Re: Using RAMD for studiying conformational changes in proteins

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Mar 24 2011 - 17:59:22 CDT

Raul,

RAMD was originally designed to study ligand pathways in proteins ...
Until now, it was only used fro that purpose quite successfully ...

If you want some qualitative view on possible conformational
transitions, you could try the way you describe .... You need to define
the ligand as the part of the protein that you expect to change its
conformation and the receptor the rest of the protein (or another region
of the protein) .... Theoretically, you should be able to do that
....The scripts I wrote for NAMD should allow you to do that ...

I would however look more at the RAMD-MD alternative rather than RAMD
alone (see documentation).

Be aware though that RAMD-MD is not yet published although there are
clear benefits and also be aware that RAMD was not originally designed
for this purpose ... You'd need some way to validate any potential
conformational changes you see ... I would first test it on a small
protein with structures available for 2 different conformations (ideally
not dramatically different).... If you start with one and you get close
to the other, it might be interesting ...Of course you need to
conformations in which the distance between the "ligand" and "receptor"
COMs are different... Otherwise it would not work. Also, choose your
force constant carefully, you can easily disturb the protein if the
perturbation is too large

I'd be happy to assist you if you decide to try it in this way ....

I have also planned some further developments of RAMD (e.g. combine it
with umbrella sampling to get free energies from it) ... Unfortunately,
I don't know if I will have time or people for that in the near future...

Best wishes
Vlad

On 03/24/2011 09:23 PM, Raul Araya wrote:
> Dear NAMD users and developers:
>
> I'm interested on studying gating phenomena in protein channels. An I
> became interested in AMD.
> I have seen the RAMD library and the examples therein contained in the
> CVS version of NAMD (an also avaliable in the 2.7 version), but they
> seem to be limited mostly to be used in ligand/protein interactionhe
> studies. Can it be used for example to induce or observe
> conformational changes in proteins?
> Being that the case, the "ligand" to be defined should correspond to a
> domain, or part of the protein in study??
>
> Any help will be appreciated
>
>
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.
>
>

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de

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