[gmx-users] allosteric effect

[Qasim Pars]

Hi Tsjerk,

I am interested in the dynamic and conformational effect of allostery on
protein. The RMSD doesn't show those effects clearly. I would appreciate if
someone gives me any example of such analysis that provides the information
about the dynamic and conformational effect of allostery on protein.

Cheers,

On 3 June 2016 at 11:10, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Hi,
>
> I wouldn't expect to be able to distinguish MWC from KNF in 200 ns but I
> imagine this could reveal at least part of the underlying communication
> mechanism. I'm also trying to use MD for this and would be interested in
> people's views.
>
> Best wishes
> James
>
> > Hi Qasim,
> >
> > Do you assume MWC or KNF like allostery, and conformational based,
> > dynamics
> > based or mixed?
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars <qasimpars at gmail.com> wrote:
> >
> >> Dear gmx users,
> >>
> >> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> >> positive allostery. Based on experimental data, the second ligand of
> >> protein has greater binding affinity than the first ligand. I would like
> >> to
> >> prove the positive allosteric effect of protein by some analyses. But I
> >> really don't know which analyses helps me to investigate/look into the
> >> allosteric effect. Could you please suggest me some useful analyses to
> >> investigate the allosteric effect (except for RMSD, RMSF)? I have
> >> simulations for singly liganded, doubly liganded and apo state.
> >>
> >> Thanks a lot, in advance.
> >> --
> >> Qasim Pars
> >> --
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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-- 
Qasim Pars