Re: modeling zinc binding site

From: Jan Kosinski (
Date: Fri Apr 28 2006 - 10:25:20 CDT


I refined my model with some de novo modeling program (rosetta). The
sidechains which should bind zinc are in much better positions now. They
are in "more or less" proper geometry for binding zinc. It still needs
some refinement but small rearangement of the sidachaing and protein
backbone in one loop should be enough. Maybe I should make a simulation
with zinc explicitly intruduced in the position between zinc binding
groups ? Should I hope that sidechains will reorganize to adjust better
to zinc binding site ?

Still I cannot find if anyone has done similar simulations/model

Jan Kosinski

Marc Q. Ma wrote:

> hi, jan,
> if your model is not ideal in terms of the binding site geometry --
> but the model is close enough ... then you may do something like the
> following:
> 1. identify the ideal distances between some residues that you would
> like the system to have
> 2. minimize the system using NAMD using the constraints on distances
> between these identified residues.
> 3. heat up --> equilibrate --> production ....
> marc
> On Apr 25, 2006, at 8:46 AM, Jan Kosinski wrote:
>> Hi,
>> I wish to model zinc binding site.
>> I have a homology model of a protein which binds zinc. The model is
>> based on the homolog which does not have the binding site for zinc.
>> I have identified potential aminoacid residues engaged in zinc
>> binding. However, the geometry of the zinc binding site in my
>> homology model is far from the geometry allowing for binding zinc -
>> the structural elements containing zinc binding residues must
>> reorganize to allow for proper geometry.
>> Thus I need to refine the model to predict the structure of a zinc
>> binding site.
>> Is it possible to model this site using namd? Coud you propose me a
>> proper approach for doing this? I cannot find if someone has done
>> similar things. Maybe I should specify constraints for to place
>> zinc binding groups around zinc ion or use steered molecular dynamics?
>> I appreciate any help,
>> Jan Kosinski

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