Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.
Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.
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DOI：
10.1016/j.bpj.2016.07.042
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发表时间：
2016-09
影响因子：
3.4
通讯作者：
M. Okuda;J. Higo;T. Komatsu;T. Konuma;K. Sugase;Y. Nishimura
中科院分区：
文献类型：
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作者：
M. Okuda;J. Higo;T. Komatsu;T. Konuma;K. Sugase;Y. Nishimura
一般转录因子II E（TFIIE）在其α亚基中含有一个富酸区（残基378-393），包括13个酸性残基和两个疏水性残基（Phe 387和Val 390）。在与TFIIH的p62亚基结合后，酸性区在p62的普列克底物蛋白同源结构域（PHD）的碱性沟上采用延伸的串状结构，并将Phe 387和Val 390插入沟中的两个浅口袋中。在这里，我们研究了这种相互作用的NMR和分子动力学（MD）模拟的动力学。虽然丙氨酸取代的Phe 387和/或Val 390大大降低结合PHD，突变体的结合模式是类似的野生型，判断的化学位移变化的PHD。核磁共振弛豫色散曲线的相互作用表现出大幅度的C-末端半串在酸性区域（苯丙氨酸387，谷氨酸388，缬氨酸390，丙氨酸391，和天冬氨酸392）的残基，表明一个两个网站的结合模式：一个对应于最终的复合物结构，和一个关闭路径的小复杂。为了探索非路径复合物的结构，结合模式的原子详细的自由能景观计算全原子多正则分子动力学。最稳定的簇对应于最终的复杂结构。下一个稳定的集群之一是关闭路径结构集群，显示了相反的取向的C-末端半串上的PHD槽，与最终的结构相比。分子动力学计算阐明，C-末端半酸性字符串形式遇到复合物，主要是围绕积极的凹槽区域，几乎有两个不同的方向的字符串，平行和反平行的最终结构。有趣的是，大多数遇到的复合物表现出平行状取向，这表明该串具有在Phe 387和/或Val 390的帮助下以适当取向结合在凹槽周围以顺利进行到最终复合物结构的趋势。
General transcription factor II E (TFIIE) contains an acid-rich region (residues 378–393) in itsα-subunit, comprising 13 acidic and two hydrophobic (Phe387 and Val390) residues. Upon binding to the p62 subunit of TFIIH, the acidic region adopts an extended string-like structure on the basic groove of the pleckstrin homology domain (PHD) of p62, and inserts Phe387 and Val390 into two shallow pockets in the groove. Here, we have examined the dynamics of this interaction by NMR and molecular dynamics (MD) simulations. Although alanine substitution of Phe387 and/or Val390 greatly reduced binding to PHD, the binding mode of the mutants was similar to that of the wild-type, as judged by the chemical-shift changes of the PHD. NMR relaxation dispersion profiles of the interaction exhibited large amplitudes for residues in the C-terminal half-string in the acidic region (Phe387, Glu388, Val390, Ala391, and Asp392), indicating a two-site binding mode: one corresponding to the final complex structure, and one to an off-pathway minor complex. To probe the off-pathway complex structure, an atomically detailed free-energy landscape of the binding mode was computed by all-atom multicanonical MD. The most thermodynamically stable cluster corresponded to the final complex structure. One of the next stable clusters was the off-pathway structure cluster, showing the reversed orientation of the C-terminal half-string on the PHD groove, as compared with the final structure. MD calculations elucidated that the C-terminal half-acidic-string forms encounter complexes mainly around the positive groove region with nearly two different orientations of the string, parallel and antiparallel to the final structure. Interestingly, the most encountered complexes exhibit a parallel-like orientation, suggesting that the string has a tendency to bind around the groove in the proper orientation with the aid of Phe387 and/or Val390 to proceed smoothly to the final complex structure.