Menachem Gutman — Page 2

PubMed2002

Gauging of the PhoE channel by a single freely diffusing proton.

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.

Arylsulfonates↗

PubMed2002

A fast in silico simulation of ion flux through the large-pore channel proteins.

The PSST program (see accompanying article) utilizes the detailed structure of a large-pore channel protein as the sole input for selection of trajectories along which negative and positive ions propagate. In the present study we applied this program to reconstruct the ion flux through five large-pore channel proteins (PhoE, OmpF, the WT R. blastica general diffusion porin and two of its mutants). The conducting trajectories, one for positive and one for negative particles, are contorted pathways that run close to arrays of charged residues on the inner surface of the channel. In silico propagation of the charged particles yielded passage time values that are compatible with the measured average passage time of ions. The calculated ionic mobilities are close to those of the electrolyte solution of comparable concentrations. Inspection of the transition probabilities along the channel revealed no region that could impose a rate-limiting step. It is concluded that the ion flux is a function of the whole array of local barriers. Thus, the conductance of the large-pore channel protein is determined by the channel's shape and charge distribution, while the selectivity also reflects the features of the channel's vestibule.

Biological Transport, Active↗