title: Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study.
abstract: A macromolecular nanopore inserted into a membrane may perturb the dynamic organization of the surrounding lipid bilayer. To better understand the nature of such perturbations, we have undertaken a systematic molecular dynamics simulation study of lipid bilayer structure and dynamics around three different classes of nanopore: a carbon nanotube, three related cyclic peptide nanotubes differing in the nature of their external surfaces, and a model of a β-barrel nanopore protein. Periodic spatial distributions of several lipid properties as a function of distance from the nanopore were observed. This was especially clear for the carbon nanotube system, for which the density of lipids, the bilayer thickness, the projection of lipid head-to-tail vectors onto the membrane plane, and lipid lateral diffusion coefficients exhibited undulatory behavior as a function of the distance from the surface of the channel. Overall, the differences in lipid behavior as a function of the nanopore structure reveal local adaptation of the bilayer structure and dynamics to different embedded nanopore structures. Both the local structure and dynamic behavior of lipids around membrane-embedded nanopores are sensitive to the geometry and nature of the outer surface of the macromolecule/molecular assembly forming the pore.
authors.affiliation: Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela , 15782 Santiago de Compostela, Spain.|Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.
authors.forename: Rebeca
authors.initials: R
authors.lastname: Garcia-Fandiño
authors.affiliation: Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela , 15782 Santiago de Compostela, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Piñeiro
authors.affiliation: Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.
authors.forename: Jemma L
authors.initials: JL
authors.lastname: Trick
authors.affiliation: Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
mesh_terms: D006860:Hydrogen Bonding; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D058608:Nanopores / Q000648:ultrastructure*; D037742:Nanotubes, Carbon / Q000737:chemistry* / Q000648:ultrastructure; D010456:Peptides, Cyclic / Q000737:chemistry*; D010713:Phosphatidylcholines / Q000737:chemistry*; D000072757:Protein Conformation, beta-Strand
chemical_list: D008051:Lipid Bilayers; D037742:Nanotubes, Carbon; D010456:Peptides, Cyclic; D010713:Phosphatidylcholines; C017251:1,2-oleoylphosphatidylcholine
keywords: carbon nanotube; cyclic peptide nanotubes; lipid bilayer; nanopores; β-barrel nanopore protein