Adeniran Charles, Hamelberg Donald
Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.
Biochemistry. 2017 Sep 19;56(37):5002-5010. doi: 10.1021/acs.biochem.7b00528. Epub 2017 Sep 6.
The molecular basis of gene regulation by Nuclear Factor-κB (NF-κB) transcription factors and their coregulators is not well understood. This family of transcription factors controls a number of essential subcellular processes. Human Pirin, a nonheme iron (Fe) binding protein, has been shown to modulate the binding affinity between p65 homodimeric NF-κB and κB DNA. However, the allosteric effect of the active Fe(III) form of Pirin on the DNA has not been established. Here, we use multiple microsecond-long molecular dynamics simulations to explore the conformational dynamics of the free DNA, the p65-DNA complex, and the Pirin-p65-DNA supramolecular complex. We show that only the Fe(III) form of Pirin enhances the affinity between p65 and the DNA in the Pirin-p65-DNA supramolecular complex, in agreement with experiments. Additionally, the results provide atomistic details of the effect of the active Fe(III) form of Pirin on the DNA upon binding to the p65-DNA complex. In general, unlike the Fe(II) form of Pirin, binding of the Fe(III) form of Pirin to the p65-DNA complex significantly alters both the conformational dynamics of the DNA and the interactions between p65 and the DNA. The results provide atomic level understanding of the modulation of the DNA as a result of a redox-specific Fe(II)/Fe(III) coregulation of NF-κB by Pirin, knowledge that is necessary to fully understand normal and aberrant subcellular processes and the role of a subtle single electron redox process in gene regulation.
核因子-κB（NF-κB）转录因子及其共调节因子对基因调控的分子基础尚未完全了解。这一家族的转录因子控制着许多重要的亚细胞过程。人松果体蛋白是一种非血红素铁（Fe）结合蛋白，已被证明可调节p65同二聚体NF-κB与κB DNA之间的结合亲和力。然而，松果体蛋白活性Fe（III）形式对DNA的变构效应尚未得到证实。在这里，我们使用多个微秒级的分子动力学模拟来探索游离DNA、p65-DNA复合物和松果体蛋白-p65-DNA超分子复合物的构象动力学。我们表明，只有松果体蛋白的Fe（III）形式增强了松果体蛋白-p65-DNA超分子复合物中p65与DNA之间的亲和力，这与实验结果一致。此外，结果提供了松果体蛋白活性Fe（III）形式与p65-DNA复合物结合后对DNA影响的原子细节。一般来说，与松果体蛋白的Fe（II）形式不同，松果体蛋白的Fe（III）形式与p65-DNA复合物的结合显著改变了DNA的构象动力学以及p65与DNA之间的相互作用。这些结果提供了对由于松果体蛋白对NF-κB进行氧化还原特异性Fe（II）/Fe（III）共调节而导致的DNA调节的原子水平理解，这是全面理解正常和异常亚细胞过程以及微妙的单电子氧化还原过程在基因调控中的作用所必需的知识。
