Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer's Disease.
Misfolding and aggregation of amyloid-β peptide and hyperphosphorylated tau are molecular markers of Alzheimer's disease (AD), and although the 3D structures of these aberrantly folded proteins have been visualized in exquisite detail, no method has been able to survey protein folding across the proteome in AD. Here, we present covalent protein painting (CPP), a mass spectrometry-based protein footprinting approach to quantify the accessibility of lysine ε-amines for covalent modification at the surface of natively folded proteins. We used CPP to survey the reactivity of 2645 lysine residues and therewith the structural proteome of HEK293T cells and found that reactivity increased upon mild heat shock. CPP revealed that the accessibility of lysine residues for covalent modification in tubulin-β (TUBB), in succinate dehydrogenase (SHDB), and in amyloid-β peptide (Aβ) is altered in human postmortem brain samples of patients with neurodegenerative diseases. The structural alterations of TUBB and SHDB in patients with AD, dementia with Lewy bodies (DLB), or both point to broader perturbations of the 3D proteome beyond Aβ and hyperphosphorylated tau.
['Bamberger|Casimir|C|0000-0002-3830-4486', 'Pankow|Sandra|S|', 'Martínez-Bartolomé|Salvador|S|0000-0001-7592-5612', 'Ma|Michelle|M|', 'Diedrich|Jolene|J|', 'Rissman|Robert A|RA|', 'Yates|John R|JR|0000-0001-5267-1672']
D000544:Alzheimer Disease D016229:Amyloid beta-Peptides D057809:HEK293 Cells D006801:Humans D023302:Protein Footprinting D020543:Proteome D016875:tau Proteins
structural proteomics neurodegenerative diseases MudPIT bottom-up proteomics chemical footprinting conformational diagnostics diffuse Lewy body disease isobaric isotopologue molecular diagnostics protein surface mapping quantitative mass spectrometry