Amyloidogenesis: What Do We Know So Far?

Abstract

The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.

Keywords: Aβ peptide; COVID-19 and amyloidosis; amyloid precursor protein; amyloid related diseases; amyloid structure analysis; amyloids; fibril formation; physical techniques in amyloid analysis; protein aggregation.

Figure 3

Common biophysical techniques used in the characterization of amyloid fibrils: (a): CD spectra of Aβ 42 fibrils in presence and absence of TTR (figure adopted from [67]; (b): the intrinsic fluorescence of nFGF-1 in various concentrations of TFE (the figure was adopted from reference [71]; (c): staining with red Congo of plant (Prasiola linearis adhesive) (the figure adopted from [76]); (d): the X-ray fiber diffraction of the n-FGF1 fibrils induced by TFE (the figure was adopted from reference [77]); (e): FTIR for native (1) and (2) fibrils TTR (the figure was adopted from [97]; (f): TEM of fibrils extracted from heart tissue samples (the figure was adopted from reference [89]); (g): AFM of Aβ 1–40: aggregation of Aβ-1–40 (the figure was adopted from [92]; (h): the linewidths of 13C NMR for CO, Cα, and Cβ location in Aβ1–40 fibrils (the figure was adopted from [94]); (i): analysis of cerebral cortex Aβ by mass spectrometry. The broad peak reveals the non-homogenous shape of the protein (figure was adopted from reference [95]).

Figure 1

Chronology of events in the history of amyloid research.

Figure 2

The structural features of amyloid fibrils: (a) 3D map of ATTR amyloid fibril constructed from cryo-EM image. Cyan depicts the N-terminus residue density and ochre depicts the C-terminus residue density (figure reproduced from [52]); (b) typical cross-beta-sheet motifs found in amyloids (the figure reproduced from [53]); (c) top and side views of the cartoon depiction of an amyloid fibril fragment showing the non-planar sub-units in a staggered conformation. The top view depicts a dry interface devoid of water formed due to interdigitation of the side chains of residues on opposite chains; (d) secondary structure and hydrophobicity mappings on the amyloid beta fibrils. The hydrophobic interactions in the core (red) bear testimony to its exceptional thermodynamic stability.

Figure 4

The canonical amyloid precursor protein (APP) processing pathways: (a) processing by α-secretase along the non-amyloidogenic pathway occurs in the amyloid-β (Aβ) region, liberates APPsα (α-secretase-generated APP ectodomain fragment) and generates p3; (b) processing along the amyloidogenic pathway generates Aβ (through β-secretase and γ-secretase cleavage) and liberates APPsβ. The schematic shows the non-canonical APP processing; (c) cleavage by δ-secretase produces three soluble APPsδ fragments and C-terminal fragment-δ (CTFδ), which are further processed by β-secretase and γ-secretase; (d) cleavage by meprin-β at three sites gives rise to three soluble fragments (top right panel). APPsβ* contains one additional residue compared with APPsβ; (e) cleavage by η-secretase gives rise to soluble APPsη and CTFη, which is further processed by α-secretase or β-secretase to generate Aη-α or Aη-β; (f) caspases cleave within the intracellular domain to yield C31 and after subsequent γ-secretase cleavage.

Figure 5

(a) Structure and sequence of human Aβ peptide; (b) amylin binds with Aβ peptide through its various interacting residues, resulting in a strong association (binding affinity energy = −8.83 kcal/mol; (c) possible interacting residues of human amylin-red (PDB ID: 2L86) and β sheet structure of Aβ1–42-magenta (PDB ID:2BEG); (d) computational analysis of disorder (red curve) and aggregation promoting(magenta) regions on human amylin-red (PDB ID: 2L86) upon binding with interacting residues (yellow) of Aβ1–42 (PDB ID:2BEG). (Figure b–d were reproduced from [151]).

Figure 6

Primary sequence of the Aβ peptide in different organisms arranged in lexicographical order. The sequence is highly conserved except for rare point amino acid mutations in some organisms.

Figure 7

Aggregation mechanisms: (a) the potential energy surface for a protein folding process. The competing basins of attractions are populated by the folding intermediates which have higher energy than the native folded protein. The native basin of attraction is a low-lying critical point, populated by the functionally folded native protein. The aggregated being thermodynamically stabler lie even more downhill, populating the lowest points of the PES; (b) various mechanisms for modeling protein aggregation: reversible oligomerization of the native monomers leading to irreversible macroaggregates; (c) conformational change of native monomer followed by b1 mechanism; (d) microaggregate/contaminant induced surface aggregation leading to irreversible polymerization and aggregation; (e) aggregation induced at phase interface or on rough surfaces.

Figure 8

Self-assembly of amyloid fibrils is triggered and facilitated by a number of preceding processes, which include prenucleation and nucleation, secondary growth, and elongation processes, occurring both chronologically and simultaneously to yield the thermodynamically stable fibrils.

Figure 9

Sigmoidal kinetic curve for amyloid formation probed by using ThT fluorescence. Thioflavin T bound to polymeric amyloid fibrils and increase in fluorescence intensity signaled increased formation of amyloid fibrils. The nascent unfolded polypeptide may either drop down into a native folding cascade via partially folded intermediates (1) and/or may directly be recruited in nucleus formation (3). The native monomer similarly can either undergo partial unfolding (2) and/or associate with the forming nucleus (4,5). When concentration of amyloid fibrils increases significantly, the secondary processes (6) take over as the dominant.

Figure 10

SARS-CoV-2 induced acute respiratory syndromes lead to upregulation of ROS and inflammation that can potentially lead to amyloidosis.