
from the other protein (P)) in the complex. They also pointed out that the
fourth coordination position on zinc may be occupied by a water molecule as
they didn't observe any water signature near zinc in the electron density

For the second case, the coordination number on zinc is satisfied by four
amino acid residues (three from P-Zn and one from P). I think this is the
case that you have mentioned in your third point.

Can you guide me on how should I proceed further?

with regards,
Satyajit Khatua

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Message: 12
Date: Tue, 3 Nov 2020 08:57:32 -0500
From: David A Case <>
Subject: Re: [AMBER] System preparation for
To: AMBER Mailing List <>
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On Tue, Nov 03, 2020, SATYAJIT KHATUA wrote:
>Thanks a lot. If you don't mind, I am asking a different scenario with two
>protein chains bound to each other through a metal center zinc & I would
>like to calculate the protein-protein interaction energy using,
>then how should I proceed?

To me, this seems like a really difficult problem. First, estimating
the energetics of zinc-ligand interactions is difficult via force
fields. You could look at the literature for trying to calibrate Mg --
ligand interactions and think about following that path.

Second, what is the reaction you are looking at? Is is 2P + Zn ->
complex (where P is protein)? Or is it P-Zn + P -> complex, where the
Zinc is pre-coordinated to one of the two proteins? The first, a
tri-molecular reaction, is outside the scope of MMPBSA.

Third, in forming the complex, presumably a water ligand on the zinc is
being replaced by coordination to some atom of a protein. Estimating this
interaction energy by continuum dielectric theories is very sensitive to
the paramters you choose, so much so that people rarely try this for
divalent ions.

That said, you might learn things by studying this, but you should
expect to put a lot of effort into the project. Of course, that is how
simulation science advances....

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Received on Tue Nov 03 2020 - 22:00:02 PST
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