Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling
Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling
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DOI：
10.1021/bi061738h
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发表时间：
2007-05-01
期刊：
影响因子：
2.9
通讯作者：
Chen, Yuan
中科院分区：
文献类型：
--
作者：
Cai, Sheng;Zhu, Lingyang;Chen, Yuan
在分子水平上理解蛋白质-DNA相互作用的机制是结构和分子生物学研究的主要焦点之一。核磁共振波谱是目前唯一能提供溶液中蛋白质-DNA识别的原子细节的方法。然而，用核磁共振波谱确定蛋白质-DNA复合体的结构依赖于分子间核Overhauser效应(NOE)的观察及其归属，而这在许多情况下是很难获得的。在这项研究中，我们已经证明了由单个自旋标记得到的分子间距离限制，再加上对接计算，已经定义了MRF2的富含AT的相互作用结构域(ARID)与其目标DNA之间的许多特定接触。MRF2主要使用L1和L2这两个柔性环与DNA接触。当L1环与磷酸骨架接触时，L2和邻近螺旋中的几个残基与DNA主沟中的AT碱基对相互作用。尽管干旱的DNA结合蛋白家族具有结构多样性，但MRf2与DNA的接触与在同源Dri-DNA复合体中观察到的相似。
Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, determining the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains contacts with DNA similar to those observed in the homologous Dri-DNA complex.