Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

• Published in: Nature communications 2024-10, Vol.15 (1), p.9310-17, Article 9310
• Main Authors: Son, Ahrum, Kim, Hyunsoo, Diedrich, Jolene K., Bamberger, Casimir, McClatchy, Daniel B., Lipton, Stuart A., Yates, John R.
• Format: Article
• Language: English
• Subjects: 631/1647/2067; 631/1647/296; 631/378/1689/1283; 631/57/2272/2273; 82/58; 82/80; Alzheimer Disease - metabolism; Alzheimer Disease - pathology; Alzheimer's disease; Animals; Complex systems; Disease Models, Animal; Footprinting; Humanities and Social Sciences; Humans; In vivo methods and tests; Lysine; Lysine - chemistry; Lysine - metabolism; Male; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Mice; Mice, Transgenic; multidisciplinary; Neurodegenerative diseases; Protein Conformation; Protein Folding; Protein Footprinting - methods; Protein structure; Proteins; Proteins - chemistry; Proteins - metabolism; Proteomes; Proteomics; Proteomics - methods; Proteostasis; Reagents; Science; Science (multidisciplinary); Therapeutic applications
• ISSN: 2041-1723; 2041-1723
• 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. This study introduces an in vivo protein footprinting method, revealing structural changes in proteome during progressing AD. It demonstrates these changes occur before expression alterations, advancing understanding of protein misfolding mechanisms.