[gmx-users] allosteric effect

[jkrieger at mrc-lmb.cam.ac.uk]

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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