Molecular dynamics simulations of YbbAP suggest the periplasmic-side pocket is a lipid-binding site.
<p><b>(A)</b> Simulation setup. <b>(B)</b> 2D histogram (bins: 30 × 30) of LysoPG phosphate head group residency in the membrane upper leaflet over 15 μs coarse-grain simulation repeats of YbbAP in its apo and nucleotide-bound states. Scale is normalized to the global m...
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| Čoahkkáigeassu: | <p><b>(A)</b> Simulation setup. <b>(B)</b> 2D histogram (bins: 30 × 30) of LysoPG phosphate head group residency in the membrane upper leaflet over 15 μs coarse-grain simulation repeats of YbbAP in its apo and nucleotide-bound states. Scale is normalized to the global maximum. A close-up view of the area encompassing the periplasmic pocket is shown inset. Protein backbone coordinates are shown in black. Residency is indicated by the frequency density of LysoPG headgroups occupying each 2.5 Å by 2.5 Å area. The highest observed frequency density across both datasets was 0.18 (n = 6, 3 per structure), from a trajectory of frames comprising of every 10th 1 ns simulation time point. Densities of LysoPE and other lipids are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003427#pbio.3003427.s010" target="_blank">S7 Fig</a>. <b>(C)</b> Vertical movement of a single LysoPG molecule that undergoes extraction from the bilayer over 1,000 ns of atomistic simulation, starting from the end point of the coarse-grain simulation where LysoPG occupies the periplasmic pocket. Repeats in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003427#pbio.3003427.s012" target="_blank">S9 Fig</a>. <b>(D)</b> Key frames from the start and end of the atomistic simulation showing LysoPG exiting the bilayer. Residues that appear to assist LysoPG extraction during the atomistic simulation are indicated. Underlying data is available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003427#pbio.3003427.s027" target="_blank">S10 Data</a>.</p> |
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