Using In Vivo Intact Structure for System-wide Quantitative Analysis of Changes in Proteins

Abstract 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 an approach using perfusion of reagents to create a whole animal in vivo protein footprinting method that adds dimethyl labels to exposed lysine residues on intact proteins to maintain information on protein conformations. When this approach was used to measure dynamic structural changes during Alzheimer’s disease (AD) progression in a mouse model, we detected 433 proteins that underwent structural changes attributed to AD, independent of aging, across 7 tissues. We identified structural changes of co-expressed proteins and linked the communities of these proteins to their biological functions. Our findings show that structural alterations of proteins precede changes in expression, thereby showing the value of in vivo protein conformation measurement. Our method represents a new 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 therapeutic interventions.