Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
J Mol Recognit. 2011 Jul-Aug;24(4):597-607. doi: 10.1002/jmr.1085. Epub 2010 Nov 26.
IκBζ (inhibitor of NF-κB (nuclear factor κB) ζ) is a nuclear protein induced upon stimulation of toll-like receptors (TLRs) and interleukin-1 receptor. Induced IκBζ, especially its C-terminal ankyrin repeat domain (ARD), interacts with NF-κB in the nucleus, where it regulates the transcriptional activity of target genes. Recent studies have shown that human ARD of IκBζ binds with p50/p65 heterodimer and inhibits the transcription of NF-κB regulated genes, whereas mouse ARD of IκBζ binds with p50/p50 homodimer and exhibits transcriptional activation activity. Since human and mouse IκBζ ARD are identical, it is unclear how IκBζ can be a positive and negative regulator of NF-κB-mediated transcription. Therefore, we generated a structural model of IκBζ ARD and constructed a detailed molecular dynamics (MD) simulation of IκBζ in explicit solvent to investigate ARD flexibility. In addition, we used molecular docking to screen for potential sites of interaction between IκBζ and the p50/p65 heterodimer and IκBζ and the p50/p50 homodimer. The docking experiments revealed that the binding of IκBζ ankyrin repeats with the p50/p65 N-terminal DNA binding domain prevents NF-κB-mediated transcriptional activation. Furthermore, the IκBζ-p50 homodimer complex, which lacks Pro, Glu (and Asp), Ser and Thr (PEST motif), facilitated gene expression. These two different binding schemes of IκBζ may be responsible for its opposite function, which is consistent with the currently available biochemical data. Moreover, our data implicate structurally highly flexible ARD residues as the prime contributors to this dual function.
IκBζ（核因子 κB（nuclear factor κB）ζ 抑制剂）是一种在刺激 Toll 样受体（TLRs）和白细胞介素-1 受体后诱导产生的核蛋白。诱导产生的 IκBζ，特别是其 C 端锚蛋白重复结构域（ankyrin repeat domain，ARD），与核内的 NF-κB 相互作用，调节靶基因的转录活性。最近的研究表明，人类 IκBζ 的 ARD 与 p50/p65 异二聚体结合，抑制 NF-κB 调节基因的转录，而小鼠 IκBζ 的 ARD 与 p50/p50 同二聚体结合，表现出转录激活活性。由于人类和小鼠 IκBζ 的 ARD 是相同的，因此尚不清楚 IκBζ 如何成为 NF-κB 介导的转录的正调节剂和负调节剂。因此，我们构建了 IκBζ ARD 的结构模型，并在显式溶剂中构建了 IκBζ 的详细分子动力学（molecular dynamics，MD）模拟，以研究 ARD 的柔性。此外，我们使用分子对接筛选 IκBζ 与 p50/p65 异二聚体和 IκBζ 与 p50/p50 同二聚体之间潜在的相互作用位点。对接实验表明，IκBζ 锚蛋白重复与 p50/p65 N 端 DNA 结合结构域的结合阻止了 NF-κB 介导的转录激活。此外，缺乏 Pro、Glu（和 Asp）、Ser 和 Thr（PEST 基序）的 IκBζ-p50 同二聚体复合物促进了基因表达。IκBζ 的这两种不同结合方案可能与其相反的功能有关，这与目前可用的生化数据一致。此外，我们的数据表明结构上高度灵活的 ARD 残基是这种双重功能的主要贡献者。
