Determination of the Three-Dimensional Structure of the Mrf2-DNA Complex Using Paramagnetic Spin Labeling

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• 作者：Sheng Cai ; Lingyang Zhu ; Ziming Zhang ; Yuan Chen
• 刊名：Biochemistry
• 出版年：2007
• 出版时间：May 1, 2007
• 年：2007
• 卷：46
• 期：17
• 页码：4943 - 4950
• 全文大小：331K
• 年卷期：v.46,no.17(May 1, 2007)
• ISSN：1520-4995

文摘

Understanding the mechanism of protein-DNA interactions at the molecular level is one ofthe main focuses in structural and molecular biological investigations. At present, NMR spectroscopy isthe 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 onthe observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which aredifficult to obtain in many cases. In this study, we have shown that intermolecular distance constraintsderived from a single spin-label in combination with docking calculations have defined many specificcontacts 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 thephosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in themajor 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.