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Soft Matter Vol - 3 Issue - 7

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A hierarchical approach for predicting the transport properties of the gramicidin A channel

Content Provider	Royal Society of Chemistry (RSC)
Author	Wang, Zheng Fried, Joel R.
Copyright Year	2007
Abstract	A hierarchical computational approach combining results of molecular dynamics (MD) simulations with continuous Poisson–Nernst–Planck (PNP) theory was used to investigate ion transport in a gramicidin A (gA) channel embedded within a 1,2-dimyristoylphosphatidylcholine (DMPC) bilayer. Molecular dynamics (MD) employing the CHARMM force field was used to investigate the diffusion of Na+ and K+ at different locations along the gA channel in both singly- and doubly-occupied states. Self-diffusion coefficients for single Na+ and K+ cations were determined to be 4.7 × 10−7 cm2 s−1 and 6.2 × 10−7 cm2 s−1, respectively. Using these values, maximum ionic conductivities calculated from the Nernst–Einstein equation were 37 pS and 49 pS for Na+ and K+, respectively, in the singly-occupied gA channel. These values agree with experimental data within an order of magnitude. Conductance of the gA channel was calculated from simulation results using the three-dimensional Poisson–Nernst–Planck (3D-PNP) model. Partial charge distributions for gA and for DMPC were assigned using the Poisson–Boltzmann module available in CHARMM. Diffusion coefficients were those obtained from the MD simulation. Results confirm that DMPC electrostatics have significant influence on channel conductivity. At low electrolyte concentrations, the channel cannot be occupied by more than one monovalent cation. Using ion diffusion coefficients obtained at different locations along the channel, current–voltage values obtained using 3D-PNP predictions for a channel immersed in an aqueous NaCl solution show good agreement with experimental values.
Starting Page	1041
Ending Page	1052
Page Count	12
File Format	HTM / HTML PDF
ISSN	1744683X
Volume Number	3
Issue Number	8
Journal	Soft Matter
DOI	10.1039/b700125h
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Einstein Molecular dynamics Ion Partial charge Planck Force field (fiction) Poisson Gramicidin Electrolyte CHARMM Diffusion Electrostatics Self-diffusion
Content Type	Text
Resource Type	Article
Subject	Chemistry Condensed Matter Physics

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