[gmx-users] conformational study of a dual domain protein

[Bert de Groot]

"K.A. Feenstra" wrote:
> 
> David wrote:
> >
> > On Fri, 2002-09-27 at 23:40, olivier walker wrote:
> > >
> > >
> > > Hi all,
> > >
> > > Thanks to David for his answer in the CCL mailing list.
> > >   I'm studying a dual domain protein and I would like to generate all
> > > possible conformations according to some restraints.
> > > Basically, I want to study all possible conformation of the link between
> > > the two domains (8 residues) and freeze the two domains (not completely
> > > because I would like to follow the shift of the domains with the
> > > conformation change of the link).
> > >
> > > the main goal is to monitor the distance between two residues (located in
> > > two different domain) when the conformation of the link is changing.
> > >
> > >
> > > In such a case, I can't use dyndom because I've only one pdb file. I tried
> > > to define an index file to specify a frozen group of atoms (typically the
> > > link is free and the two domains are frozen) but I want the two domains to
> > > move with reorientation of the link (like two balls attached by a rope).
> > >
> > > I'm sure this is possible to do in gromacs but I'm not comfortable enough
> > > with this program to find the right way to do so immediately.
> > >
> > > has anybody experienced such a problem?  Any help is welcome
> > This is not trivial. You probably realize you cannot study *all*
> > conformations... You could probably generate some from the original pdb
> > file using pymol by rotating a few torsions, then do short simulations
> > and throw everything together in an essential dynamics analysis...
> > Most important is that you ask yourself the question what you want to
> > get out of it....
> 
> Couldn't concoord (written by Bert de Groot) do something in this respect?
> I know it is good at creating a multitude of sensible possible conformations.
> 

Hi,

it all depends on what kind of restraints you have between the domains.
If these can be translated into distance restraints (or actually distance
bounds), then concoord could indeed be used to obtain insight in the
conformational freedom of the two domains wrt each other.

the software can be downloaded from:
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot/concoord.html

Some manual intervention might be required to include your additional
interdomain restraints. Let me know if you need help.

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________