Extended Data Figure 5: Summary of molecular dynamics simulations.

a–c, Conformational stability of the AT₂R structure is illustrated by representative conformations (c) from a total of 4 μs of molecular dynamics simulations (8 independent 500 ns runs), clustered by r.m.s.d. Traces of distances measured between different helices are shown for apo AT₂R (a) and for the AT₂R–compound 1 complex (b). Distances were calculated between the centres of mass of residues Ser79^2.39-Ile83^2.43 for helix II, Arg142^3.50-Val146^3.54 for helix III, Gln253^6.32-Met257^6.36 for helix VI, and Phe325-Lys328 for helix VIII. d, e, Conformational stability of helix VIII upon perturbations, using eight starting conformations of helix VIII (d) is revealed by r.m.s.d. traces (e), which all converge by ~250 ns of simulations. r.m.s.d. values are calculated for the centre of mass of C_α atoms of residues Phe325-Lys328 compared to the crystal structure of AT₂R. Tick marks on the y axis show the starting frame r.m.s.d. values. Coloured lines are plotted using values averaged over a 500 ps window. f–h, Results of molecular dynamics simulations for a modified AT₂R model with the backbone of helix VIII aligned with helix VIII from AT₁R structure (PDB code 4YAY). Conformational snapshots of the AT₂R model (f) are shown for every 100 ns (blue to red spectrum) from one of the six independent 700 ns molecular dynamics simulation runs (simulation 5). Green cartoon shows inactive-state conformation of CCR5 (PDB code 4MBS), helix VIII of which was found to be the closest to the final conformations of AT₂R helix VIII in molecular dynamics simulations. Intracellular view (g) of snapshots from the same molecular dynamics simulation is shown, but at t = 0 and t = 700 ns. Traces of the distance between helices VI and II (h, top curves), calculated between the centres of mass of C_α atoms of residues Gln253^6.32-Met257^6.36 in helix VI and residues Ser79^2.39-Ile83^2.43 in helix II, show a change from 21 Å (active state) to under 16 Å (inactive state). Traces of the distance between helix VIII and the membrane (h, bottom curves), calculated between the centre of mass of C_α atoms of residues Arg330-Val332 and the closest phosphate atoms of lipid molecules, indicate a gradual shift of helix VIII towards the lipid bilayer, with the distance decreasing from ~10 Å to under 3 Å.