NMR spectroscopy

NMR 光谱学
  • 文章类型: Journal Article
    TG相互作用因子-1同源域(TGIF1-HD)通过其三氨基酸环延伸(TALE)型同源域与基因启动子中的共有DNA基序5'-TGTCA-3'结合,然后招募共同调节因子来调节基因表达。尽管以前已经报道了人TGIF1-HD的溶液NMR结构,对其DNA结合机制知之甚少。NMR滴定已被广泛用于研究配体与靶蛋白结合的机制;然而,当用共有DNA滴定时,主要在游离状态和结合状态的TGIF1-HD之间发生中间交换,这导致质量较差的NMR光谱,并阻止了对其相互作用界面和构象动力学的进一步探索。这里,通过氢-氘交换质谱(HDX-MS)实验推测TGIF1-HD的螺旋α3为特异性DNA结合界面,随后通过化学交换饱和转移(CEST)光谱证实。此外,其他区域的同时构象变化,包括α1和α2,由DNA结合诱导,解释了除了位于α3中的残基之外的广泛残基对化学位移扰动的观察。Further,低填充DNA结合的TGIF1-HD以130.2±3.6s-1的速率缓慢交换来自CEST数据的分析,和两个残留物,位于α3中间的R220和R221被鉴定为对于DNA结合至关重要。我们的研究提供了对TGIF1-HD识别广泛启动子DNA的机制的结构和动态见解。
    The TG interacting factor-1 homeodomain (TGIF1-HD) binds with the consensus DNA motif 5\'-TGTCA-3\' in gene promoters through its three-amino acid loop extension (TALE) type homeodomain, and then recruits co-regulators to regulate gene expression. Although the solution NMR structure of human TGIF1-HD has been reported previously, little is known about its DNA binding mechanism. NMR titrations have been extensively used to study mechanisms of ligand binding to target proteins; however, an intermediate exchange occurred predominantly between TGIF1-HD in the free and bound states when titrated with the consensus DNA, which resulted in poor-quality NMR spectra and precluded further exploration of its interaction interface and conformational dynamics. Here, the helix α3 of TGIF1-HD was speculated as the specific DNA binding interface by hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, and subsequently confirmed by chemical exchange saturation transfer (CEST) spectroscopy. In addition, simultaneous conformational changes in other regions, including α1 and α2, were induced by DNA binding, explaining the observation of chemical shift perturbations from extensive residues besides those located in α3. Further, low-populated DNA-bound TGIF1-HD undergoing a slow exchange at a rate of 130.2 ± 3.6 s-1 was derived from the analysis of the CEST data, and two residues, R220 and R221, located in the middle of α3 were identified to be crucial for DNA binding. Our study provides structural and dynamic insights into the mechanisms of TGIF1-HD recognition of extensive promoter DNA.
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