title: Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels.
abstract: We examine the validity and utility of the electrodiffusion (ED) equation, i.e., the generalized Nernst-Planck equation, to characterize, in combination with molecular dynamics, the electrophysiological behavior of simple ion channels. As models, we consider three systems-two naturally occurring channels formed by α-helical bundles of peptaibols, trichotoxin, and alamethicin, and a synthetic, hexameric channel, formed by a peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. Starting with equilibrium properties, such as the potential of mean force experienced by an ion traversing the channel and diffusivity, obtained from molecular dynamics simulations, the ED equation can be used to determine the full current-voltage dependence with modest or no additional effort. The potential of mean force can be obtained not only from equilibrium simulations, but also, with comparable accuracy, from nonequilibrium simulations at a single voltage. The main assumptions underlying the ED equation appear to hold well for the channels and voltages studied here. To expand the utility of the ED equation, we examine what are the necessary and sufficient conditions for Ohmic and nonrectifying behavior and relate deviations from this behavior to the shape of the ionic potential of mean force.
authors.affiliation: Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.|Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States.
authors.forename: Andrew
authors.identifier: 0000-0001-8562-6595
authors.initials: A
authors.lastname: Pohorille
authors.affiliation: Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.|SETI Institute , 189 N Bernardo Ave #200, Mountain View, California 94043, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Wilson
authors.affiliation: Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.|Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States.
authors.forename: Chenyu
authors.initials: C
authors.lastname: Wei
mesh_terms: D004058:Diffusion; D004553:Electric Conductivity; D055664:Electrochemical Techniques; D007473:Ion Channels / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D015203:Reproducibility of Results
chemical_list: D007473:Ion Channels