Water has a profound effect on the dynamics of biomolecules and governs many biological processes, leading to the concept that function is slaved to solvent dynamics within and surrounding the biomolecule. Protein conformational changes on μs-ms time scales are frequently associated with protein function, but little is known about the behavior of protein-bound water on these time scales. Here we have used NMR relaxation dispersion measurements to probe the tryptophan indoles in the enzyme dihydrofolate reductase (DHFR). We find that during structural changes on the μs-ms time scale, large chemical shift changes are often observed for the NH proton on the indole ring, while relatively smaller chemical shift changes are observed for the ring nitrogen atom. Comparison with experimental chemical shifts and density functional theory-based chemical shift predictions show that during the structural change the tryptophan indole NHs remain bound to water, but the geometry of the protein-bound water networks changes. These results establish that relaxation dispersion measurements can indirectly probe water dynamics and indicate that water can influence, or be influenced by, protein conformational changes on the μs-ms time scale. Our data show that structurally conserved bound water molecules can play a critical role in transmitting information between functionally important regions of the protein and provide evidence that internal protein motions can be coupled through the mediation of hydrogen-bonded water bound in the protein structure.

中文翻译：

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蛋白质中色氨酸-水网络的缓慢动态

水对生物分子的动力学有着深远的影响，并控制着许多生物过程，导致了功能受制于生物分子内部和周围的溶剂动力学的概念。μs-ms 时间尺度上的蛋白质构象变化通常与蛋白质功能相关，但对这些时间尺度上蛋白质结合水的行为知之甚少。在这里，我们使用 NMR 弛豫分散测量来探测酶二氢叶酸还原酶 (DHFR) 中的色氨酸吲哚。我们发现，在 μs-ms 时间尺度上的结构变化期间，吲哚环上的 NH 质子经常观察到较大的化学位移变化，而环氮原子的化学位移变化相对较小。与实验化学位移和基于密度泛函理论的化学位移预测的比较表明，在结构变化期间，色氨酸吲哚 NHs 仍然与水结合，但蛋白质结合水网络的几何形状发生了变化。这些结果表明，弛豫分散测量可以间接探测水动力学，并表明水可以影响或受μs-ms 时间尺度上的蛋白质构象变化的影响。我们的数据表明，结构上保守的结合水分子可以在蛋白质功能重要区域之间传递信息方面发挥关键作用，并提供证据表明内部蛋白质运动可以通过蛋白质结构中结合的氢键水的介导来耦合。