Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Abstract

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Figure 1.

Schematic representation of the amyloidogenic processing of APP. Aβ is produced by sequential processing of APP by bS and gS to produce either a soluble and nontoxic mixture of Aβ or a more amyloidogenic Aβ mixture with a propensity to form oligomers that bind PrP^c and potentially induce AD.

Figure 2.

(A) Overview of the gS and APP structures and pathogenic AD mutations. (A) Depiction of the gS complex (PDB 6IYC). NCT subunit (blue), APH-1A (green), PEN-2 (yellow), and the catalytic PSN subunit (pink) bound to a C99 fragment (red). C-alpha atoms from the PSN disease-causing mutations that affect C99 processing are shown (purple spheres). C99 disease causing mutations available in the 6IYC structure are shown (yellow spheres). (B) gS structure with the same color code as part A in a surface representation. (C) Depiction of a C99 structure model (gray) with the Aβ sequence highlighted (red). C-alpha atoms from disease causing mutations are shown in yellow spheres with the protective Icelandic mutant (green). (D) C99 sequence with mutations highlighted in the same color code representation and showing the two main Aβ production lines. The structures in parts A, B, and C from the PDB were drawn using VMD.

Figure 3.

Domain organization, isoforms of tau, and binding to microtubules. (A) Schematic of tau domain architecture and assigned functions. The MT-binding domain of four repeats is defined as residues 242 to 367. The inset shows the sequence alignment of the four repeat sequences, R1 to R4, that make up the repeat domain. Ser262 is marked by the asterisk. (B) Schematic representation of the six human tau isoforms and two tau constructs. Tau isoforms differ by the absence or presence of one or two 29-amino acid inserts in the amino-terminal part, in combination with either three (R1, R3, and R4) or four (R1–R4) repeat regions (black boxes) in the carboxy-terminal part. Isoform sizes range from 352 amino acids (aa) to 441 aa. (C) Model of full-length tau binding to microtubules and tubulin oligomers. (D) Schematic representation of the largest isoform of tau with specific phosphorylation sites. Serine, threonine, and tyrosine residues that can be phosphorylated in AD, PD, and dementia with Lewy bodies (DLB) are indicated.

Figure 4.

Key αS domains having a role in functional and pathological contexts. The membrane-binding domain (residues 1 to 90), the NAC region (residues 61 to 95), and the C-terminal domain (residues 98 to 140) are shown in blue, orange, and red, respectively. The diagram also shows the main pathological mutations (black) and key post-translational modifications (red) such as the N-terminal acetylation and phosphorylation of residues Ser87, Ser129, and Tyr39.

Figure 5.

Orthogonal view of the three-dimensional structural models of tau filaments and α-synuclein amyloid fibrils. NTD and CTD are the N-terminal and C-terminal domains. (A) Solid-state tau paired PHF spanning residues 306–378 in the right protofilament. (B) Cryo-EM PHF and SF tau amyloid cores in AD. In chronic traumatic encephalopathy (CTE), tau filaments contain predominantly the type I (90%) and type II filaments. The interprotofilament interfaces are different compared to those in AD. (C) Amyloid core of human α-synuclein amyloid fibrils (PDB 2NOA), containing a Greek-key fold. (D and E) Amyloid core fibril structure of α-synuclein: polymorph rod 1a (PDB entry 6CU7) and polymorph twister 1b (PDB entry 6CU8). The authors prepared the figure with pymol.

Figure 6.

(A) Orthogonal view of Aβ40 structures (PDB entries 2LMN and 2LMP) spanning residues 9–40 and Aβ42 structures (PDB entries 2NAO and 5OQV) spanning residues 1–42. (B) Cryo-EM structure of Aβ42 showing the staggered arrangement of nonplanar Aβ42 subunits. (C) Cryo-EM structure of IAPP grown at physiological pH (PDB 6Y1A) spanning residues 13–37. The authors designed the figure with pymol.

Figure 7.

