Nguyen Dan, Hoffpauir Zoe A, Iwahara Junji
Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555, United States.
Biochemistry. 2017 Nov 7;56(44):5866-5869. doi: 10.1021/acs.biochem.7b00885.
Basic side chains play crucial roles in protein-DNA interactions. In this study, using NMR spectroscopy, we investigated the dynamics of Arg and Lys side chains of the fruit fly Antennapedia homeodomain in the free state and in the complex with target DNA. We measured N relaxation for Arg and Lys side chains at two magnetic fields, from which generalized order parameters for the cationic groups were determined. Mobility of the R5 side chain, which makes hydrogen bonds with a thymine base in the DNA minor groove, was greatly dampened. Several Lys and Arg side chains that form intermolecular ion pairs with DNA phosphates were found to retain high mobility with the order parameter being <0.6 in the DNA-bound state. Interestingly, some of the interfacial cationic groups in the complex were more mobile than in the free protein. The retained or enhanced mobility of the Arg and Lys side chains in the complex should mitigate the overall loss of conformational entropy in the protein-DNA association and allow dynamic molecular recognition.
碱性侧链在蛋白质与DNA的相互作用中起着至关重要的作用。在本研究中，我们使用核磁共振光谱法，研究了果蝇触角足同源结构域中精氨酸（Arg）和赖氨酸（Lys）侧链在游离状态以及与靶DNA形成复合物状态下的动力学。我们在两个磁场下测量了Arg和Lys侧链的N弛豫，由此确定了阳离子基团的广义序参数。与DNA小沟中的胸腺嘧啶碱基形成氢键的R5侧链的流动性大大降低。发现几个与DNA磷酸基团形成分子间离子对的Lys和Arg侧链在与DNA结合的状态下保持高流动性，序参数<0.6。有趣的是，复合物中的一些界面阳离子基团比游离蛋白质中的更具流动性。复合物中Arg和Lys侧链保留或增强的流动性应可减轻蛋白质-DNA缔合中构象熵的总体损失，并实现动态分子识别。
