Alzheimer's disease (AD) is the most common representation of
dementia, with brain pathological hallmarks of
protein abnormal aggregation, such as with
amyloid beta and
tau protein. It is well established that posttranslational modifications on
tau protein, particularly phosphorylation, increase the likelihood of its aggregation and subsequent formation of neurofibrillary tangles, another hallmark of AD. As additional misfolded
proteins presumably exist distinctly in AD disease states, which would serve as potential source of AD
biomarkers, we used limited proteolysis-coupled with mass spectrometry (LiP-MS) to probe
protein structural changes. After optimizing the LiP-MS conditions, we further applied this method to human cerebrospinal fluid specimens collected from healthy control,
mild cognitive impairment (MCI), and AD subject groups to characterize
proteome-wide misfolding tendencies as a result of
disease progression. The fully tryptic
peptides embedding LiP sites were compared with the half-tryptic
peptides generated from internal cleavage of the same region to determine any structural unfolding or misfolding. We discovered hundreds of significantly up- and down-regulated
peptides associated with MCI and AD indicating their potential structural changes in AD progression. Moreover, we detected 53 structurally changed regions in 12
proteins with high confidence between the healthy control and disease groups, illustrating the functional relevance of these
proteins with AD progression. These newly discovered conformational
biomarker candidates establish valuable future directions for exploring the molecular mechanism of designing therapeutic targets for AD.