Extended Data Fig. 10: Molecular Dynamics simulations of β₂AR-Gs^GTP intermediate structures.

a Weakened interactions of β₂AR and Gs in simulations seeded by later cryo-EM intermediate structures. Chord diagrams show interactions between receptor regions (purple) with Gα regions (gold) coarse-grained to domain segments. Interactions are defined as residue pairs having at least one pair of heavy atoms less than 4 Å apart. Each chord diagram is generated using all the data from triplicate 3 μsec MD trajectories for each seed/condition. The average sum of total contacts for each triplicate #16–20 are 41.6, 35.4, 30.6, 28.2, and 20.6, respectively. b-g, Quantification of movement of TM5 (b, c) and TM6 (d, e) on the extracellular and intracellular sides of β₂AR; of the ionic lock with contact frequencies at 4 Å shown inset (f), and of c-Epi ligand (g). Dashed vertical lines represent values of seed structures. h, Sampling of ligand poses over the MD trajectories shown both as discrete transitions between poses (color-coded time traces, see adjacent ligand pose key below panel), as well as in terms of RMSD to the initial pose (solid black line). i, Principal component analysis of the sampled ligand poses, with the positions of selected representative poses superimposed as color-coded circled numbers. j, Superimposition of selected ligand poses shown in ‘i’, showing coverage of the entire ligand binding pocket volume shaded in light purple. k, Representative models of selected ligand pose clusters. TM6 shown in solid purple, c-Epi ligand in orange, transparent lilac colored cloud represents the volume sampled by the ligand across all MD trajectories. The extracellular half of TM7 is hidden to show ligand binding pocket. See also Supplementary Table 6 for detailed population information of ligand poses.