title: Gauging of the PhoE channel by a single freely diffusing proton.
abstract: In the present study we combined a continuum approximation with a detailed mapping of the electrostatic potential inside an ionic channel to define the most probable trajectory for proton propagation through the channel (propagation along a structure-supported trajectory (PSST)). The conversion of the three-dimensional diffusion space into propagation along a one-dimensional pathway permits reconstruction of an ion motion by a short calculation (a few seconds on a state-of-the-art workstation) rather than a laborious, time-consuming random walk simulations. The experimental system selected for testing the accuracy of this concept was the reversible dissociation of a proton from a single pyranine molecule (8-hydroxypyrene-1,2,3-trisulfonate) bound by electrostatic forces inside the PhoE ionic channel of the Escherichia coli outer membrane. The crystal structure coordinates were used for calculation of the intra-cavity electrostatic potential, and the reconstruction of the observed fluorescence decay curve was carried out using the dielectric constant of the intra-cavity space as an adjustable parameter. The fitting of past experimental observations (Shimoni, E., Y. Tsfadia, E. Nachliel, and M. Gutman. 1993. Biophys. J. 64:472-479) was carried out by a modified version of the Agmon geminate recombination program (Krissinel, E. B., and N. Agmon. 1996. J. Comp. Chem. 17:1085-1098), where the gradient of the electrostatic potential and the entropic terms were calculated by the PSST program. The best-fitted reconstruction of the observed dynamics was attained when the water in the cavity was assigned epsilon </= 55, corroborating the theoretical estimation of Sansom (Breed, J. R., I. D. Kerr, and M. S. P. Sansom. 1996. Biophys. J. 70:1643-1661). The dielectric constant calculated for reversed micelles of comparable size (Cohen, B., D. Huppert, K. M. Solntsev, Y. Tsfadia, E. Nachliel, and M. Gutman. 2002. JACS. 124:7539-7547) allows us to set a margin of epsilon = 50 +/- 5.
authors.affiliation: Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
authors.forename: Sharron
authors.initials: S
authors.lastname: Bransburg-Zabary
authors.forename: Esther
authors.initials: E
authors.lastname: Nachliel
authors.forename: Menachem
authors.initials: M
authors.lastname: Gutman
mesh_terms: D001190:Arylsulfonates / Q000737:chemistry*; D001693:Biological Transport, Active / Q000502:physiology; D003198:Computer Simulation; D004058:Diffusion; D004553:Electric Conductivity; D004563:Electrochemistry / Q000379:methods; D029968:Escherichia coli Proteins; D007473:Ion Channels / Q000737:chemistry / Q000502:physiology; D046911:Macromolecular Substances; D008823:Micelles; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D018272:Porins / Q000737:chemistry* / Q000502:physiology; D011522:Protons; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055672:Static Electricity
chemical_list: D001190:Arylsulfonates; D029968:Escherichia coli Proteins; D007473:Ion Channels; D046911:Macromolecular Substances; D008823:Micelles; D018272:Porins; D011522:Protons; C082922:PhoE protein, E coli; C005047:pyranine