[gmx-users] a question about membrane simulation

[Peter C. Lai]

It also coincides with the 1.5A RMSD change of the active site in those time 
periods (see figure 2).  As to the interpretation of this, maybe you should
ask the paper's authors directly? (Since they do not provide any graphs of
ligand conformation changes) And yes, I have seen chi changes like that 
when there is a hydrophobic interaction between a PHE sidechain with 
ligands of that nature (large hydrophobic region + polar head group) in 
exogenous-ligand-activating-GPCRs.

On 2012-02-06 04:39:26PM +0100, Albert wrote:
> Dear:
> 
>    I am reading a membrane protein simulation paper by GROMACS which
> published on PLOS Computational Biology (
> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001053
> ),
> titled 'Predicting Novel Binding Modes of Agonists to β Adrenergic
> Receptors Using All-Atom Molecular Dynamics Simulations', PLoS Comput Biol
> 7(1): e1001053. doi:10.1371/journal.pcbi.1001053. The author performed a
> 800 ns large scale MD simulation in GROMACS and obtained some residues'
> conformations changes during the long time simulations.
> 
>    I found a very strange phenomena in this paper,i.e: in supplementary
> figure S4,(
> http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1001053.s007)
> the author indicated us the chi angle change of a Phe. As we can see
> from
> the plot that the conformation of this residue in 40-50 ns is the same with
> that at 700-800 ns which has been conclude to be something active. So, I am
> wondering, does such phenomena frequently happen in general membrane
> protein simulation? Why this active conformation absent during 60-700 ns
> period and present again in 700-800 time scale level? Can we also expect
> that around 50 ns time scale level, agonist bound GPCR should also expect
> such kind of side chain switches and it may lost at 100 ns time scale?
> 
>   I would be very appreciated if someone could give me some comments on
> this issue.
> 
> Thank you very much
> 
> best wishes
> Albert

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