Polymorphic structures of Alzheimer's β-amyloid globulomers

Abstract

Background: Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation.

Methods and findings: Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR.

Conclusions: Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils.

Figure 1. A three-step assembly procedure for constructing Aβ_17–42 globulomers by using monomer or dimer building blocks.

Step 1: Aβ monomer/dimer aligns parallel to the z axis (i.e. core axis) and then is rotated and replicated to form an annular structure. Step 2: each building block (i.e. monomer or dimer) is self-rotated along its β-strand axis at the center of mass by 5° interval from 0° to 360° to generate 72 candidates. Step 3: each candidate is energy minimized using GBSW implicit solvent model to obtain preliminary energy profiles of monomer-based globulomers (red) and dimer-based globulomers (black). Six lowest-energy globulomers with different peptide packings are preselected as initial conformations for subsequent explicit-solvent MD simulations to examine their structural stability.

Figure 2. Conformational energy landscapes with respect to backbone RMSD and Rg for (A) MWT0, (B) MWT90, (C) MWT170, and (D) MMT0.

Labels of 1 and 2 in the landscapes represent the initial (left) and the final (right) structures at 0 ns and 40 ns, respectively. Color codes: negatively charged residues (red), positively charged residues (blue), hydrophilic residues (green), and hydrophobic residues (white). C_β atoms of Met35 are shown by VDW spheres to guide eyes. All cartoon structures are rendered by VMD .

Figure 3. Conformational energy landscapes with respect to backbone RMSD and Rg for (A) DWT25, (B) DWT265, (C) DWT330, and (D) DMT25.

Labels of 1 and 2 in the maps represent the initial (left) and the final (right) structures at 0 ns and 40 ns, respectively. Color codes: negatively charged residues (red), positively charged residues (blue), hydrophilic residues (green), and hydrophobic residues (white). C_β atoms of Met35 are shown by VDW spheres to guide eyes.

Figure 4. Averaged structures of monomer-based Aβ globulomers of (A) MWT0, (B) MWT90, (C) MWT170, and (D) MMT0 and dimer-based Aβ globulomers of (E) DWT25, (F) DWT265, (G) DWT330, and (H) DMT25 from the last 5-ns MD simulations.

The residue-based RMSF is imposed on each averaged structure using a blue-white-red scale, with low RMSF of <3 Å (blue), intermediate RMSF of 3∼6 Å (white), and high RMSF of >6 Å (red).

Figure 5. Comparison of secondary structure populations between the initial 5 ns (left column) and final 5 ns (right column) conformations for six wild-types and two mutants of Aβ globulomers.

Figure 6. Time evolution of globulomer sphericity for DWT25 (black), DWT265 (red), DWT330 (green), MWT0 (yellow), MWT90 (blue), MWT170 (pink), D25M (cyan), and M0M (gray).

Figure 7. Comparison of solvent accessible surface area of hydrophobic C-terminal residues Ile31-Ala42, charged/hydrophilic N-terminal residues Leu17-Ser26, and turn residues Asn27-Ala30 between the initial 5 ns (left column) and the final 5 ns (right column) trajectories for all globulomers.

Figure 8. Energy decomposition for all globulomers averaged from the last 10 ns simulations.

Figure 9. Residue-residue interaction maps including sidechain contacts (upper left triangular corner) and hydrogen bonds (lower right triangular corner) for (A) MWT0, (B) MWT90, (C) MWT170, (D) MMT0, (E) DWT25, (F) DWT265, (G) DWT330, and (H) DMT25.

A sidechain contact is defined if the center of mass of sidechains between two residues is less than 6.0 Å. A hydrogen bond is defined if donor-acceptor distance is <3.5 Å and accepter-donor-hydrogen angle is >120°.

Figure 10. Number of dimers formed in the Aβ globulomers during 40 ns MD simulations.

Figure 11. The most populated Aβ dimeric clusters extracted from the condensed areas of principle component analysis maps for (A) MWT0, (B) MWT90, (C) MWT170, (D) DWT25, (E) DWT265, and (F) DWT330.