High-resolution structures of amyloid oligomers in solution or membrane-bound state solved using X-ray and NMR methods, with the exception being the model of Aβ40 assembly toxic surface (top, right).

Figure 8.

Protein representations from all-atom to coarse-grained models. (A) All-atom. (B) OPEP. (C) Geometric representation of the protein intermediate-resolution model, PRIME, for polyalanine. Covalent bonds are shown with thick gray lines connecting united atoms for N–H, C=O, Cα-H, and CH3 side chain. At least one of each type of pseudobond is shown with a colored line. Pseudobonds are used to maintain backbone bond angles, consecutive Cα distances, and l-isomerization. The united atoms are not shown full size for ease of viewing. (D) UNRES. (E) Shea’s model.

Figure 9.

Protein representations from coarse-grained to mesoscopic models. (A) SIRAH. (B) SOP-IDP. (C) Caflisch’s model. (D) Frenkel’s model.

Figure 10.

(A–E) Simulation snapshots of non-HB oligomer; HB oligomer; and two, three, and four β-sheet fibrils, respectively. The peptides in the five aggregates and in solution are shown in green and magenta, respectively. (F) Phase diagram for Aβ_16–22 peptide. Solubility, C_e, versus temperature data for the oligomer and fibril. The fibril and solution phases are colored yellow and cyan, respectively. (G) Summary of both the simulation-predicted temperature-dependent solubility line, C_e(T), for Aβ_16–22 peptide (black curve) and the fibrillation experiments performed under given conditions. Red dots and red circles indicate conditions at which fibrils have been found to form and not to form, respectively, via TEM. Blue dots indicate that fibrils have been reported in the literature^– to form under these conditions. (H) Six selected TEM images (i–vi) showing that Aβ_16–22 forms fibrils under conditions that correspond to the six red dots labeled i–vi in part A. (Scale bar: 200 nm.) Reprinted with permission from ref . Copyright 2019 National Academy of Science.

Figure 11.

(A) Schematic representation of two extreme scenarios, the one-step and the two-steps nucleation process for early steps of amyloid aggregation. (B) Characteristic steps and kinetics of Aβ42 amyloid proliferation determined experimentally, with the reaction rates at a concentration of 5 microM. (C) Description of the dock and lock mechanism, left chart schematically reproduces the results, where the evolution of the β-structure of a monomer is followed in time during the dock and lock phases. (D) Effect of hydrodynamic interactions on the aggregation process of Aβ_16–22 peptides (left) and protofibril elongation due to oligomer fusion (right) as observed in LBMD simulations.^,

Figure 12.

Unfolding and stability of SOD1 in crowded conditions.^, (A) Snapshot from a 1 μs coarse-grain LBMD simulation of loop-truncated SOD1 monomers immersed in a 200 g/L BSA solution. (B) Representative states of local packing around SOD1 extracted from the coarse-grain simulation and converted into a fully all-atom representation. (C) Thermal stability—calculated using enhanced-sampling all-atom simulations—of SOD1 in the different states of local packing. The stability of the SOD1 monomer is expressed by means of the secondary-structure content of the protein. Comparison with a result obtained in dilute conditions reveals only a weak effect induced by crowding. (D) Semiunfolded intermediate state observed in the enhanced-sampling all-atom simulations. The blue clouds, representing the spatial distribution of BSA atoms in contact with SOD1, show that the denaturated region has an increased probability to interact with the crowder.

Figure 13.

(A) N-terminus (blue, 1–15), CHC (green, 16–21), loop (gray, 22–29), and C-terminus (purple, 30–40/42). (B) Schematic free energy landscape of Aβ monomers. Switching between some conformations occurs within 35 ns, as reported by FRET data. The conformation of S-shape N* from the fibril structure with PDB ID 2NAO was also sampled in CG simulations. (C) Representative structure of the Aβ42 tetramer, obtained by using multiscale MD simulation. Blue and orange balls refer to the first and last residues, respectively, of monomer subunits. (D) Population of oligomer sizes obtained from simulations of 20-peptides.

Figure 14.

