Dissecting the Structural Organization of Multiprotein Amyloid Aggregates Using a Bottom-Up Approach

Deposition of fibrillar
amyloid β (Aβ) in senile plaques
is a pathological signature of Alzheimer’s disease. However,
senile plaques also contain many other components, including a range
of different proteins. Although the composition of the plaques can
be analyzed in post-mortem tissue, knowledge of the molecular details
of these multiprotein inclusions and their assembly processes is limited,
which impedes the progress in deciphering the biochemical mechanisms
associated with Aβ pathology. We describe here a bottom-up approach
to monitor how proteins from human cerebrospinal fluid associate with
Aβ amyloid fibrils to form plaque particles. The method combines
flow cytometry and mass spectrometry proteomics and allowed us to
identify and quantify 128 components of the captured multiprotein
aggregates. The results provide insights into the functional characteristics
of the sequestered proteins and reveal distinct interactome responses
for the two investigated Aβ variants, Aβ(1–40)
and Aβ(1–42). Furthermore, the quantitative data is used
to build models of the structural organization of the multiprotein
aggregates, which suggests that Aβ is not the primary binding
target for all the proteins; secondary interactions account for the
majority of the assembled components. The study elucidates how different
proteins are recruited into senile plaques and establishes a new model
system for exploring the pathological mechanisms of Alzheimer’s
disease from a molecular perspective.