School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
Biochem Biophys Res Commun. 2013 Feb 1;431(1):65-9. doi: 10.1016/j.bbrc.2012.12.091. Epub 2013 Jan 3.
We have developed a new methodology that determines protein structures using small-angle X-ray scattering (SAXS) data. The current bottlenecks in determining the protein structures require a new strategy using the simple design of an experiment, and SAXS is suitable for this purpose in spite of its low information content. First we demonstrated that SAXS constraints work additively to NMR-derived information in calculating structures. Next, structure calculations for nine proteins taking different folds were performed using the SAXS constraints combined with the NMR-derived distance restraints for local geometry such as secondary structures or those for tertiary structure. The results show that the SAXS constraints complemented the tertiary-structural information for all the proteins, and that accuracy of the structures thus obtained with SAXS constraints and local geometrical restraints ranged from 1.85 to 4.33Å. Based on these results, we were able to construct a coarse-grained protein model at amino acid residue resolution.
我们开发了一种新的方法，利用小角 X 射线散射（SAXS）数据来确定蛋白质结构。目前确定蛋白质结构的瓶颈需要使用实验的简单设计来制定新策略，而 SAXS 非常适合这种用途，尽管它的信息量较低。首先，我们证明了 SAXS 约束可以与 NMR 衍生信息相加，用于计算结构。接下来，使用 SAXS 约束和 NMR 衍生的距离约束（用于局部几何形状，如二级结构或三级结构）对九个具有不同折叠的蛋白质进行了结构计算。结果表明，SAXS 约束补充了所有蛋白质的三级结构信息，并且使用 SAXS 约束和局部几何约束获得的结构的准确性在 1.85 到 4.33Å 之间。基于这些结果，我们能够构建一个在氨基酸残基分辨率的粗粒度蛋白质模型。
