Journal
ACS NANO
Volume 10, Issue 3, Pages 3693-3701Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acsnano.6b00202
Keywords
nanopores; lipid bilayer; carbon nanotube; cyclic peptide nanotubes; beta-barrel nanopore protein
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Funding
- Spanish Ministry of Science and Innovation MICINN
- ERDF [CTQ2013-43264-R, MAT2011-25501, MAT2015-71826-P, GPC2013-039, EM 2012/117]
- Xunta de Galicia
- Spanish Ministry of Education
- BBSRC [BB/L002558/1]
- Leverhulme Foundation [RPG-2013-393]
- Wellcome Trust [WT02970MA]
- BBSRC [BB/L002558/1, BB/I019855/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/I019855/1, 1107206, BB/L002558/1] Funding Source: researchfish
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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 beta-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 assembly forming the pore.
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