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. 2016 May 13;12(5):e1004935. doi: 10.1371/journal.pcbi.1004935

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© 2016 Scholes, Weinzierl

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 3 — Panels A—C show the GAL11-ABD1 in grey surface representation and the GCN4-cAD as a purple ribbon. The key hydrophobic residues GCN4-W120 and F124 are shown as liquorice models in light blue and green, respectively. The time-frame shown in the right corner of each panel corresponds to the 4 x 1000 ns aggregate trajectory shown in Panel D. A. GCN4-F124 located in the ABD1 pocket near the beginning of aMD_no2. B. Co-occupancy of GCN4-W120 and F124 inside the ABD1 pocket. Note that the cAD α-helix is additionally rotated by 90° in comparison to (A) and (C). C. GCN4-W120 located within the ABD1 pocket towards the end of aMD_no4. Note that this simulation, just like the other three started out with GCN4-F124 in the pocket. D. Distance measurement [Å] between residue GAL11-A216, which forms the floor of the ABD1 pocket, and GCN4-W120 (blue trace) or F124 (green trace). For this analysis the four aMD simulations trajectories were concatenated to a single trajectory before processing to allow cross-comparison of the data under identical conditions.