Ma Peixiang, Xue Yi, Coquelle Nicolas, Haller Jens D, Yuwen Tairan, Ayala Isabel, Mikhailovskii Oleg, Willbold Dieter, Colletier Jacques-Philippe, Skrynnikov Nikolai R, Schanda Paul
Université Grenoble Alpes, IBS, F-38044 Grenoble, France.
CEA, Institut de Biologie Structurale, F-38044 Grenoble, France.
Nat Commun. 2015 Oct 5;6:8361. doi: 10.1038/ncomms9361.
The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall 'rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.
绝大多数生物大分子的三维结构是通过晶体样品的X射线衍射确定的。高分辨率结构测定关键取决于蛋白质晶体的均匀性。晶体中分子的整体“摇摆”运动预计会影响衍射质量，因此这种运动可能会影响晶体结构解析过程。然而，到目前为止，尚未在蛋白质晶体中直接观察到整体分子运动，而且这种动力学的时间尺度仍不清楚。在这里，我们使用固态核磁共振、X射线衍射方法和微秒级分子动力学模拟，直接表征不同晶体形式下蛋白质的刚体运动。对于本研究中所研究的泛素晶体，我们确定了摇摆运动可能的相关时间范围为0.1至100微秒。摇摆幅度因晶体形式而异，并且与X射线衍射实验中可获得的分辨率相关。
