Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) has emerged as a powerful technique to explore the conformational dynamics of proteins and protein complexes in solution. The bottom-up approach to MS uses peptides to represent an average of residues, leading to reduced resolution of deuterium exchange and complicates the interpretation of the data. Here, we introduce ReX, a method to infer residue-level uptake patterns leveraging the overlap in peptides, the temporal component of the data and the correlation along the sequence dimension. This approach infers statistical significance for individual residues by treating HDX-MS as a multiple change-point problem. By fitting our model in a Bayesian non-parametric framework, we perform parameter number inference, differential HDX confidence assessments, and uncertainty estimation for temporal kinetics. Benchmarking against existing methods using a three-way proteolytic digestion experiment shows our method's superior performance at predicting unseen HDX data. Moreover, it aligns HDX-MS with the reporting standards of other structural methods by providing global and local resolution metrics. Using ReX, we analyze the differential flexibility of BRD4's two Bromodomains in the presence of I-BET151 and quantify the conformational variations induced by a panel of seventeen small molecules on LXRalpha. Our analysis reveals distinct residue-level HDX signatures for ligands with varied functional outcomes, highlighting the potential of this characterisation to inform mode of action analysis.

中文翻译：

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使用 ReX 推断氢氘交换的残留水平

氢-氘交换质谱 (HDX-MS) 已成为探索溶液中蛋白质和蛋白质复合物构象动力学的强大技术。自下而上的 MS 方法使用肽来代表残基的平均值，导致氘交换的分辨率降低，并使数据的解释变得复杂。在这里，我们介绍 ReX，这是一种利用肽的重叠、数据的时间成分以及沿序列维度的相关性来推断残基水平摄取模式的方法。该方法通过将 HDX-MS 视为多变化点问题来推断单个残基的统计显着性。通过将我们的模型拟合到贝叶斯非参数框架中，我们可以执行参数数推断、差分 HDX 置信度评估以及时间动力学的不确定性估计。使用三向蛋白水解消化实验对现有方法进行基准测试表明，我们的方法在预测看不见的 HDX 数据方面具有卓越的性能。此外，它通过提供全局和局部分辨率指标，使 HDX-MS 与其他结构方法的报告标准保持一致。使用 ReX，我们分析了 I-BET151 存在下 BRD4 的两个 Bromodomain 的差异灵活性，并量化了 LXRalpha 上由 17 个小分子组成的组诱导的构象变化。我们的分析揭示了具有不同功能结果的配体的独特残基水平 HDX 特征，突出了这种表征为作用模式分析提供信息的潜力。