Figure 4.

Proton conductance in the BR trimer. (A) Proton collection surface of the cytosolic side. (B) Proton exit surface of the extracellular side. Electrostatic surface potentials were calculated with grasp (44) and shown from −20 kcal/mol (red) to +20 kcal/mol (blue). The internal residues D96, D115, and E204 were assumed to be protonated. (C) Internal cavities of BR. Twelve cavities were found by voidoo (45) using a probe radius of 1 Å and a primary grid spacing of 0.25 Å for enhanced sensitivity. Eight cavities (blue) fulfilled the criteria to be discontinuous from the molecular surface and capable of accommodating at least one water. White numbers indicate the maximal number of waters per cavity. (D) Proton exit pathway with the E194/E204 dyad (white). Cavities are shown in blue, H bonds within a 3.5-Å cutoff in white.