Dynamics of Metastable β-Hairpin Structures in the Folding Nucleus of Amyloid β-Protein

The amyloid beta-protein (A beta), which is present predominately as a 40- or 42-residue peptide, is postulated to play a seminal role in the pathogenesis of Alzheimer's disease (AD). Folding of the A beta(21-30) decapeptide region is a critical step in the aggregation of A beta. We report results of constant temperature all-atom molecular dynamics simulations in explicit water of the dynamics of monomeric A beta(21-30) and its Dutch [Glu22Gln], Arctic [Glu22Gly], and Iowa [Asp23Asn] isoforms that are associated with familial forms of cerebral amyloid angiopathy and AD. The simulations revealed a variety of loop conformers that exhibited a hydrogen bond network involving the Asp23 and Ser26 amino acids. A population of conformers, not part of the loop population, was found to form metastable beta-hairpin structures with the highest probability in the Iowa mutant. At least three beta-hairpin structures were found that differed in their hydrogen bonding register, average number of backbone hydrogen bonds, and lifetimes. Analysis revealed that the Dutch mutant had the longest beta-hairpin lifetime (>= 500 ns), closely followed by the Iowa mutant (approximate to 500 ns). A beta(21-30) and the Arctic mutant had significantly lower lifetimes (approximate to 200 ns). Hydrophobic packing of side chains was responsible for enhanced beta-hairpin lifetimes in the Dutch and Iowa mutants, whereas lifetimes in A beta(21-30) and its Arctic mutant were influenced by the backbone hydrogen bonding. The data suggest that prolonged beta-hairpin lifetimes may impact peptide pathogenicity in vivo.