Molecular dynamics studies of hexamers of amyloid-β peptide (16–35) and its mutants: Influence of charge states on amyloid formation

To study the early stage of amyloid-β peptide (Aβ) aggregation, hexamers of the wild-type (WT) Aβ_16–35 and its mutants with amyloid-like conformations have been studied by molecular dynamics simulations in explicit water for a total time of 1.7 μs. We found that the amyloid-like structures in the WT oligomers are destabilized by the solvation of ionic D23/K28 residues, which are buried in the fibrils. This means that the desolvation of D23/K28 residues may contribute to the kinetic barrier of aggregation in the early stage. In the E22Q/D23N, D23N/K28Q, and E22Q/D23N/K28Q mutants, hydration becomes much less significant because the mutated residues have neutral amide side-chains. These amide side-chains can form linear cross-strand hydrogen bond chains, or “polar zippers”, if dehydrated. These “polar zippers” increase the stability of the amyloid-like conformation, reducing the barrier for the early-stage oligomerization. This is in accord with experimental observations that both the D23/K28 lactamization and the E22Q/D23N mutation promote aggregation. We also found that the E22Q/D23N mutant prefers an amyloid-like conformation that differs from the one found for WT Aβ. This suggests that different amyloid structures may be formed under different conditions. Proteins 2007. © 2006 Wiley-Liss, Inc.