Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.
Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea.
Nat Commun. 2024 Oct 29;15(1):9310. doi: 10.1038/s41467-024-53582-x.
Mass spectrometry-based methods can provide a global expression profile and structural readout of proteins in complex systems. Preserving the in vivo conformation of proteins in their innate state is challenging during proteomic experiments. Here, we introduce a whole animal in vivo protein footprinting method using perfusion of reagents to add dimethyl labels to exposed lysine residues on intact proteins which provides information about protein conformation. When this approach is used to measure dynamic structural changes during Alzheimer's disease (AD) progression in a mouse model, we detect 433 proteins that undergo structural changes attributed to AD, independent of aging, across 7 tissues. We identify structural changes of co-expressed proteins and link the communities of these proteins to their biological functions. Our findings show that structural alterations of proteins precede changes in expression, thereby demonstrating the value of in vivo protein conformation measurement. Our method represents a strategy for untangling mechanisms of proteostasis dysfunction caused by protein misfolding. In vivo whole-animal footprinting should have broad applicability for discovering conformational changes in systemic diseases and for the design of therapeutic interventions.
基于质谱的方法可以提供复杂系统中蛋白质的全局表达谱和结构读数。在蛋白质组学实验中，保持蛋白质在其天然状态下的体内构象是具有挑战性的。在这里，我们引入了一种使用灌注试剂的整体动物体内蛋白质足迹分析方法，将二甲基标签添加到完整蛋白质上暴露的赖氨酸残基上，从而提供有关蛋白质构象的信息。当我们使用这种方法来测量阿尔茨海默病（AD）小鼠模型中进展过程中的动态结构变化时，我们在 7 种组织中检测到 433 种蛋白质发生了与 AD 相关的结构变化，而与衰老无关。我们确定了共表达蛋白质的结构变化，并将这些蛋白质的社区与其生物学功能联系起来。我们的研究结果表明，蛋白质结构的改变先于表达的改变，从而证明了体内蛋白质构象测量的价值。我们的方法代表了一种用于解决由蛋白质错误折叠引起的蛋白质稳态功能障碍机制的策略。体内整体动物足迹分析应该具有广泛的适用性，可以用于发现系统性疾病中的构象变化，并设计治疗干预措施。
