Van Benschoten Andrew H, Liu Lin, Gonzalez Ana, Brewster Aaron S, Sauter Nicholas K, Fraser James S, Wall Michael E
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025;
Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4069-74. doi: 10.1073/pnas.1524048113. Epub 2016 Mar 28.
X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.
X射线衍射有潜力提供关于大分子结构动力学的丰富信息。为了实现这一潜力，必须同时测量目前用于推导大分子结构的布拉格散射以及反映电荷密度变化相关性的漫散射。到目前为止，由于收集漫散射数据需要额外的努力，来自蛋白质晶体的漫散射测量很少。在此，我们展示了从亲环素A和胰蛋白酶晶体收集的漫散射强度的三维测量结果。这些测量是从与布拉格数据相同的X射线衍射图像中获得的，采用了标准数据收集的最佳方法。为了以一种可用于结构精修的实用方式对潜在动力学进行建模，我们测试了蛋白质运动的平移-摆动-螺旋（TLS）、类液体运动（LLM）和粗粒度正常模式（NM）模型。LLM模型提供了运动的全局图像，并根据漫散射数据进行了精修，而TLS和NM模型提供了更详细和独特的原子位移描述，并且仅使用了来自布拉格数据的信息。虽然不同的TLS分组产生了相似的布拉格强度，但它们产生了不同的漫散射强度，且没有一个与数据完全吻合。相比之下，LLM和NM模型都与漫散射数据基本吻合。这些结果展示了一条切实可行的途径，可增加更广泛的生物科学领域可用的漫散射数据集数量，并表明受动力学启发的NM结构模型可以同时与布拉格散射和漫散射相吻合。
