Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
Protein J. 2010 Nov;29(8):545-50. doi: 10.1007/s10930-010-9291-z.
In the last decade, several studies have reported that Wide-Angle X-ray Scattering (WAXS) from protein in solution contains valuable information about protein secondary and tertiary structures. Nevertheless, the use of such information will remain limited until a clear understanding of the correlation between protein structural elements and WAXS profile regions is established. In this work, large number of possible protein conformations is generated using comparative modeling (LOOPP & PHYRE servers) of nine different proteins representing six main protein classes (SCOP database). After model validation (SAVES server), protein structural elements of the selected models are retrieved (Swiss PDB Viewer & VORONOIA) and their corresponding WAXS profiles are generated (CRYSOL). The correlations between seven elements of protein structure (alpha helix, beta sheet and random coil content, alpha to beta ratio, alpha to random coil ratio, average packing density and number of residues) and seven WAXS profile parameters (Full Width at Half Maximum of two main scattering peaks of interest, their areas, positions and ratio of intensities) are investigated. Results revealed high (up to 0.75) and moderate (0.30-0.50) correlations between some of the suggested profile parameters and investigated protein structural elements indicating that these parameters represent a useful probe of protein conformation. Moreover, a high observed correlation between the degree of fitting of model to reference structures and the degree of fitting of their corresponding WAXS profiles suggests that the latter can be used in experimental model validation.
在过去的十年中，已有多项研究报告称，溶液中蛋白质的广角 X 射线散射（WAXS）包含有关蛋白质二级和三级结构的有价值信息。然而，除非明确了解蛋白质结构元素与 WAXS 谱区之间的相关性，否则此类信息的应用仍将受到限制。在这项工作中，使用比较建模（LOOPP 和 PHYRE 服务器）对代表六个主要蛋白质类别的九种不同蛋白质生成了大量可能的蛋白质构象（SCOP 数据库）。在模型验证（SAVES 服务器）之后，检索所选模型的蛋白质结构元素（Swiss PDB Viewer 和 VORONOIA）并生成其相应的 WAXS 谱（CRYSOL）。研究了蛋白质结构的七个元素（α螺旋、β片层和无规卷曲含量、α/β比、α/无规卷曲比、平均堆积密度和残基数）与七个 WAXS 谱参数（两个主要感兴趣散射峰的半峰全宽、它们的面积、位置和强度比）之间的相关性。结果表明，一些建议的谱参数与所研究的蛋白质结构元素之间存在高度（高达 0.75）和中度（0.30-0.50）相关性，表明这些参数代表了蛋白质构象的有用探针。此外，模型对参考结构的拟合程度与相应 WAXS 谱的拟合程度之间存在高度相关性，这表明后者可用于实验模型验证。