Representative structures of the αS conformational ensemble obtained by short-distance cross-linking constraint-guided DMD simulations. Conformers A, B, C, and D represent the first four clusters. Structures are colored from blue (N-terminus) to red (C-terminus). The figure was created using Pymol.

Figure 15.

(A) Sequence alignment of the R1–R4 repeats and the sequence after R4 that are part of the CBD and AD fibril cores. The positions of filamentous β strands in both diseases are shown. PTMs detected by MS in tau fibrils from CBD case 1 and AD. The cryo-EM structures are shown with acetylation, ubiquitination, trimethylation, and phosphorylation sites marked with blue, orange, red, and green balls, respectively. Side chains with multiple PTMs detected are shown with two colors. (B and C) PTMs mapped onto schematics of the protofilament structures from (B) CBD case 1 and (C) AD. The same color scheme as described above is used to depict PTMs. (D) cis pT231-tau is highly neurotoxic and acts as an early driver of tauopathy, with bipolar illustrated here. (E) Snapshot from the simulation showing the α-helix and two salt bridge interactions (pThr231-Arg242 and pSer235-Arg242) of peptide htau_225–250.

Figure 16.

Schematic diagram of 4-repeat (2N4R) and 3-repeat (2N3R) human tau isoforms. The microtubules binding region (MBD) is highlighted, and the sequences for the repeat units are shown along with the hexapeptides PHF6* and PHF6.

Figure 17.

(a) Schematic representation of Tau and RNA models. Tau and RNA are modeled as chains of bonded monomeric units with size b in implicit solvent. The charge of each monomer is determined from the corresponding amino acid in the tau sequence at pH = 7. RNA is modeled as a uniformly charged polyanion. (b) Tau solution phases at fixed total density: (b-1) single phase solution in weak electrostatic strength and good solvent conditions (l_B = 0.16 b, v = 0.02 b³); (b-2) two phase coacervate in relatively strong electrostatic interaction and low solvent quality (l_B = 3.25 b, v = 0.0068 b³). (c) Coexistence phase boundary determined from FTS as a function of the Bjerrum length and tau density at fixed excluded volume of v = 0.0068 b3. (d) Binodal points as a function of the excluded volume at fixed Bjerrum length l_B = 1.79 b.

Figure 18.

Coexistence points obtained from parametrized FTS at low salt (filled green circles) and at 120 mM NaCl (open green circles) as compared to experimental cloud point temperature as measured in turbidity experiments performed at 20 mM NaCl (filled red circles) and 120 mM (filled blue circles). The experimentally determined cloud point temperature corresponds to the low-density branch of the phase diagram. FTS simulations also predict the corresponding high-density branch of the binodal curve.

Figure 19.

Different interaction models of full-length Aβ_40/42 peptides with lipid membranes. (a) Aβ transmembrane pores with high Ca²⁺ permeability and selectivity. (b) Tetrameric Aβ₄₂ β-barrel pores in PC/PS/cholesterol/sphingomyelin and DPPC bilayers. (c) Tetrameric Aβ₄₂ α-helix-bundle pores in a DPPC bilayer with Ca²⁺ transport across the bilayer. (d) Aβ₄₂ monomer with both α-helical and β-structure conformations being adsorbed on cholesterol-rich POPC bilayers, where increase of cholesterol promotes Aβ-membrane interactions and adsorption. (e) Aβ dimers on the GM1-clustering membrane, with C-terminal residues being inserted into the membrane. (f) Aβ tetramers with typical U-bent β-structure being preferentially adsorbed on and inserted into the POPE bilayer over the POPC bilayer, as driven by electrostatic interactions. (g) Aβ₄₂ pentamer being adsorbed onto a POPC/POPG bilayer via Ca²⁺ ionic bridges between Glu22 and Asp23 and anionic headgroups of the lipid bilayer.

Figure 20.

