Dhavan G M, Lapham J, Yang S, Crothers D M
Departments of Chemistry, Yale University, New Haven, CT 06511, USA.
J Mol Biol. 1999 May 14;288(4):659-71. doi: 10.1006/jmbi.1999.2690.
Integration Host Factor, IHF, is an E. coli DNA binding protein that imposes a substantial bend on DNA. Previous footprinting studies and bending assays have characterized several recognition sequences in the bacterial and lambda phage genome as unique in the way they are bound by IHF. We have chosen one of the lambda phage sites, H1, for study because it presents a small yet sequence-specific substrate for NMR analysis of the complex. A 19 base-pair duplex, H19, corresponding to the recognition sequence at the H1 site was constructed by isotopically labeling one of the strands with 15N. (1H, 15N) heteronuclear NMR experiments aided in assigning the imino proton resonances of the DNA alone and in complex with IHF. The NMR results are consistent with a mode of binding observed in the recent crystal structure of IHF bound to another of its sites from the lambda phage genome. Additionally, the dramatic change that IHF imposes on the imino proton chemical shifts is indicative of a severe deviation from canonical B-DNA structure. In order to understand the dynamic properties of the DNA in the complex with IHF, the exchange rates of the imino protons with the solvent have been measured for H19 with and without IHF bound. A drastic reduction in exchange is observed for the imino protons in the IHF bound DNA. In the DNA-protein complex, groups of adjacent base-pair exchange at the same rate, and appear to close more slowly than the rate of imino proton exchange with bulk water, since their exchange rate is independent of catalyst concentration. We infer that segments of the double helix as large as 6 bp open in a cooperative process, and remain open much longer than is typical for opening fluctuations in naked duplex DNA. We discuss these results in terms of the specific protein-DNA contacts observed in the crystal structure.
整合宿主因子(IHF)是一种大肠杆菌DNA结合蛋白,它能使DNA发生显著弯曲。先前的足迹分析研究和弯曲分析已将细菌和λ噬菌体基因组中的几个识别序列鉴定为与IHF结合方式独特的序列。我们选择了λ噬菌体的一个位点H1进行研究,因为它为该复合物的核磁共振分析提供了一个小而序列特异的底物。通过用15N对其中一条链进行同位素标记,构建了一个与H1位点识别序列相对应的19个碱基对的双链体H19。(1H,15N)异核核磁共振实验有助于确定单独的DNA以及与IHF结合的DNA的亚氨基质子共振。核磁共振结果与最近在与λ噬菌体基因组中另一个位点结合的IHF晶体结构中观察到的结合模式一致。此外,IHF对亚氨基质子化学位移产生的显著变化表明其与标准B-DNA结构存在严重偏差。为了了解与IHF结合的复合物中DNA的动态特性,已测量了结合和未结合IHF的H19中亚氨基质子与溶剂的交换率。在结合了IHF的DNA中,观察到亚氨基质子的交换急剧减少。在DNA-蛋白质复合物中,相邻碱基对以相同的速率交换,并且似乎比亚氨基质子与大量水的交换速率关闭得更慢,因为它们的交换速率与催化剂浓度无关。我们推断,长达6个碱基对的双螺旋片段在协同过程中打开,并且保持打开的时间比裸双链DNA中打开波动的典型时间长得多。我们根据晶体结构中观察到的特定蛋白质-DNA接触来讨论这些结果。