Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region.
Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region.
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DOI：
10.1039/c5cp06197k
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发表时间：
2016-02-17
期刊：
影响因子：
--
通讯作者：
Palmer AG III
中科院分区：
文献类型：
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作者：
Gill ML;Byrd RA;Palmer AG III
内源性无序蛋白（IDP）和具有内源性无序区（IDR）的蛋白质在调节和信号转导通路中起着重要作用。这些功能的一个关键方面是IDP/IDR与靶分子形成高度特异性复合物的能力。然而，阐明的构象动力学功能的贡献一直受到限制的IDP/IDR的结构异质性相关的挑战。利用在14.1 ~ 21.1T的四个静磁场下收集的NMR自旋弛豫参数（15 NR 1、15 NR 2和{1H}-15N杂环NOE），我们分析了酿酒酵母转录因子GCN 4的碱性亮氨酸拉链（bZip）结构域的骨架动力学。我们证明了扩展的无模型分析可以应用于具有IDR的蛋白质，例如apo GCN 4，并且这些结果显著扩展了使用11.74 T的单个静磁场进行的GCN 4动力学的先前NMR研究[Bracken等人（1999）J. Mol. Biol.生物学：285，2133-2146]并且与分子动力学模拟很好地相关[Robustelli等人（2013）J. Chem. Theory Comput.，9，5190-5200]。与早期的工作相比，在多个静态字段的数据允许GCN 4的内部动态的时间尺度进行可靠的量化。在DNA结合区的大幅度动态波动具有与两步机制一致的相关时间（τs = 1.4-2.5 ns），其中GCN 4的部分有序bZip构象与DNA形成初始相遇复合物，然后快速重排到具有完全形成的碱性区域识别螺旋的高亲和力状态。
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways. A critical aspect of these functions is the ability of IDP/IDRs to form highly specific complexes with target molecules. However, elucidation of the contributions of conformational dynamics to function has been limited by challenges associated with structural heterogeneity of IDP/IDRs. Using NMR spin relaxation parameters (15N R1, 15N R2, and {1H}-15N heteronuclear NOE) collected at four static magnetic fields ranging from 14.1 to 21.1 T, we have analyzed the backbone dynamics of the basic leucine-zipper (bZip) domain of the Saccharomyces cerevisiae transcription factor GCN4, whose DNA binding domain is intrinsically disordered in the absence of DNA substrate. We demonstrate that the extended Model-free analysis can be applied to proteins with IDRs such as apo GCN4 and that these results significantly extend previous NMR studies of GCN4 dynamics performed using a single static magnetic field of 11.74 T [Bracken, et al. (1999) J. Mol. Biol., 285, 2133–2146] and correlate well with molecular dynamics simulations [Robustelli, et al. (2013) J. Chem. Theory Comput., 9, 5190–5200]. In contrast to the earlier work, data at multiple static fields allows the time scales of internal dynamics of GCN4 to be reliably quantified. Large amplitude dynamic fluctuations in the DNA-binding region have correlation times (τs ≈ 1.4–2.5 ns) consistent with a two-step mechanism in which partially ordered bZip conformations of GCN4 form initial encounter complexes with DNA and then rapidly rearrange to the high affinity state with fully formed basic region recognition helices.