Numerous studies have investigated changes in protein expression at the system level using proteomic mass spectrometry, but only recently have studies explored the structure of proteins at the proteome level. We developed covalent protein painting (CPP), a protein footprinting method that quantitatively labels exposed lysine, and have now extended the method to whole intact animals to measure surface accessibility as a surrogate of in vivo protein conformations. We investigated how protein structure and protein expression change as Alzheimer's disease (AD) progresses by conducting in vivo whole animal labeling of AD mice. This allowed us to analyze broadly protein accessibility in various organs over the course of AD. We observed that structural changes of proteins related to 'energy generation,' 'carbon metabolism,' and 'metal ion homeostasis' preceded expression changes in the brain. We found that proteins in certain pathways undergoing structural changes were significantly co-regulated in the brain, kidney, muscle, and spleen.
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.
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