Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer

Abstract

The relationship between amyloid deposition and cellular toxicity is still controversial. In addition to fibril-forming oligomers, other soluble Aβ forms (amyloid β-derived diffusible ligands (ADDLs)) were also suggested to form and to present different morphologies and mechanisms of toxicity. One ADDL type, the "globulomer," apparently forms independently of the fibril aggregation pathway. Even though many studies argue that such soluble Aβ oligomers are off fibril formation pathways, they may nonetheless share some structural similarity with protofibrils. NMR data of globulomer intermediates, "preglobulomers," suggested parallel in-register C-terminal β-sheets, with different N-terminal conformations. Based on experimental data, we computationally investigate four classes of Aβ dodecamers: fibril, fibril oligomer, prefibril/preglobulomer cluster, and globulomer models. Our simulations of the solvent protection of double-layered fibril and globulomer models reproduce experimental observations. Using a single layer Aβ fibril oligomer β-sheet model, we found that the C-terminal β-sheet in the fibril oligomer is mostly curved, preventing it from quickly forming a fibril and leading to its breaking into shorter pieces. The simulations also indicate that β-sheets packed orthogonally could be the most stable species for Aβ dodecamers. The major difference between fibril-forming oligomers and ADDL-like oligomers (globulomers) could be the exposure of Met-35 patches. Although the Met-35 patches are necessarily exposed in fibril-forming oligomers to allow their maturation into fibrils, the Met-35 patches in the globulomer are covered by other residues in the orthogonally packed Aβ peptides. Our results call attention to the possible existence of certain "critical intermediates" that can lead to both seeds and other soluble ADDL-like oligomers.

FIGURE 1.

The structure and dynamics of two Aβ fibril models (F1 and F2) indicate the importance of the Met-35 patch in fibril formation. Each model consists of two hexamers organized in parallel that are packed together to yield a dodecamer. Each hexamer is a layer. The monomer has the well accepted U-shaped conformation. In the figure, the two U-shaped β-sheet layers are depicted in red and green ribbons. The Met-35 surface patches are highlighted (yellow balls are sulfur atoms, and red balls Met-35 are backbone oxygen). The coordinates are taken at the end of 60-ns simulations. A, the F1 model with turn structure based on the Luhrs structure (3). B, F2 model with turn structure based on Tycko's and our models (31, 33). C and D, the RMSD from averaged structures for both F1 (C) and F2 (D) show a flexible N-terminal and stable core structure. E, the distribution of the distances between the Cα atoms of the C-terminal residues 31–39 of two layers. F, the distribution of the distances between the heavy atoms of Met-35 with the heavy atoms in the C terminus of the next layer. The distance distributions for profibril oligomer P2 are also reported in E and F for comparison.

FIGURE 2.

Comparison of simulations with experiment: the simulated amide hydrogen protection factor (NH solvation on the y axis) versus the experimental H/D exchange NMR observations (x axis). On the x axis, the residue number and type are listed, and the H/D exchange NMR factors are also indicated following reference (30). The black circles indicate highly protected residues, and the white dots show the decreasing protection; the dashes indicate no protection. A, fibril (F1 and F2) and fibril oligomer (FO1 and FO2) models. B, prefibril (P1 and P2) and preglobulomer (P3 and P4) models. C, globulomer models.

FIGURE 3.

Single layer fibril oligomer models have different structure and dynamics as compared with fibril models. The fracture and C-terminal distortions are in the middle of the β-strands. A, FO1 model. The panel on the left provides a view from residues 10–24, showing the even fracture. On the right is the view from the C-terminal (residues 20–42) side, showing that Met-35 patch is partially covered. The yellow balls are sulfur atoms. B, FO2 model. On the left is the view from the side of residues 10–24, showing the large uneven fracture. On the right is the view from C-terminal (residues 20–42) side, showing that the Met-35 patch is partially covered. C, RMSD for the FO1 model. D, RMSD for the FO2 model.

FIGURE 4.

This figure summarizes the essence of the paper from the mechanistic standpoint: the C-terminal distortions and β-sheet fracture explain why a fibril oligomer cannot directly convert to fibril. A shows the fibril model represented by two U-shaped β-sheets associated via the C-terminal regions. Ideally, the fibril can be formed through binding of two ideal U-shaped β-sheets as represented in B. However, experiments indicate that B to A conversion is not straightforward. In our simulations, we found that the ideal “fibril” oligomer (B) is not stable in solution. Instead, the ideal fibril oligomer is better represented as the “real” fibril oligomer shown in C, with a fracture in the middle of the oligomer and nonplanar C terminus, in which Met-35 patch is covered. The longer structure of C would break into short pieces as indicated in D, which in turn either recruit more monomers or slowly convert to fibril in A. It is difficult to convert a longer fibril oligomer as in C to A because of the distortion of the C terminus.

FIGURE 5.

The arrangement and secondary structure stabilities of prefibril oligomers (P1 and P2) and preglobulomer (P3 and P4). A, the differences in Met-35 patch interactions. In each model, the Met-35 patches are shown in a surface representation with the yellow balls representing sulfur atoms. In the top row, six β-strands are represented as red ribbons, and another six as green ribbons, for comparison with Fig. 1. In the middle, there are two ways of arranging the C-terminal Met-35 patches as illustrated by block arrows. In models P1 and P2, the Met-35 patches are available to be associated as in fibril (Fig. 1). However, in P3 and P4 the Met-35 patches are not available, because they are covered by residues 1–20. In P3 and P4, the C terminus can be associated without Met-35 patches. The orientation of the C-terminal β-sheets can be parallel (P1), antiparallel (P2 and P3), or with an angle up to 90 degree (orthogonally, P4). In the bottom row, only four core strands are shown for clarity. B, the backbone hydrogen bond in C-terminal region along the simulation trajectories for the four models. C, the total number of backbone hydrogen bond. D, the number of hydrogen bonds in the hairpin region of residues Val-18 to Ile-32.

FIGURE 6.

The structure and dynamics of the globulomer models. The two sets of six β-strands are represented as red and green ribbons. Lys-28 residues sit in the turn regions and are represented as balls. Met-35 patches are represented by surface patches, with sulfur atoms in yellow. A, the starting conformation for GO1 model, showing that with the Luhrs turn, two sets of six β-strands can fit exactly into an orthogonal C-terminal interaction, forming a dodecamer. B, the starting conformation for the GO2 model, showing that alternatively, two sets of six β-strands can also form an orthogonal C-terminal interaction with room for an additional strand in each set to form oligomer with 14 β-strands. C, starting conformation for the GO3 model with two sets of anti-parallel β-sheets (each with six strands), which also can form orthogonal C-terminal interactions. D–F, RMSDs of all three models exhibit large fluctuations of the N-terminal and stable core structures. G and H, surface model of residues 10–42 in the globulomer model, under the assumption that the flexible 1–9 region is not observable in EM.

FIGURE 7.

The box illustrates that the fibril- and ADDL-forming pathways may share common critical intermediates and subsequently diverge into different structures. The key step may involve the formation of critical intermediate (CI) with a C-terminal parallel β-sheet. The subsequent association of the critical intermediate may underlie the divergence of fibril and ADDL pathways. If the critical intermediate associates, leaving the Met-35 patches available, the fibril may eventually form. If the critical intermediates interact otherwise with Met-35 patches covered by other parts, ADDLs may be formed. The ribbon models (with six strands in red and six strands in green) highlight that critical intermediate interaction without Met-15 patches can mature into globulomer with orthogonal C-terminal interaction, with no conversion to fibril.