Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy.
Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy.
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DOI：
10.1021/ja312314b
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发表时间：
2013-03-06
影响因子：
15
通讯作者：
Iwahara, Junji
中科院分区：
文献类型：
--
作者：
Anderson, Kurtis M.;Esadze, Alexandre;Manoharan, Mariappan;Brueschweiler, Rafael;Gorenstein, David G.;Iwahara, Junji
离子配对是最基本的化学相互作用之一，对于生物大分子的分子识别至关重要。从实验的角度来看，目前对生物大分子系统中的离子对动力学知之甚少。吸收、红外和拉曼光谱方法以前被用来表征离子对的动力学性质，但这些方法只能应用于小的化合物。在这里，使用NMR 15 N弛豫和氢键标量15 N-31 P J-耦合（h3 JNP），我们研究了赖氨酸侧链NH3+氨基和DNA磷酸基团之间的离子对在HoxD 9同源结构域-DNA复合物的分子界面的动力学。我们确定了赖氨酸NH ~（3+）基团的C-N键旋转和重取向的序参数和相关时间。我们的数据表明，分子间离子对中的NH3+基团在蛋白质-DNA界面处是高度动态的，这应该降低蛋白质-DNA缔合的熵成本。从C-N键旋转的相关时间沿着与实验和量子化学衍生的h3 JNP氢键标量耦合，它似乎发生在一个亚纳秒的时间尺度上的离子对中的氢键断裂。有趣的是，发现DNA磷酸基团中的氧硫取代增强了分子间离子对中NH3+基团的迁移率。这可以部分地解释通过氧-硫取代的蛋白质-DNA缔合的亲和力增强，这是先前观察到的但知之甚少的现象。
Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR 15N relaxation and hydrogen-bond scalar 15N-31P J-couplings (h3JNP), we have investigated the dynamics of the ion pairs between lysine side-chain NH3+ amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain-DNA complex. We have determined the order parameters and the correlation times for C-N bond rotation and reorientation of the lysine NH3+ groups. Our data indicate that the NH3+ groups in the intermolecular ion pairs are highly dynamic at the protein-DNA interface, which should lower the entropic costs for protein-DNA association. Judging from the C-N bond-rotation correlation times along with experimental and quantum-chemically derived h3JNP hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond timescale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3+ group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein-DNA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.
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