Protein dynamics involving higher-energy sparsely populated conformational substates are frequently critical for protein function. This study describes the dynamics of the homodimer (p50)2 of the p50 Rel homology region (RHR) of the transcription factor NF-κB, using 13C relaxation dispersion experiments with specifically (13C, 1H)-labeled methyl groups of Ile (δ), Leu and Val. Free (p50)2 is highly dynamic in solution, showing μs-ms relaxation dispersion consistent with exchange between the ground state and higher energy substates. These fluctuations propagate from the DNA-binding loops through the core of the domain. The motions are damped in the presence of κB DNA, but the NMR spectra of the DNA complexes reveal multiple local conformations of the p50 RHR homodimer bound to certain κB DNA sequences. Varying the length and sequence of κB DNA revealed two factors that promote a single bound conformation for the complex: the length of the κB site in the duplex and a symmetrical sequence of guanine nucleotides at both ends of the recognition motif. The dynamic nature of the DNA-binding loops, together with the multiple bound conformations of p50 RHR with certain κB sites, is consistent with variations in the transcriptional activity of the p50 homodimer with different κB sequences.

中文翻译：

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使用甲基 NMR 光谱法研究 NF-κB p50 RHR 同二聚体 DNA 识别的结构和动态研究

涉及高能稀疏构象亚态的蛋白质动力学通常对于蛋白质功能至关重要。本研究描述了转录因子 NF-κB 的 p50 Rel 同源区 (RHR) 的同型二聚体 (p50)2 的动力学，使用 13C 弛豫分散实验和专门 (13C, 1H) 标记的 Ile (δ) 甲基进行、亮氨酸和缬氨酸。游离 (p50)2 在溶液中具有高度动态性，显示出与基态和高能亚态之间交换一致的 μs-ms 弛豫色散。这些波动从 DNA 结合环通过结构域的核心传播。κB DNA 存在时，运动会受到抑制，但 DNA 复合物的 NMR 谱揭示了与某些 κB DNA 序列结合的 p50 RHR 同二聚体的多个局部构象。改变 κB DNA 的长度和序列揭示了促进复合物形成单一结合构象的两个因素：双链体中 κB 位点的长度和识别基序两端鸟嘌呤核苷酸的对称序列。DNA 结合环的动态性质，以及 p50 RHR 与某些 κB 位点的多重结合构象，与具有不同 κB 序列的 p50 同二聚体的转录活性的变化一致。