Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
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DOI：
10.1063/4.0000087
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发表时间：
2021-07
期刊：
影响因子：
--
通讯作者：
Wilson MA
中科院分区：
文献类型：
--
作者：
Su Z;Dasgupta M;Poitevin F;Mathews II;van den Bedem H;Wall ME;Yoon CH;Wilson MA
蛋白质的结构和动力学可以用x射线晶体学来探测。而布拉格峰只敏感的平均单位细胞的电子密度，布拉格峰之间的信号-扩散散射-是敏感的电子密度变化的空间相关性。虽然漫散射包含有价值的信息，蛋白质动力学，扩散信号是更难以从背景中分离相比，布拉格信号，和扩散信号的再现性还没有得到很好的理解。我们提出了一个系统的研究，从异氰水合酶在三种不同的蛋白质形式的漫散射的再现性。在成对比较中，从不同突变体获得的重复弥散数据集和数据集相似（Pearson相关系数≥0.8）。这些数据的处理方式受到先前发表的方法的启发，使用具有模块化设计的定制软件，使我们能够对各种数据处理选择进行分析，以确定如何获得使用对称性和再现性的无偏测量评估的最高质量数据。然后使用扩散数据来表征原子的流动性，使用类液体运动（LLM）模型。这种表征是能够区分不同的各向异性原子位移参数（ADP）模型所产生的不同的各向异性缩放选择，同意与布拉格数据。我们的研究结果强调了数据再现性的重要性，作为一个无模型的漫数据质量的措施，说明漫散射的LLM分析的能力，选择替代ADP模型，并提供成功的漫散射实验设计的见解。
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
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DOI：
10.1107/s0907444905036693
发表时间：
2006-01-01
影响因子：
2.2
作者：
Evans, P
通讯作者：
Evans, P
影响因子：
2.5
作者：
Holton JM
通讯作者：
Holton JM
影响因子：
64.8
作者：
CASPAR, DLD;CLARAGE, J;CLARAGE, M
通讯作者：
CLARAGE, M
影响因子：
4.8
作者：
Lakshminarasimhan, Mahadevan;Madzelan, Peter;Wilson, Mark A.
通讯作者：
Wilson, Mark A.
影响因子：
5.6
作者：
Héry, S;Genest, D;Smith, JC
通讯作者：
Smith, JC