Extended Data Fig. 8: Time-traces for selected parameters of a composite trajectory leading to GDP release.
From: Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor
The composite trajectory consists of run 2 of the β2AR-GsGDP simulations followed by a 4.5 µs biased simulation, followed by 2.5 µs unbiased simulation (Methods, Table S1, movie 5). A) Increasing Solvent-Accessible-Surface-Area (SASA, in nm2) of GDP in the GsGDP nucleotide binding pocket. The SASA value of GDP in solution (ca. 6 nm2), was estimated for the same frames after eliminating all non-GDP atoms and re-computing SASA. B) Decreasing number of GDP contacts (interaction cutoff is 4 Å). C) αN-α5 opening as tracked by the H41αN-H387α5 interaction. D) αF-α1 distance, as tracked by the distance between their respective center of masses (COMs). E) Distance traveled by the COM of GDP during the composite trajectory. In panels A)-E) a smoothing window of 20 frames is applied (solid lines) with the raw data as gray backdrop. F) First (in gray) and last (in color) frames of the composite trajectory, showing how far away from the nucleotide binding pocket the GDP is dislodged. Also shown are the displacements of α1 and αG.
