Shevchuk Roman, Hub Jochen S
Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
Göttingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.
PLoS Comput Biol. 2017 Oct 18;13(10):e1005800. doi: 10.1371/journal.pcbi.1005800. eCollection 2017 Oct.
Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state.
小角X射线散射是一种越来越受欢迎的技术，用于检测溶液中的蛋白质结构和集合体。然而，由于小角X射线散射数据的信息含量低、未知的系统误差以及溶剂未知的散射贡献，根据小角X射线散射数据对结构和集合体进行精修往往具有不确定性。我们通过将贝叶斯推理与全原子分子动力学模拟以及显式溶剂小角X射线散射计算相结合，为这类问题提供了一个解决方案。贝叶斯公式正确地权衡了小角X射线散射数据与先前的物理知识，它量化了拟合结构和集合体的精度或不确定性，并且考虑了由于缓冲液匹配不佳导致的未知系统误差。该方法还提供了一个概率标准，用于确定解释小角X射线散射数据所需的状态数。通过针对计算出的小角X射线散射曲线精修周质结合蛋白的集合体，对该方法进行了验证。随后，我们根据实验小角X射线散射数据推导出真核伴侣热休克蛋白90（Hsp90）的溶液集合体。我们发现，Hsp90的无配体状态的小角X射线散射数据与单一的大开构象兼容，而与ATP或ATP类似物结合的Hsp90的小角X射线散射数据强烈表明存在封闭状态和大开状态的异质集合体。
