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Membranes 2016, 6(1), 20; doi:10.3390/membranes6010020

Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A

School of Physics, University of Sydney, Sydney NSW 2006, Australia
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Author to whom correspondence should be addressed.
Academic Editor: Shiro Suetsugu
Received: 10 February 2016 / Revised: 8 March 2016 / Accepted: 8 March 2016 / Published: 18 March 2016
(This article belongs to the Special Issue Membranes and Ion Channels)
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Abstract

Membrane proteins are embedded in a lipid bilayer and interact with the lipid molecules in subtle ways. This can be studied experimentally by examining the effect of different lipid bilayers on the function of membrane proteins. Understanding the causes of the functional effects of lipids is difficult to dissect experimentally but more amenable to a computational approach. Here we perform molecular dynamics simulations and free energy calculations to study the effect of two lipid types (POPC and NODS) on the conductance of the gramicidin A (gA) channel. A larger energy barrier is found for the K+ potential of mean force in gA embedded in POPC compared to that in NODS, which is consistent with the enhanced experimental conductance of cations in gA embedded in NODS. Further analysis of the contributions to the potential energy of K+ reveals that gA and water molecules in gA make similar contributions in both bilayers but there are significant differences between the two bilayers when the lipid molecules and interfacial waters are considered. It is shown that the stronger dipole moments of the POPC head groups create a thicker layer of interfacial waters with better orientation, which ultimately is responsible for the larger energy barrier in the K+ PMF in POPC. View Full-Text
Keywords: gramicidin A; ion permeation; molecular dynamics; potential of mean force; ceramides gramicidin A; ion permeation; molecular dynamics; potential of mean force; ceramides
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Setiadi, J.; Kuyucak, S. Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A. Membranes 2016, 6, 20.

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