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Molecular dynamics study of the KcsA potassium channel

Allen, Toby; Kuyucak, Serdar; Chung, Shin-Ho

Description

The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions....[Show more]

dc.contributor.authorAllen, Toby
dc.contributor.authorKuyucak, Serdar
dc.contributor.authorChung, Shin-Ho
dc.date.accessioned2015-12-13T23:23:11Z
dc.identifier.issn0006-3495
dc.identifier.urihttp://hdl.handle.net/1885/91796
dc.description.abstractThe structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to ~1/3 of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion within this multiple ion channel.
dc.publisherBiophysical Society
dc.sourceBiophysical Journal
dc.subjectKeywords: ion channel; potassium channel; potassium ion; sodium ion; water; article; diffusion; hydration; hydrophobicity; molecular dynamics; molecular model; protein structure; simulation; thermodynamics; Bacterial Proteins; Diffusion; Electricity; Molecular Dyna
dc.titleMolecular dynamics study of the KcsA potassium channel
dc.typeJournal article
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.citationvolume77
dc.date.issued1999
local.identifier.absfor030505 - Physical Organic Chemistry
local.identifier.ariespublicationMigratedxPub22665
local.type.statusPublished Version
local.contributor.affiliationAllen, Toby, 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.startpage2502
local.bibliographicCitation.lastpage2516
dc.date.updated2015-12-12T09:14:22Z
local.identifier.scopusID2-s2.0-0032750783
CollectionsANU Research Publications

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