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. 2018 May 23;15:39. doi: 10.1186/s12977-018-0422-5

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© The Author(s) 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 9 — Molecular dynamics analysis (MD) of CDK9/Cyclin T1/Tat complex with phosphorylated Tat Ser-16 and Ser-46. a Spatial superposition of the CDK9/Cyclin T1/Tat complexes with non-phosphorylated Tat (S16&S46) and Tat phosphorylated on Ser-16 and Ser-46 (S16P&S46P) at 20 ns MD time, protein main chains are shown as follows: Cyclin T1—in blue and grey colors, CDK9—in green and carrot colors and Tat—in yellow and cyan colors, respectively. CDK9 Thr-186 was phosphorylated in all the MD simulations. ATP⁺Mg2⁺ is shown in ball-and-stick presentation. Initial conformation of the complexes were built by homology with crystal structure (PDB: 3MIA) as described in Methods. Arrows indicates the position of Ser-16 and phosphorylated Ser-16 (Sep16) and phosphorylated Thr 186 (Tpo186). Phosphorylated Ser-46 is abbreviated as Sep46. b Enlarged picture showing interaction of Tat Ser-16 with Cyclin T1 Val-54. b, c Enlarged pictures showing conformational change of Tat protein due to its phosphorylation. Initial interaction of Tat Ser-16 with Cyclin T1 Val-54 (b) is lost upon Ser-16 phosphorylation and the interaction with Tat Met-1 is formed (c). d, e Enlarged pictures showing interaction of Tat Glu-9 with CDK9 Lys-144 when Tat was phosphorylated (e) and no interaction when Tat was not phosphorylation (d)