Structural polymorphism and cytotoxicity of brain-derived β-amyloid extracts

Abstract

To date, more than 37 amyloidogenic proteins have been found to form toxic aggregates that are implicated in the progression of numerous debilitating protein misfolding diseases including Alzheimer's disease (AD). Extensive literature highlights the role of β-amyloid (Aβ) aggregates in causing excessive neuronal cell loss in the brains of AD patients. In fact, major advances in our understanding of Aβ aggregation process, including kinetics, toxicity, and structures of fibrillar aggregates have been revealed by examining in vitro preparations of synthetic Aβ peptides. However, ongoing research shows that brain-derived Aβ aggregates have specific characteristics that distinguish them from in vitro prepared species. Notably, the molecular structures of amyloid fibrils grown in the human brain were found to be markedly different than synthetic Aβ fibrils. In addition, recent findings report the existence of heterogeneous Aβ proteoforms in AD brain tissue in contrast to synthetically produced full-length aggregates. Despite their high relevance to AD progression, brain-derived Aβ species are less well-characterized compared with synthetic aggregates. The aim of this review is to provide an overview of the literature on brain-derived Aβ aggregates with particular focus on recent studies that report their structures as well as pathological roles in AD progression. The main motivation of this review is to highlight the importance of utilizing brain-derived amyloids for characterizing the structural and toxic effects of amyloid species. With this knowledge, brain-derived aggregates can be adopted to identify more relevant drug targets and validate potent aggregation inhibitors toward designing highly effective therapeutic strategies against AD.

Keywords: Cryo-EM; cortical brain extracts; in vitro aggregation; natural amyloids; neurotoxicity; polymorphism; soluble oligomers; structural biology.

FIGURE 1

Schematic illustration of the overall extraction process of Aβ aggregates from brain tissues of deceased AD patients. Freshly frozen cortical brain samples are homogenized/soaked with extraction buffer and then centrifuged to obtain a soluble brain fraction supernatant and a mixture of insoluble brain fraction pellet. The insoluble pellet (1) is subjected to detergent‐containing buffer and/or formic acid to obtain solubilized amyloid‐enriched fibrils. On the other hand, the soluble brain fraction supernatant (2) is further subjected to ultracentrifugation and/or immunoprecipitation to selectively purify soluble Aβ oligomers and dimers.

FIGURE 2

Resolved ssNMR/Cryo‐EM structures of synthetically prepared Aβ_1–42/Aβ_1–40 fibrils. Top view representation was used to demonstrate the fibril symmetry (i.e., conformation and number of molecules per fibril layer). (a–i) Fibrillar models are generated on PyMol using the protein data bank entries and are colored based on secondary structure (yellow for β‐sheets and green for loops). The terms, positive and negative stagger, in panels f–i describe the conformation of Aβ_1–40 which spans two different z‐planes implying that each fibril layer is not occupied by a single Aβ_1–40 molecule.

FIGURE 3

Resolved ssNMR/Cryo‐EM structures of natural brain‐derived Aβ_1–42/Aβ_1–40 fibrils extracted from deceased AD cases. Top view representation was used to demonstrate the fibril symmetry (i.e., conformation and number of molecules per fibril layer). (a–e) Fibrillar models of brain‐derived fibrils are generated on PyMol using the protein data bank entries and are colored based on secondary structure (yellow for β‐sheets and green for loops). (a) Threefold morphology of brain derived Aβ_1–40 fibrils, PDB: 2M4J, from occipital, parietal and temporal cortical AD brain tissues. Structural calculations were performed to accurately determine the fibril structure of Aβ_1–40 (PDB: 2M4J) that is fully consistent with the experimental data. (b) Twofold morphology of brain‐derived Aβ_1–40 fibrils, PDB: 6SHS, from the meninges of severe AD and CAA (cerebral amyloid angiopathy). (c) Twofold morphology of brain‐derived Aβ_1–40 fibrils, PDB: 6W0O, from cortical tissues of AD patients with slightly left‐handed twist as revealed by cryo‐EM. (d and e) Twofold morphologies of brain‐derived Aβ_1–42 fibrils, extracted from cortical brain tissues of sporadic (type I in d) and familial (type II in e) AD cases.