[gmx-users] allosteric effect

[sun]

Hi Qasim
You can read below mentioned paper for analysis:
http://www.nature.com/articles/srep23830

Sent from my iPhone

> On 03-Jun-2016, at 3:28 pm, Qasim Pars <qasimpars at gmail.com> wrote:
> 
> 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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>> 
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> 
> 
> -- 
> Qasim Pars
> -- 
> Gromacs Users mailing list
> 
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