Linking folding with aggregation in Alzheimer's beta-amyloid peptides

Abstract

Growing evidence suggests that the beta-amyloid (Abeta) peptides of Alzheimer's disease are generated in early endosomes and that small oligomers are the principal toxic species. We sought to understand whether and how the solution pH, which is more acidic in endosomes than the extracellular environment, affects the conformational processes of Abeta. Using constant pH molecular dynamics simulations of two model peptides, Abeta(1-28) and Abeta(10-42), we found that the folding landscape of Abeta is strongly modulated by pH and is most favorable for hydrophobically driven aggregation at pH 6. Thus, our theoretical findings substantiate the possibility that Abeta oligomers develop intracellularly before secretion into the extracellular milieu, where they may disrupt synaptic activity or act as seeds for plaque formation.

Fig. 1.

pH-dependent helix formation. (A) Residue-based helix propensity of Aβ(1–28) and Aβ(10–42) computed from simulations at pH 2 (red), 4 (orange), 6 (green), and 8 (blue). Nascent helices containing ionizable residues are depicted in cyan, and those in the CHC and C-terminal hydrophobic regions are depicted in brown. (B) Total helix content as a function of pH computed as the percentage of helical residues (open symbols) and from the theoretical mean residue ellipticity at 222 nm (filled symbols).

Fig. 2.

Probability density for the solvent-accessible surface area (SAS) of the CHC residues, Leu-17-Ala-21, in Aβ(1–28) and Aβ(10–42) at pH 2 (red), 4 (orange), 6 (green), and 8 (blue).

Fig. 3.

Correlation between the formation of a β-turn in residues 23–26 and the electrostatic interaction between Glu-22 and Lys-28. (A) Probability density for the formation of a β-turn as a function of pH. (B) Relative free energy, ΔG, as a function of the Glu-22-Lys-28 distance in the presence (solid lines and absence (dashed lines) of the turn from simulations at pH 4. The distance between Glu-22 and Lys-28 is defined as the minimum separation between the carboxylate oxygen atom in Glu-22 and the amino nitrogen atom in Lys-28. ΔG is defined as −RTlnP, where P is the probability density for the distance to fall into one of the 22 bins between 2 and 24 Å.

Fig. 4.

Correlation between the backbone hydrogen bond formation and the side-chain electrostatic or hydrophobic interactions. Relative free energy, ΔG (in kcal/mol), as a function of the backbone CO… NH distance between Val-18 and Glu-22 (x axis) and the side-chain distance between Glu-22 and Lys-28 (y axis) in the simulation of Aβ(1–28) (A) and Aβ(10–42) (B) at pH 4. The distance between Glu-22 and Lys-28 is defined as the minimum separation between the carboxylate oxygen atom of Glu-22 and the amino nitrogen atom of Lys-28.

Fig. 5.

Representative conformations of Aβ(10–42) at pH 8. (A) Centroid of the largest conformational cluster. This conformation contains a β-turn at residues 23–26 and a parallel orientation of the CHC region with respect to the C-terminal residues. The latter is stabilized by a β-bridge between Phe-19 and Ile-41 as well as the side-chain hydrophobic interactions between the CHC residues Leu-17, Val-18, and Phe-19 and the C-terminal residues Val-40, Ile-41, and Ala-42. (B) Centroid of the second largest conformational cluster. This conformation contains a helix at residues 23–28 as well as a hydrophobic cluster composed of residues Val-18, Phe-19, Val-40, and Ile-41.

Fig. 6.

A proposed mechanism for the pH-dependent aggregation of Aβ. Depicted are representative structures obtained as the centroids of the most populated conformational clusters under the pH conditions of 2, 4, 6, and 8, respectively. The N-terminal residues 1–28 are shown in blue; the C-terminal residues 29–42 are shown in red. In the most aggregation-prone state (pH 6), the side chains of Leu-17, Val-18, Phe-19, Phe-20, and Ala-21 are shown as van der Waals spheres in pink, gray, cyan, purple, and green, respectively.