Structure of PorB. (A) Cartoon model of the PorB trimer (A) viewed from the extracellular side. (B) and (C) Electrostatic surface potential calculated using Adaptive Poisson–Boltzmann Solver (61) (B) viewed from extracellular side and (C) rotated 180° and viewed from periplasmic space. Positive potential is colored blue, and negative potential is colored red. Potentials are contoured from +20 kT/e to -20 kT/e.

Binding of AMP–PNP and regulation of channel conductance by pNTPs. (A) Binding of AMP–PNP. |F_o| - |F_c| omit maps contoured at 3σ calculated after the omission of AMP–PNP (Black). (B) Specific side chain contacts to AMP–PNP (C) Comparison of the electrostatic surface potential calculated with APBS (61) of PorB with no ligands bound (PDBID:3A2R, Left) to the electrostatic surface potential with AMP–PNP bound (PDBID:3A2U, Right). Positive potential is colored blue, and negative potential is colored red. Potentials are contoured from +20 kT/e to -20 kT/e. The diameter of pore is 8 × 10 Å without AMP–PNP, and narrows to 4 × 5 Å when AMP–PNP is bound. The view is from the extracellular side of the channel. (D) Binding sites and putative transport pathways through PorB. The binding sites for sugars are indicated with magenta (galactose) and cyan (sucrose) circles, the binding site for AMP–PNP is indicated with a black rectangle, the binding site for cations is indicated with orange circle, and the binding site for antibiotics is shown with a red triangle. A putative cation translocation pathway lined by negatively charged amino acids is highlighted with orange shading, whereas the putative anion translocation pathways lined with positively charged side chains is highlighted with blue shading.

Specific transport of sugars by PorB. (A) Representative sugar-induced swelling time course for PorB-containing liposomes upon dilution in 70 mM of the indicated sugars (Thick Colored Lines). Swelling is measured for each experiment as a decrease in absorption at 400 nm relative to the maximum absorption for each time course. For comparison, thin gray lines are protein-free liposomes diluted in isoosmotic concentrations (35 mM) of all the sugars tested with PorB-containing liposomes. The isoosmotic external sugar concentrations are determined separately for protein-free (35 mM) and PorB (70 mM) liposomes as detailed in methods. (B) PorB-mediated sugar uptake for the same sugars as in A (same color coding, as indicated) averaged over three liposomal preparations. Filled symbols are mean ± SEM of 3 experiments. (C)–(E) Identification of a specific binding site for sugars in the channel pore. (C) Specific side chain contacts to galactose (D) Specific side chain contacts to sucrose. (E) |F_o| - |F_c| omit maps contoured at 3σ calculated after the omission of galactose (Magenta) and sucrose (Cyan).

Model for the binding mode between TLR ectodomains and outer membrane porins. (A) Electrostatic surface potentials calculated using APBS (61) and contoured to ± 20 kT/e for both TLR1/2 ectodomain heterodimer [PDBID 2Z7X; (57)] (B) PorB viewed through the membrane. Note the ring of positively charged residues that orient PorB in the membrane and the highly negative charge of the TLR ectodomains. (C) A model consistent with the electrostatics and the 2∶6 TLR2:PorB stoichiometry of the complex.