Dear:
I am reading a membrane protein simulation paper 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 â 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 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 (plot in red) 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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Received on Mon Feb 06 2012 - 05:30:03 PST
