Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study

Abstract

Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

Figure 1

Oligomer size distributions for Aβ_1–40 (black curve) and Aβ_1–42 (red curve) obtained in silico using DMD with the four-bead protein model at T = 0.130. Each distribution is an average over eight 20 × 10⁶ simulation steps long trajectories. All conformations for time frames at 19 × 10⁶, 19.5 × 10⁶, and 20 × 10⁶ simulation steps were included in the analysis. Each trajectory involved 32 peptides, initially spatially separated and each in a random coil conformation enclosed in a 25-nm-length cubic box. The error bars represent SEM. For comparison, old simulation data reported by Urbanc et al. for Aβ_1–40 (thin black curve) and Aβ_1–42 (thin red curve), obtained at T = 0.150 by averaging over eight 10 × 10⁶ simulation steps long trajectories, are shown.

Figure 2

Oligomer size distributions for (a) Aβ_1–40 and (b) Aβ_1–42 obtained by DMD simulations using the four-bead protein model at T = 0.130 at different effective electrostatic interactions. Each distribution is an average over eight 20 × 10⁶ simulation steps long trajectories. All conformations for time frames of 19 × 10⁶, 19.5 × 10⁶, and 20 × 10⁶ simulation steps were included in the analysis. Each trajectory involved 32 peptides, initially spatially separated and each in a random coil conformation, enclosed in a 25-nm-length cubic box. The error bars represent SEM.

Figure 3

Effective electrostatic interactions speed up the conversion from hexamers (n = 6) to elongated protofibrillar assemblies (e.g., n = 28). β-Strands are depicted as yellow ribbons, turns as light-blue ribbons, and random coils as white ribbons. Amino acid D1, marking the N-termini, is represented by red spheres.

Figure 4

Oligomer size distributions for Arctic mutants [E22G] Aβ_1–40 (dotted black curve) and [E22G] Aβ_1–42 (dotted red curve) obtained by DMD simulations using the four-bead protein model at T = 0.130. Each distribution is an average over eight 20 × 10⁶ simulation steps long trajectories. The oligomer size distributions for Aβ_1–40 (solid black curve) and Aβ_1–42 (solid red curve) are shown for comparison. All conformations for time frames of 19 × 10⁶, 19.5 × 10⁶, and 20 × 10⁶ simulation steps were included in the analysis. Each trajectory involved 32 peptides, initially spatially separated and each in random coil conformation, enclosed in a 25-nm-length cubic box. The error bars represent SEM. The inset adapted from Bitan et al. shows the experimental data obtained by PICUP/SDS-PAGE for (a) Aβ_1–40, (b) Aβ_1–42, (c) [E22G] Aβ_1–40, and (d) [E22G] Aβ_1–42.

Figure 5

Average propensities for (a) a β-strand and (b) turn formation in monomers, dimers, trimers, tetramers, pentamers, and hexamers for Aβ_1–40 (solid black curve), Aβ_1–42 (solid red curve), [E22G]Aβ_1–40 (dotted black curve), and [E22G]Aβ_1–42 (dotted red curve). The error bars correspond to SEM.

Figure 6

Average β-strand propensity per amino acid for (a) dimers and (b) hexamers of Aβ_1–40 (solid black curve), Aβ_1–42 (solid red curve), [E22G]Aβ_1–40 (dotted black curve), and [E22G]Aβ_1–42 (dotted red curve). The error bars correspond to SEM.

Figure 7

Average turn propensity per amino acid for (a) dimers and (b) hexamers of Aβ_1–40 (solid black curve), Aβ_1–42 (solid red curve), [E22G]Aβ_1–40 (dotted black curve), and [E22G]Aβ_1–42 (dotted red curve). The error bars correspond to SEM.

Figure 8

Formation of an Aβ_1–40 hexamer from a tetramer and a dimer for (A) 19.0 × 10⁶ and (B) 19.6 × 10⁶ simulation steps. β-Strands are depicted as yellow ribbons, turns as light blue ribbons, and random coils as white ribbons. Amino acid D1, marking the N-termini, is represented by red spheres, and V39 and V40 are represented by orange spheres.

Figure 9

Relative distances of individual residues from the center of mass of Aβ_1–40 (solid black curve), Aβ_1–42 (solid red curve), [E22G]Aβ_1–40 (dotted black curve), and [E22G]Aβ_1–42 (dotted red curve) (a) dimers and (b) hexamers. The error bars correspond to SEM.

Figure 10

Intra- and intermolecular contact maps of Aβ_1–42 oligomers: (a, b) n = 12 for E_CH = 0 (average taken over 12 conformers) and (c, d) n = 11 for E_CH = 10⁻² (average taken over 30 conformers). The lower triangle contains the average number of contacts between two amino acids, and the upper triangle contains the average number of hydrogen bonds for each pair of amino acids. The scale on the right shows the color mapping. The two types of maps have different scales: the scale on the left corresponds to the average number of contacts, and the scale on the right corresponds to the average number of hydrogen bonds. The two thin diagonal lines are drawn through the diagonal elements of the two types of contact maps. The rectangular gray boxes with numbers mark regions of interest.