A model of interdomain mobility in a multidomain protein
A model of interdomain mobility in a multidomain protein
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DOI：
10.1021/ja067667r
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发表时间：
2007-03-21
影响因子：
15
通讯作者：
Fushman, David
中科院分区：
文献类型：
--
作者：
Ryabov, Yaroslav E.;Fushman, David
结构域迁移率在多结构域系统的生物学功能中起着至关重要的作用。磁畴运动的特征时间落在从纳米到毫秒的区间内，适合于NMR研究。适当的分析NMR弛豫数据，这些系统在解决方案中占域间的运动，除了整体翻滚和本地intradomain动态。在这里，我们提出了一个多结构域蛋白质的结构域间流动性模型，它认为结构域的重新取向的交换/相互转换之间的两个不同的构象状态的分子，结合完全各向异性的整体翻滚。在pH 4.5和6.8的Lys 48连接的双泛素的N-15-弛豫数据的分析表明，该模型充分拟合的实验数据，并允许表征双泛素的结构和运动特性，从而提供信息的泛素结构域在两个相互转换状态的相对取向。分析表明，这两个结构域重新定向的时间尺度为9-30 ns，振幅足以让蛋白质配体访问的结合位点隔离在界面上的封闭构象。对控制双泛素中相互转化状态之间平衡的可能机制的分析指向His 68的质子化，这导致分子的三种不同的带电状态，零，+e和+2e净电荷。三种状态中只有两种在pH 4.5或6.8时明显聚集，这确保了双态模型在这些条件下对双泛素的适用性。我们还比较了我们的模型与“扩展无模型”的方法，并讨论了该模型未来可能的发展。
Domain mobility plays an essential role in the biological function of multidomain systems. The characteristic times of domain motions fall into the interval from nano- to milliseconds, amenable to NMR studies. Proper analysis of NMR relaxation data for these systems in solution has to account for interdomain motions, in addition to the overall tumbling and local intradomain dynamics. Here we propose a model of interdomain mobility in a multidomain protein, which considers domain reorientations as exchange/interconversion between two distinct conformational states of the molecule, combined with fully anisotropic overall tumbling. Analysis of N-15-relaxation data for Lys48-linked diubiquitin at pH 4.5 and 6.8 showed that this model adequately fits the experimental data and allows characterization of both structural and motional properties of diubiquitin, thus providing information about the relative orientation of ubiquitin domains in both interconverting states. The analysis revealed that the two domains reorient on a time scale of 9-30 ns, with the amplitudes sufficient for allowing a protein ligand access to the binding sites sequestered at the interface in the closed conformation. The analysis of a possible mechanism controlling the equilibrium between the interconverting states in diubiquitin points toward protonation of His68, which results in three different charged states of the molecule, with zero, +e, and +2e net charge. Only two of the three states are noticeably populated at pH 4.5 or 6.8, which assures applicability of the two-state model to diubiquitin at these conditions. We also compare our model with the "extended model-free" approach and discuss possible future developments of the model.