Ramsey Kristen M, Dembinski Holly E, Chen Wei, Ricci Clarisse G, Komives Elizabeth A
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA.
J Mol Biol. 2017 Apr 7;429(7):999-1008. doi: 10.1016/j.jmb.2017.02.017. Epub 2017 Feb 27.
We recently discovered that IκBα enhances the rate of release of nuclear factor kappa B (NFκB) from DNA target sites in a process we have termed molecular stripping. Coarse-grained molecular dynamics simulations of the stripping pathway revealed two mechanisms for the enhanced release rate: the negatively charged PEST region of IκBα electrostatically repels the DNA, and the binding of IκBα appears to twist the NFκB heterodimer so that the DNA can no longer bind. Here, we report amide hydrogen/deuterium exchange data that reveal long-range allosteric changes in the NFκB (RelA-p50) heterodimer induced by DNA or IκBα binding. The data suggest that the two Ig-like subdomains of each Rel-homology region, which are connected by a flexible linker in the heterodimer, communicate in such a way that when DNA binds to the N-terminal DNA-binding domains, the nuclear localization signal becomes more highly exchanging. Conversely, when IκBα binds to the dimerization domains, amide exchange throughout the DNA-binding domains is decreased as if the entire domain is becoming globally stabilized. The results help understand how the subtle mechanism of molecular stripping actually occurs.
我们最近发现，IκBα在一个我们称为分子剥离的过程中提高了核因子κB（NFκB）从DNA靶位点的释放速率。对剥离途径的粗粒度分子动力学模拟揭示了释放速率提高的两种机制：IκBα带负电荷的PEST区域与DNA发生静电排斥，并且IκBα的结合似乎会扭曲NFκB异二聚体，从而使DNA无法再结合。在此，我们报告了酰胺氢/氘交换数据，这些数据揭示了由DNA或IκBα结合诱导的NFκB（RelA-p50）异二聚体中的长程变构变化。数据表明，每个Rel同源区域的两个Ig样亚结构域在异二聚体中通过柔性接头相连，并以这样一种方式进行通信：当DNA与N端DNA结合结构域结合时，核定位信号的交换变得更加频繁。相反，当IκBα与二聚化结构域结合时，整个DNA结合结构域的酰胺交换减少，就好像整个结构域在整体上变得更加稳定。这些结果有助于理解分子剥离的微妙机制实际上是如何发生的。
