Hi Donghui,
It’s going to be tricky. Perhaps, you can predict some local rotamer variations
around the ligand interacting regions. Predicting the global changes is
difficult, particularly if you are anticipating a big conformational change.
For example, in one of our structure, the active site of the unliganded protein
is in an open conformation and adopted closed conformation upon ligand binding
(JBC, Vol. 282, 27334-27342). You can find many such examples in the
literature, including the text book example of cAMP receptor protein.
I would try to crystallize the apo form. If this is not possible, you can try
studying the dynamics by solution studies or through molecular dynamics
simulation (http://ambermd.org/).
All the best
Satheesh
Palaninathan Satheesh , PhD
Research Scientist
Department of Biochemistry and Biophysics
Texas AM University, 2128 TAMU
College Station, TX - 77843-2128
USA.
Ph. 1-979-862-7639
Date: Mon, 10 Aug 2009 11:10:42 +0800
From: wdh0...@gmail.com
Subject: Re: [ccp4bb] How to model apo protein structure from solved ligand
bound high resolution structure?
To: CCP4BB@JISCMAIL.AC.UK
More information about the two ligand bound structures, each protein is
composed of two globular domains, between the two globular domains, there lies
a deep cleft and ligand sits or buried there comfortably. These two domains are
connected by a hinge region, here we want to model how this hinge region moves
upon ligand binding. Any recommendation for any program which can do this task
well. Thanks ahead.
Donghui
On Sun, Aug 9, 2009 at 8:37 PM, wu donghui wdh0...@gmail.com wrote:
Dear CCP4ers,
Recently we have solved two structures from E.coli in high resolution, which
have bound two different ligands tightly already. Here I want to know if there
is any program which can let us model the structure of our apo proteins
confidently. Thanks ahead for any comment and input.
Regards,
Donghui
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