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. 2017 Aug 14;7:8075. doi: 10.1038/s41598-017-08747-8

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© The Author(s) 2017

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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Volume dynamics of AP in the Loose protomer of AcrB and AcrD. (Left Panels) Distribution of the volume of AP within the Loose protomer of AcrB (a) and AcrD (c), calculated for the 10 top cluster representatives extracted from equilibrium MD trajectories. Histograms refer to the values of the volume, lines to the relative population of the corresponding clusters. The volumes calculated for the pre-MD structures of AcrB and AcrD are shown as dashed line. (Right Panels) Porcupine plots representing collective motions along the first principal-component eigenvector for AP in AcrB (b) and AcrD (d) simulations shown as arrows (>2 Å) attached to Cα atoms indicating the magnitude of the corresponding eigenvalues. The loop lining the base of AP (‘bottom-loop’) showing large rearrangement in AcrB but not in AcrD are coloured yellow in both.