Typical interaction model of hIAPP monomer with lipid bilayers via a three-step approaching–adsorption–insertion process. The hIAPP monomers with the disordered structures approach the cell membrane to establish initial contacts with their N-terminal residues via electrostatic interactions, then adjust their orientation parallel to membrane surfaces with hydrophobic residues facing toward hydrophobic tails of lipids, and finally tend to insert partially or fully into cell membranes. During the whole process, hIAPP monomers always involve the conformational changes from the bulk phase to the membrane surface to the membrane interior for inducing their potential membrane-disruption activity.

Figure 21.

Different interaction models of full-length hIAPP_1–37 oligomers with lipid membranes. (a) hIAPP dimers with α-helical structure insert into POPG bilayers with different insertion depths, strongly depending on interactive contacts of hIAPP dimers with POPG bilayers. (b) hIAPP pentamer with U-bent β-structures to be partially inserted into (left) DPPG and (right) DPPC/DPPG bilayers via the turn region. (c) hIAPP pentamer with U-bent β-structures to be adsorbed on (left) POPC and (right) POPG/POPE bilayers with different hIAPP orientations. (d) Double hIAPP pores with different (left) “turn-to-tail” and (right) “tail-to-turn” orientations in DOPC bilayers to show nonselective, ion-permeable activity.

Figure 22.

Pathological process of tau production, hyperphosphorylation, oligomerization, fibrillization, and interaction with cell membranes.

Figure 23.

Membrane binding by monomeric and oligomeric αS. (A) Monomeric αS is disordered in solution (red) and binds the membrane with three regions having distinct structural and dynamical properties. The N-terminal region (blue) acts as a rigid membrane anchor. The central region (gray) is in conformational exchange between membrane-bound (helical) and detached (disordered) conformations. The C-terminal region (green) remains essentially unbound from the membrane. (B) The membrane binding by toxic αS oligomers involves N-terminal regions (blue) of αS molecules from the oligomer, strongly anchoring the oligomers to the membrane surface in a cooperative manner, and the prefibrilar β-sheeted rigid core (red), inserting into the lipid bilayer and disrupting its integrity.

Figure 24.

Coordination spheres of Aβ, αS, IAPP, and tau peptides and some variants with Cu(I), Cu(III), and Zn(II). Generally, the most populated states at pH 7.4 are shown. Often several coordination spheres (states) are present and differently populated. They are in fast equilibrium. An exception is Cu(II)-Aβ4–40/2 which has a well-defined coordination sphere. Abbreviations: NH₂, N-terminal amine; N^Im, nitrogen of imidazole ring of a His; N⁻, nitrogen of an amidate; N, any nitrogen of unknown ligand. Review and references.^–

Figure 25.

Proposed mechanism of ROS production by a Cu–peptide (Cu-P) in the presence of a reducing agent (Red⁻) and dioxygen.

Figure 26.

High-resolution structural characterization of zinc binding sites to Alzheimer’s Aβ. (A) At physiological pH (7.4), zinc was proposed to tetrahedrally bind with Aβ where the coordination sphere is contributed from two of three histidine (H6, H13, and H14) residues and two carboxylate side chains (E11 and one from D1, E3, or D7). (B) Superimposition of 20 NMR model structures of Taiwanese mutant Aβ fragment (D7H-Aβ_1–10) showing zinc (gray sphere) induced formation of a homodimer. The dimer is stabilized by two zinc ions where one coordinates to D1 and H6 of one Aβ subunit and the other to H7 and E3 orienting the H6 residue of both subunits to form stacking interactions.^,

Figure 27.

High-resolution NMR model structure of IAPP in the absence or presence of zinc. Full-length NMR structure of IAPP (top) and Zn-IAPP complex (bottom). Zinc binding to His18 (green sticks) induces helical perturbation and formation of a helix–kink–helix conformation. NMR model structures of IAPP_1–19 and IAPP_1–19 obtained from 2D ¹H/¹H TOCSY and NOESY experiments. Zinc binding transforms the disordered N-terminus (left) to an ordered structure (right).^,

Figure 28.

