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 A&M 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 _________________________________________________________________ We all see it as it is. But on MSN India, the difference lies in perspective. http://in.msn.com
