Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France.
J Am Chem Soc. 2016 May 18;138(19):6240-51. doi: 10.1021/jacs.6b02424. Epub 2016 May 6.
The dynamic modes and time scales sampled by intrinsically disordered proteins (IDPs) define their function. Nuclear magnetic resonance (NMR) spin relaxation is probably the most powerful tool for investigating these motions delivering site-specific descriptions of conformational fluctuations from throughout the molecule. Despite the abundance of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rates remains poorly understood. Here we measure an extensive range of auto- and cross-correlated spin relaxation rates at multiple magnetic field strengths on the C-terminal domain of the nucleoprotein of Sendai virus, over a large range of temperatures (268-298 K), and combine these data to describe the dynamic behavior of this archetypal IDP. An Arrhenius-type relationship is used to simultaneously analyze up to 61 relaxation rates per amino acid over the entire temperature range, allowing the measurement of local activation energies along the chain, and the assignment of physically distinct dynamic modes. Fast (τ ≤ 50 ps) components report on librational motions, a dominant mode occurs on time scales around 1 ns, apparently reporting on backbone sampling within Ramachandran substates, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. Extending the study to three protein constructs of different lengths (59, 81, and 124 amino acids) substantiates the assignment of these contributions. The analysis is shown to be remarkably robust, accurately predicting a broad range of relaxation data measured at different magnetic field strengths and temperatures. The ability to delineate intrinsic modes and time scales from NMR spin relaxation will improve our understanding of the behavior and function of IDPs, adding a new and essential dimension to the description of this biologically important and ubiquitous class of proteins.
无规卷曲蛋白（IDPs）的动态模式和时间尺度决定了它们的功能。核磁共振（NMR）自旋弛豫可能是研究这些运动最有力的工具，它可以提供整个分子中构象波动的位点特异性描述。尽管有大量关于 IDPs 中弛豫的实验测量，但测量弛豫率的物理起源仍知之甚少。在这里，我们在多个磁场强度下，在温度范围为 268-298 K 的范围内，对仙台病毒核蛋白的 C 末端结构域进行了广泛的自相关和互相关自旋弛豫率测量，并结合这些数据描述了这种典型 IDP 的动态行为。我们使用 Arrhenius 型关系同时分析了整个温度范围内每个氨基酸多达 61 个弛豫率，从而可以测量链上的局部活化能，并分配物理上不同的动态模式。快速（τ≤50 ps）成分报告了旋转运动，主导模式出现在 1 ns 左右的时间尺度上，显然报告了在 Ramachandran 亚态范围内的骨架采样，而较慢的模式（5-25 ns）报告了由蛋白质链状性质主导的片段动力学。将研究扩展到三个不同长度（59、81 和 124 个氨基酸）的蛋白质构建体，证实了这些贡献的分配。该分析被证明具有很强的稳健性，可以准确预测在不同磁场强度和温度下测量的广泛弛豫数据。从 NMR 自旋弛豫中划分出内在模式和时间尺度的能力将提高我们对 IDPs 行为和功能的理解，为描述这种具有生物学意义且无处不在的蛋白质类别增加了一个新的、必不可少的维度。
