Fig. 5
From: PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore
MD simulations of OmpF corroborate experimentally observed permeability and selectivity trends. a Typical simulation system. (Top) Cut-away view of the system revealing a transmembrane water passage through an OmpF monomer. The OmpF monomer is depicted in purple, the lipid-bilayer in cyan, water molecules as red and white spheres, and Na+ and Cl– ions as orange and green spheres, receptively. (Bottom) Top-down view of the system. The OmpF trimer is drawn using a cartoon representation, the lipid-bilayer as cyan bonds; water and ions are not shown. b Simulated osmotic permeability (averaged over 12,500 frames) of OmpF variants (red) and the corresponding experimental values (gray). c Ionic conductance of OmpF trimers obtained from applied field simulations under a 500 mV transmembrane voltage and averaged over 10,417 frames. d Water occupancy of OmpF variants. The green volume depicts the average location of water molecules in each channel characterized as a 0.3 g/cm3 isosurface of water oxygen density. For reference, each channel is shown using a semitransparent cartoon representation. e Major axis dimensions of the pores measured from PoreDesigner before MD (gray) and from the last 100 frames of MD (red). The error bars represent standard deviations. A 0.4 nm line represents the PoreDesigner design constraint of identifying pore designs smaller than 0.4 nm. f The average number of hydrogen bonds made between water and an OmpF monomer in each of the regions depicted in panel d and averaged over 14,583 frames
