Extended Data Fig. 2: Time-traces of selected parameters describing structural changes at the nucleotide binding pocket in the β2AR-GsGDP simulations.
From: Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor
As a reference, the same parameters are also shown for the GssGDP simulations. The panels on the left show the time-trace of run 2 of the β2AR-GsGDP simulations (solid blue curve, example trajectory in Fig. 2) and all runs of the GsGDP simulations (black curves, mostly invariant), whereas the panel on the right shows the distributions for all runs of the β2AR-GsGDP and GsGDP simulations. A) R201SwitchI-E50Ploop residue-residue distance. All β2AR-GsGDP simulations show increased fluctuations of this interaction compared with GsGDP simulations. B) Solvent-Accessible-Surface-Area, SASA, of GDP in the Gs nucleotide binding pocket. All β2AR-GsGDP simulations show increased SASA compared with GsGDP simulations. C) Distance between the center of mass (COM) of the helices αF-α1, showing a clear increase only in run2 of the β2AR-GsGDP simulations. A smoothing window of 20 ns is applied (solid lines) with the raw data as gray backdrop.
