Extended Data Fig. 9: MD simulation of Hoechst 33342 in solution, using the newly-developed CHARMM-compatible forcefield.
From: An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity
a, Comparison of the geometry of Hoechst 33342 in simulation and the experimental structure observed in complex with LmrP, in terms of the RMS difference between simulated and experimental geometries for each of the constituent chemical groups. The RMSD data is shown as histograms, derived from time-series of 100 ns. b, Evaluation of the interaction of Hoechst with water. For each snapshot in a 100-ns trajectory, water molecules in the first hydration shell were mapped onto a 3D number-density distribution (oxygen and hydrogen atoms separately), which was then time-averaged. Iso-density surfaces/meshes are shown for water oxygen (red, 0.07 σ) and hydrogen (cyan, 0.14 σ), to highlight the most persistent interaction sites and relative ligand-water orientations.
