Incorporation of D2O-Induced Fluorine Chemical Shift Perturbations into Ensemble-Structure Characterization of the ERalpha Disordered Region.
Incorporation of D2O-Induced Fluorine Chemical Shift Perturbations into Ensemble-Structure Characterization of the ERalpha Disordered Region.
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DOI：
10.1021/acs.jpcb.2c05456
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发表时间：
2022-11
期刊：
影响因子：
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通讯作者：
Wenwei Zheng;Zhanwen Du;Soobin Ko;Nalinda P. Wickramasinghe;Sichun Yang
中科院分区：
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作者：
Wenwei Zheng;Zhanwen Du;Soobin Ko;Nalinda P. Wickramasinghe;Sichun Yang
内在无序蛋白质（IDP）的结构表征需要实验和计算之间的协同努力，通过占其构象异质性。由于提供局部和全局结构信息的实验工具的多样性，构建一个实验约束满足结构合奏仍然具有挑战性。在这里，我们使用雌激素受体α（ER α）的无序N-末端结构域（NTD）作为模型系统，结合联合收割机现有的小角X射线散射（SAXS）和羟基自由基蛋白质足迹（HPF）数据和新获得的溶剂可及性数据，通过D2O诱导的氟化学位移（DFCS）测量。添加了一组新的DFCS数据的溶剂暴露的一组12个氨基酸的位置，以补充先前获得的HRPF测量的溶剂暴露的其他16个不重叠的氨基酸，从而大大提高了NTD合奏表征。我们还发现，虽然选择从不同的原子级力场或采样/建模方法生成的结构的初始系综可以导致不同的接触图，即使当相同的实验测量集用于系综拟合时，这些初始系综的比较分析揭示了它们的系综平均接触图中常见的重复结构特征。具体而言，非本地或远程瞬态相互作用被发现一致的N-末端片段和中心区域之间，足以介导的构象合奏和调节如何的NTD与其共激活蛋白相互作用。
Structural characterization of intrinsically disordered proteins (IDPs) requires a concerted effort between experiments and computations by accounting for their conformational heterogeneity. Given the diversity of experimental tools providing local and global structural information, constructing an experimental restraint-satisfying structural ensemble remains challenging. Here, we use the disordered N-terminal domain (NTD) of the estrogen receptor alpha (ERalpha) as a model system to combine existing small-angle X-ray scattering (SAXS) and hydroxyl radical protein footprinting (HRPF) data and newly acquired solvent accessibility data via D2O-induced fluorine chemical shifting (DFCS) measurements. A new set of DFCS data for the solvent exposure of a set of 12 amino acid positions were added to complement previously acquired HRPF measurements for the solvent exposure of the other 16 nonoverlapping amino acids, thereby improving the NTD ensemble characterization considerably. We also found that while choosing an initial ensemble of structures generated from a different atomic-level force field or sampling/modeling method can lead to distinct contact maps even when the same sets of experimental measurements were used for ensemble-fitting, comparative analyses from these initial ensembles reveal commonly recurring structural features in their ensemble-averaged contact map. Specifically, nonlocal or long-range transient interactions were found consistently between the N-terminal segments and the central region, sufficient to mediate the conformational ensemble and regulate how the NTD interacts with its coactivator proteins.