Abstract

Recent advances in artificial intelligence have addressed a long-standing question in protein biophysics: What is the relationship between a protein’s primary sequence and its native three-dimensional structure? On the other hand, the process by which proteins navigate to these native states during their biosynthesis or following their denaturation is perilous, complex, and much less predictable. Many proteins misfold, a process which can sometimes be reverted through chaperones, but which is also associated with a wide range of ailments, particularly neurodegenerative diseases. We became interested in delineating which (kinds of) proteins are capable of refolding into their native conformations spontaneously versus which ones require chaperone assistance. To do so, we developed limited proteolysis mass spectrometry (LiP-MS) methods, a structural proteomic approach that can interrogate protein conformation and misfolding on the proteome scale. These experiments provide a holistic view of what properties facilitate refoldability and have highlighted an important and unexpected role for intrinsically disordered regions. I will also highlight a more recent study wherein we discovered a link between nonrefoldability and cognitive decline, by using LiP-MS to compare hippocampal proteins in old rats that have impaired cognition to those from age-matched animals that retain their spatial memory. These experiments uncover several hundred proteins that endure cognition-associated structural changes (CASCs), and provide evidence that the intersection between protein misfolding and age-related neurological disease expands beyond a small number of amyloid-forming proteins.