Metal binding sites and post-translational modifications of αS. αS harbors three binding sites for metal ions (displayed with colored circles): the low affinity, nonspecific metal binding site at the acidic DPDNEA segment in the C-terminal, the His50 site, and the first five residues at the N-terminal. His50 can anchor transition-metal ions such as Zn(II), Fe(III), and Fe(II), but the highest affinity is found for Cu(II) and Cu(I) ions. The N-terminus of αS is a high affinity and highly specific site for Cu ions. Reprinted with permission from ref . Copyright 2021 John Wiley and Sons.

Figure 29.

Mutations, modifications, and structural elements of SOD1. The crystal structure of SOD1^WT is shown in the top panel (pdb: 2V0A) with the zinc binding loop, loop IV, spanning residues 49–84 (yellow) and the electrostatic loop, loop VII, spanning residues 122–143 (orange). The most prevalent ALS associated mutations are shown on the left monomer (green), and three SOD1 destabilizing post-translational modifications are shown on the right monomer (green). The bottom panel shows a possible trimeric structure of SOD1 modeled by Procter et al. The authors designed the figure with Pymol.

Figure 30.

Chemical structures of a few selected small molecules that are shown to inhibit amyloid aggregation, remodel aged fibers, and/or promote Aβ or IAPP fibrillation.

Figure 31.

Chemical structures and the binding poses of the seven natural ligands to (A) 4Aβ_11–42 peptides (PDB 2MXU),, (B) αS (2X6M), (C) hIAPP (6Y1A), (D) insulin (1GUJ), and (E) SOD1 (6FLH). Binding poses were obtained by Autodock vina with exhaustiveness of 8 and a grid of 60 × 60 × 60 Å covering the whole receptor. Astaxanthin, brazilin, curcumin, dopamine, EGCG, resveratrol, and rosmarinic acid are highlighted in red, green, light blue, blue, yellow, magenta, and orange, respectively.

Figure 32.

Schematic representation of the molecular mechanisms by which carbon nanoparticles (CNPs) and small molecules inhibit the aggregation of proteins/peptides discussed in this review. Amyloid proteins can self-assemble into toxic β-sheet-rich oligomers (such as β-barrels) and protofibrils/fibrils. CNPs/small molecules can prevent β-sheet formation and disassemble preformed protofibrils/fibrils through physical interactions and finally lead to the inhibition of protein amyloid formation. CNPs include graphene, fullerene, carbon nanotube (CNT), and their derivatives (such as hydroxylated CNT/fullerene, graphene oxide, and graphene quantum dot). Many small-molecule inhibitors have been reported in the literature, such as dopamine, EGCG, curcumin, and resveratrol. Due to space limitations, only fullerene, carbon nanotube, dopamine, and EGCG are illustrated in the diagram.

Figure 33.

Images of the GNNQQNY fibril sample prior to and after laser irradiation of the GNNQQNY obtained from scanning EM experiment (A) and simulation (B). Their secondary structures are in (C).

Figure 34.

Co-occurring pathologies across common neurodegenerative diseases. Schematic illustrating the relative proportions (numbers within colored disks) of amyloid pathologies formed of Aβ (blue), tau (pink), and αS (green) within each disease class. Question marks indicate unknown proportions for hybrid assemblies (i.e., Aβ/tau, Aβ/αS, αS/tau, and Aβ/αS/tau). The numbers inserted within the colored disks are taken from ref .

Figure 35.

Cross-seeding and coaggregation of amyloid proteins. Schematic illustrating the in vitro formation of amyloids (depicted by different shapes) including oligomers, protofibrils, and fibrils from tau (pink), αS (green), Aβ (blue), IAPP (orange), and PrP (gray) proteins. This scheme also summarizes the in vitro formation of coaggregates (αS:tau, Aβ:αS, Aβ:IAPP, Aβ:PrP, tau:PrP) by cross-seeding/coaggregation mechanism demonstrated in various studies. Different shapes, colors, and their numbers used here arbitrarily represent amyloid aggregates; they do not indicate aggregates of any specific size or shape.