Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
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结合同源建模、蛋白质-蛋白质对接、分子动力学模拟和虚拟丙氨酸突变，深入了解Keap1和IKK beta之间的分子间识别机制
DOI：
10.1371/journal.pone.0075076
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Sun HP
中科院分区：
文献类型：
--
作者：
Jiang ZY;Chu HX;Xi MY;Yang TT;Jia JM;Huang JJ;Guo XK;Zhang XJ;You QD;Sun HP
通过泛素-蛋白酶体途径降解某些蛋白质是负责应激反应的关键调节剂所采取的常见策略。Kelch样ECH相关蛋白-1（Keap 1）是基于Cullin 3（Cul 3）的泛素E3连接酶复合物的底物接头组分，介导两种关键调节剂NF-E2相关因子2（Nrf 2）和IκB激酶β（IKKβ）的泛素化，这两种调节剂参与基因转录的氧化还原控制。然而，与Keap 1-Nrf 2蛋白质-蛋白质相互作用（PPI）相比，Keap 1和IKKβ的分子间识别机制研究较少。为了探讨Keap 1与IKKβ的结合模式，我们建立了Keap 1与IKKβ的PPI模型。以已报道的非洲爪蟾IKKβ的晶体结构为模板，采用同源模建方法构建了人IKKβ的结构。采用蛋白质-蛋白质对接的方法建立了Keap 1-IKKβ复合物模型。在对对接蛋白进行细化和可视化分析后，通过分子动力学模拟进一步优化了所选择的位姿。利用所得结构进行虚拟丙氨酸突变，以探索对分子间相互作用有意义的热点。总体而言，我们的结果提供了对Keap 1-IKKβ的PPI模型的结构见解，并表明Keap 1的底物特异性取决于与关键酪氨酸（即Tyr 525，Tyr 574和Tyr 334）的相互作用。目前项目中提出的研究可能有助于设计选择性调节Keap 1的分子。Keap 1与IKKβ或Nrf 2的选择性识别机制将有助于进一步了解NF-κB与Nrf 2信号通路之间的相互作用。
Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1), a substrate adaptor component of the Cullin3 (Cul3)-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2) and IκB kinase β (IKKβ), which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI), the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.
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影响因子：
4.8
作者：
Carayol, Nathalie;Chen, Ji;Wang, Cun-Yu
通讯作者：
Wang, Cun-Yu
DOI：
10.1073/pnas.0607260103
发表时间：
2006-10-10
影响因子：
11.1
作者：
Clements, Casey M.;McNally, Richard S.;Ting, Jenny P-Y.
通讯作者：
Ting, Jenny P-Y.
DOI：
10.1073/pnas.172398899
发表时间：
2002-09-03
影响因子：
11.1
作者：
Dinkova-Kostova, AT;Holtzclaw, WD;Talalay, P
通讯作者：
Talalay, P
影响因子：
5.5
作者：
Hess, Berk
通讯作者：
Hess, Berk
DOI：
10.1074/jbc.m109.096545
发表时间：
2010-05-28
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Copple IM;Lister A;Obeng AD;Kitteringham NR;Jenkins RE;Layfield R;Foster BJ;Goldring CE;Park BK
通讯作者：
Park BK