Key Residue for Aggregation of Amyloid-β Peptides

Abstract

It is known that oligomers of amyloid-β (Aβ) peptide are associated with Alzheimer's disease. Aβ has two isoforms: Aβ40 and Aβ42. Although the difference between Aβ40 and Aβ42 is only two additional C-terminal residues, Aβ42 aggregates much faster than Aβ40. It is unknown what role the C-terminal two residues play in accelerating aggregation. Since Aβ42 is more toxic than Aβ40, its oligomerization process needs to be clarified. Moreover, clarifying the differences between the oligomerization processes of Aβ40 and Aβ42 is essential to elucidate the key factors of oligomerization. Therefore, to investigate the dimerization process, which is the early oligomerization process, Hamiltonian replica-permutation molecular dynamics simulations were performed for Aβ40 and Aβ42. We identified a key residue, Arg5, for the Aβ42 dimerization. The two additional residues in Aβ42 allow the C-terminus to form contact with Arg5 because of the electrostatic attraction between them, and this contact stabilizes the β-hairpin. This β-hairpin promotes dimer formation through the intermolecular β-bridges. Thus, we examined the effects of amino acid substitutions of Arg5, thereby confirming that the mutations remarkably suppressed the aggregation of Aβ42. Moreover, the mutations of Arg5 suppressed the Aβ40 aggregation. It was found by analyzing the simulations that Arg5 is important for Aβ40 to form intermolecular contacts. Thus, it was clarified that the role of Arg5 in the oligomerization process varies due to the two additional C-terminal residues.

Keywords: amyloid-β peptide; generalized-ensemble algorithm; molecular dynamics simulation; protein aggregation.

Figure 1

Dimerization propensities of Aβ42 (green) and Aβ40 (red).

Figure 2

Intermolecular contact probabilities of C_α atoms for (a) Aβ42 and (b) Aβ40. Probabilities with which the residues in (c) Aβ42 and (d) Aβ40 form β-strands with the corresponding length.

Figure 3

Intramolecular contact probabilities of C_α atoms for (a) Aβ42 and (b) Aβ40. Probability distributions with respect to the number of intramolecular and intermolecular β-bridges for (c) Aβ42 and (d) Aβ40.

Figure 4

Free-energy landscapes for (a) Aβ42 and (b) Aβ40 with respect to the corresponding first and second principal components (PC1 and PC2). The local-minimum free-energy states are labeled as (a) states A–E for Aβ42 and (b) states A′–E′ for Aβ40. The units of the free-energy landscapes are kcal/mol. Representative dimer structures in (a) states A–E and (b) states A′–E′ are also shown.

Figure 5

Intramolecular contact probabilities between residues for (a) Aβ42 and (b) Aβ40. Here, all atoms, including the side-chain atoms, except the hydrogen atoms, are considered in calculating the contact probabilities. (c) Schematic illustration where the β-hairpin of Aβ42 is stabilized by the contacts between the C-terminus and Arg5 and between E22 and K28.

Figure 6

(a) Time series of distances between residue 5 and C-terminal residue for the wild type and mutants. Representative structures for the time periods indicated by red circles are also shown. Residues 5 and 42 are shown in the ball-and-stick model. (b) Probability distributions of distances between residue 5 and C-terminal residue for the wild type and mutants. (c) Time series of the average numbers of β-bridges between the β1 and β2 regions calculated from 20 MD simulations for each system.

Figure 7

Intramolecular contact probabilities of C_α atoms in the three Aβ42 monomers: (a) the wild type, (b) R5G, and (c) R5E.

Figure 8

Aggregation of (a) the wild type, (b) R5G, and (c) R5E of Aβ42s monitored by ThT assay in 20 mM sodium phosphate buffer, pH 7.4. Aggregation of (d) the wild type, (e) R5G, and (f) R5E of Aβ40s monitored by ThT assay in 20 mM sodium phosphate buffer, pH 7.4.

Figure 9

Intermolecular contact probabilities between residues for (a) Aβ42 and (b) Aβ40. Here, all atoms, including the side-chain atoms, except the hydrogen atoms, are considered in calculating the contact probabilities.