[gmx-users] Help: Analysis large interdomain motion

[Karsten Suhre]

Dear Gao,

for the study large conformational changes, I would suggest Normal Mode 
Analysis (NMA) as the computational tool of choice, since large protein 
movements are still without reach of molecular dynamics simulations.

The following paper gives a number of examples of proteins with large 
conformational changes and describe their analysis using NMA:

Tama, F. & Sanejouand, Y.H., Conformational change of proteins arising from 
normal mode calculations. Protein Engineering vol.14, p1-6, 2001.

A very complete list of observed protein movements (i.e. based on structures 
from protein cristallography) is also accessible on this server:

http://www.molmovdb.org/

You can do a normal mode analysis of your own protein using our server elNemo:

http://igs-server.cnrs-mrs.fr/elnemo/

In particular, if you have two structures of the same (or homologous) proteins 
in different conformations at hand, you can use elNemo to determine the 
normal modes that describe best the observed movement and compute a series of 
intermediate PDB structures (that can for example be analysed using VMD).

I hope this helps,

Kind regards,

Karsten.

PS: You will find related papers on the elNemo reference page 
http://igs-server.cnrs-mrs.fr/elnemo/refs.html


On Tuesday 19 April 2005 13:44, Zhenting Gao wrote:
> Hi  gmx-users ,
>
> I am currently working on a protein with 3 domains: left, middle and right
> domain. While the 3 domains' internal structure remain almost
> unchanged(rmsd of each domain is below 2.5A if fit to itself), the
> interdomain motion between the left and right domains are comparably large,
> i.e. the rmsd of right domain is more than 12A if fit to the hydrolase
> domain.
>
> Does anyone know a protein like this? As I concern mostly at the residues
> which are indispensable for the large interdomain motion, what can I do to
> persue this?
>
> Any suggestion or papers are heartily appreciated.
>
> Yours sincerely,
> Zhenting Gao