Sugimura Sawako, Crothers Donald M
Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA.
Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18510-4. doi: 10.1073/pnas.0608337103. Epub 2006 Nov 20.
Integration host factor (IHF) is a prokaryotic protein required for the integration of lambda phage DNA into its host genome. An x-ray crystal structure of the complex shows that IHF binds to the minor groove of DNA and bends the double helix by 160 degrees [Rice PA, Yang S, Mizuuchi K, Nash HA (1996) Cell 87:1295-1306]. We sought to dissect the complex formation process into its component binding and bending reaction steps, using stopped-flow fluorimetry to observe changes in resonance energy transfer between DNA-bound dyes, which in turn reflect distance changes upon bending. Different DNA substrates that are likely to increase or decrease the DNA bending rate were studied, including one with a nick in a critical kink position, and a substrate with longer DNA ends to increase hydrodynamic friction during bending. Kinetic experiments were carried out under pseudofirst-order conditions, in which the protein concentration is in substantial excess over DNA. At lower concentrations, the reaction rate rises linearly with protein concentration, implying rate limitation by the bimolecular reaction step. At high concentrations the rate reaches a plateau value, which strongly depends on temperature and the nature of the DNA substrate. We ascribe this reaction limit to the DNA bending rate and propose that complex formation is sequential at high concentration: IHF binds rapidly to DNA, followed by slower DNA bending. Our observations on the bending step kinetics are in agreement with results using the temperature-jump kinetic method.
整合宿主因子(IHF)是一种原核蛋白,是λ噬菌体DNA整合到其宿主基因组中所必需的。该复合物的X射线晶体结构表明,IHF与DNA的小沟结合,并使双螺旋弯曲160度[赖斯·PA、杨·S、水内·K、纳什·HA(1996年)《细胞》87卷:1295 - 1306页]。我们试图将复合物形成过程分解为其组成的结合和弯曲反应步骤,使用停流荧光法观察与DNA结合的染料之间共振能量转移的变化,这反过来又反映了弯曲时的距离变化。研究了可能增加或降低DNA弯曲速率的不同DNA底物,包括在关键扭结位置有一个切口的底物,以及具有更长DNA末端以增加弯曲过程中流体动力学摩擦力的底物。动力学实验是在准一级条件下进行的,其中蛋白质浓度大大超过DNA浓度。在较低浓度下,反应速率随蛋白质浓度线性上升,这意味着双分子反应步骤是速率限制因素。在高浓度下,速率达到一个平稳值,该值强烈依赖于温度和DNA底物的性质。我们将这种反应极限归因于DNA弯曲速率,并提出在高浓度下复合物形成是顺序性的:IHF迅速与DNA结合,随后是较慢的DNA弯曲。我们对弯曲步骤动力学的观察结果与使用温度跳跃动力学方法得到的结果一致。