Skip navigation
Skip navigation

Continuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel

Edwards, Scott; Corry, Ben; Kuyucak, Serdar; Chung, Shin-Ho

Description

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...[Show more]

dc.contributor.authorEdwards, Scott
dc.contributor.authorCorry, Ben
dc.contributor.authorKuyucak, Serdar
dc.contributor.authorChung, Shin-Ho
dc.date.accessioned2015-12-13T23:24:20Z
dc.identifier.issn0006-3495
dc.identifier.urihttp://hdl.handle.net/1885/92182
dc.description.abstractWe 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.
dc.publisherBiophysical Society
dc.sourceBiophysical Journal
dc.subjectKeywords: gramicidin A; gramicidin; ion channel; article; calculation; channel gating; dielectric constant; drug structure; drug transport; electric field; ion transport; molecular dynamics; structure activity relation; validation process; biophysics; chemistry; co
dc.titleContinuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel
dc.typeJournal article
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.citationvolume83
dc.date.issued2002
local.identifier.absfor029901 - Biological Physics
local.identifier.ariespublicationMigratedxPub23188
local.type.statusPublished Version
local.contributor.affiliationEdwards, Scott, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationCorry, Ben, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationKuyucak, Serdar, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationChung, Shin-Ho, College of Physical and Mathematical Sciences, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.startpage1348
local.bibliographicCitation.lastpage1360
dc.date.updated2015-12-12T09:20:07Z
local.identifier.scopusID2-s2.0-0036708445
CollectionsANU Research Publications

Download

File Description SizeFormat Image
01_Edwards_Continuum_Electrostatics_Fails_2002.pdf432.85 kBAdobe PDF    Request a copy


Items in Open Research are protected by copyright, with all rights reserved, unless otherwise indicated.

Updated:  19 May 2020/ Responsible Officer:  University Librarian/ Page Contact:  Library Systems & Web Coordinator