Fig. 2: Signalling state distribution of VMR_FL by MD simulations.

a, Selected VMR_FL conformations obtained by MD simulations. An ‘upright’ conformation is observed exclusively for the ligand-bound receptor and enables high communication between sensor and responder. The ligand-free receptor adopts exclusively a ‘bent’ conformation with reduced communication capacity. Upright and bent conformations likely encode signalling active and inactive states, respectively. b, PCA decomposition of all (top) and TM (bottom) coordinates. In both cases, the PCA space is defined by the bound MD coordinates only. While K-means clustering is applied independently to the different datasets, points are coloured based on their K-means assignment in the all-coordinate PCA space only: ligand-bound (circle), ligand-unbound (hollow squares) data, cluster centres (black). Left insets: representative conformations observed in the unbound (for example, yellow cluster) and bound (green) states characterized by low angles versus the membrane and low coupling between ligand-binding and signalling domains. Right inset: conformations only observed in the ligand-bound state (blue cluster) characterized by high angles versus the membrane and high coupling. Parts of these figure panels were generated with bioRender (a,b). c, Probability of C–C termini distance between the two protomers at (left) the D2 domain and (right) the TM domain over the course of the MD simulation. d, Root mean square fluctuation (RMSF) along the protein. e, Schematic of VMR_FL, zoomed on the RWQFP CT JM motif. Top: ligand-bound snapshot with close interfacial contacts at Q516 (boxed). Bottom: ligand-unbound snapshot with the cation–π bond between R514 and W515 (light orange dotted line). Part of this figure was generated with bioRender. f, Residue side-chain contact maps for ligand bound (top), unbound (bottom) MD simulations. Contacts are defined with an 8 Å threshold. R514–W515 cation–π bond and Q516 interfacial contacts are shown with light and dark orange boxes, respectively. They highlight the increase in cation–π residence time for the unbound state, a known stabilizing interaction for the inactive state, and the increased Q516 participation at the active interface in the bound state. g, Average helicity measured via DSSP of TM–JM residues over the simulation time.