Fig. 2: Ligand directly affects the intracellular receptor surface by rotating intracellular loop 2.

a Simulations of the receptor with AP8 bound (blue) favor one stable ICL2 conformation (PR state) while simulations without AP8 (orange) favor a distinct negatively rotated ICL2 conformation (NR state). Both simulations were started from the same structure. Representative simulation snapshots are shown at indicated time points overlaid on the AP8-bound crystal structure (light grey). Simulation trajectories show the ICL2 angle as measured by the rotation of L112 and Y114 around the ICL2 helix axis (see Methods). The dashed horizontal line at 0 degrees is the distance in the starting structure. b AP8 alters a network of polar interactions; the frequency of water-mediated hydrogen bonds between key ICL2 residues was quantified in the presence and absence of AP8. Data presented as mean with 68% CI (N = 10 independent simulations for each condition). Only simulation frames where ICL2 remained folded were used. c Simulation frames show representative hydrogen bonds (yellow dashes) formed with and without AP8 bound. With AP8 bound, a stable water molecule forms a hydrogen bond network bridging AP8 and the ICL2 backbone. In the absence of AP8, the water molecule reorients to form a new stable network of hydrogen bonds, necessitating a rotation of ICL2.