Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

The 3D structures of aberrant protein folds have been visualized in exquisite detail, yet no method has been able to quantitatively measure protein misfolding across a proteome. Here, we present Covalent Protein Painting (CPP), a mass spectrometry-based structural proteomics approach to quantify the accessibility of lysine {varepsilon}-amines for chemical modification at the surface of natively folded proteins. We used CPP to survey 2,645 lysine residues in the proteome of HEK293T cells in vivo and found that mild heat shock increased rather than decreased lysine accessibility for chemical modification. CPP was able to differentiate patients with Alzheimer disease (AD) or Lewy body disease (LBD) or both from controls based on relative accessibility of lysine residues K147, K137, and K28 in Tubulin-{beta}, Succinate dehydrogenase, and amyloid-{beta} peptide, respectively. The alterations of Tubulin-{beta} and Succinate dehydrogenase hint to broader perturbations of the proteome in AD beyond amyloid-{beta} and hyper-phosphorylated tau.