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Int. J. Mol. Sci. 2014, 15(8), 14247-14268; doi:10.3390/ijms150814247

The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation

Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany
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Received: 22 May 2014 / Revised: 14 July 2014 / Accepted: 6 August 2014 / Published: 15 August 2014
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Abstract

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA. View Full-Text
Keywords: Glycophorin A dimerization; dimer interface formation; bitopic transmembrane α-helix; fatty acid dependency; MARTINI force field Glycophorin A dimerization; dimer interface formation; bitopic transmembrane α-helix; fatty acid dependency; MARTINI force field
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Flinner, N.; Mirus, O.; Schleiff, E. The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation. Int. J. Mol. Sci. 2014, 15, 14247-14268.

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