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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 7 — GCN4-cAD residues W120 and F124 are displayed in liquorice representation in light blue and green, respectively, on a portion of the GCN4 α-helix shown as a purple ribbon. Key residues participating in the formation of Pocket #1 on the GAL11-ABD1 surface are drawn as van der Waals structures and labelled according to amino acid identiy (V170 white; M173 pink; Y220 red; K217 and K 221 in light blue). V170 and M173 are part of GAL11-ABD1 α-helix 1 (see Fig 2B for helix nomenclature) marked in dark grey. K217, K221 and Y220 are on GAL11-ABD1 α-helix 4 shown in light grey. The changing orientation of the GCN4 α-helical axis is marked by a purple arrow. A. Structure near beginning of simulation (30 ns of GAL11-ABD1/GCN4-cAD _aMD_no1). GCN4-F124 occupies Pocket #1 formed by GAL11-Y220 and -K217 (among other residues not shown here), while GCN4-W120 engages in hydrophobic interactions with the non-polar section of the GAL11-K221 side-chain. B. Structure after 120 ns simulation (GAL11-ABD1/GCN4-cAD _aMD_no1). GCN4-F124 has moved towards GAL11-M173, freeing up Pocket #1 for GCN4-W120 to move in while maintaining hydrophobic engagements with GAL11-K217 and -K221. C. Structure after 220 ns simulation (GAL11-ABD1/GCN4-cAD _aMD_no1). GCN4-F124 binds now to GAL11-M173 and -V170, and Pocket #1 is now fully occupied by GCN4-W120.