Continuum electrostatics fails to describe ion permeation in the gramicidin channel

Scott Edwards, Ben Corry, Serdar Kuyucak, Shin Ho Chung*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    103 Citations (Scopus)

    Abstract

    We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure. The potential and electric field acting on ions in and around the channel are computed by solving Poisson's equation. These are then used in Brownian dynamics simulations to obtain concentration profiles and the current passing through the channel. We show that regardless of the effective dielectric constant used for water in the channel or the channel protein, it is not possible to reproduce all the experimental data on gramicidin A; thus, continuum electrostatics cannot provide a valid framework for the description of ion dynamics in gramicidin channels. Using experimental data and molecular dynamics simulations as guides, we have constructed potential energy profiles that can satisfactorily describe the available physiological data. These profiles provide useful benchmarks for future potential of mean force calculations of permeating ions from molecular dynamics simulations of gramicidin A. They also offer a convenient starting point for studying structure-function relationships in modified gramicidin channels.

    Original languageEnglish
    Pages (from-to)1348-1360
    Number of pages13
    JournalBiophysical Journal
    Volume83
    Issue number3
    DOIs
    Publication statusPublished - Sept 2002

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