Extended Data Fig. 4: Molecular dynamics simulations of the LmrP-Hoechst complex with and without POPG bound.

a, View of outward-facing LmrP along the membrane plane, with structural regions of seemingly distinct dynamics color-coded. Ligands are omitted for clarity. The peripheral regions, or Set 1 (blue), comprise TM helices 3, 4 and 6 in the N-lobe and TM 9, 10 and 12 in the C-lobe. Set 2 (orange) comprises the intracellular half of TM helices 1, 2 and 5, and TM 7, 8 and 11, respectively. Set 3 (yellow) includes the remainder of these 6 helices. b) Analysis of the structural dynamics of the N-lobe in terms of the root-mean-square deviation of the protein backbone relative to the X-ray structure (after least-squares self-fit). For each of the regions defined in (a) (Sets 1, 1 + 2 or 1 + 2 + 3), the plot shows the evolution of RMSD as a function of simulation time. Left and right plots compare simulations with only Hoechst bound to LmrP, and with both Hoechst and POPG bound, respectively. For clarity, only one of the two trajectories calculated in each case is analyzed. c, Same as b, for the C-lobe. d, Summary of the RMSD time-series data, in terms of time-averages alongside the corresponding standard deviations, for two independent simulations of each system. Data are compared for simulations of LmrP bound to Hoechst 33342, and of LmrP bound to Hoechst and a POPG lipid. Red arrows indicate regions for which a significant change was observed between simulation systems. e, Dynamics of the N- and C-lobes relative to each other, in the presence or absence of bound POPG. The plot quantifies the variability in distance between the two lobes, defined as the distance between the centers-of-mass of the peripheral regions in each lobe (Set 1, blue). The histograms shown derive from the time-series of this distance, combining the two simulations calculated with and without bound POPG. The value of this distance in the LmrP crystal structure is also indicated (vertical gray dashed line).