Fig. 3: MD simulations of lipids bound to BmrCD_OF.
a Kernel Density Estimation analysis. Lipid phosphorous atoms in the outer leaflet have been binned in their XY projections, with high density appearing yellow and low density appearing dark purple. b Molecular rendering of POV15 entering into the cleft and attracting Hoechst molecules. Gray and color models are the MD simulation results at 0 ns and 140 ns, respectively. Loops are omitted for clarity. c Time series of fraction of native contacts. Each color in the trace belongs to an independent replica simulation. Native contacts are defined as any protein residue with heavy atoms within 4.5 Å of the Hoechst molecules in the initial structure. d Distribution of Hoechst tilt angles as measured with respect to the positive Z-axis. This was measured by defining the vector going from the piperazine to the ethoxy group of Hoechst and measuring the angle formed with the vector (0, 0, 1). e Time series for the salt-bridge distance between E33 and R345 of BmrC and BmrD, respectively. Each trace represents an independent replica. f Distribution of E33BmrC-R345BmrD salt-bridge distances over all the simulations.
