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. 2017 Jul 4;8:15948. doi: 10.1038/ncomms15948

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Copyright © 2017, The Author(s)

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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In this simulation (Sim 1), the lid loop is embedded into the lipid membrane. (a) Overall conformations of Lnt and surrounding lipid molecules. The Nit and TM domains are shown as cyan and grey cartoon model, respectively, and the lid loop region is shown in cyan stick model. For the lipid bilayer, only the phospho-atoms from the lipid molecules are shown as spheres, except for one lipid molecule inside the cavity, which is shown as green stick model. (b) More detailed interactions between lid loop residues (thick stick models) and surrounding lipid molecules (thin line models) for three snapshots. (i) The initial energy-minimized model; (ii) a snapshot after 20 ns simulations with Lnt constrained; (iii) a snapshot after 150-ns free dynamics simulations. (Also see a Supplementary Movie 1).