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

• Main Authors: Cruz, L, Rao, J Srinivasa, Teplow, DB, Urbanc, B
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: eScholarship, University of California 2012
• Subjects: Acquired Cognitive Impairment; Dementia; Neurodegenerative; Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD); Aging; Alzheimer's Disease; Brain Disorders; Neurosciences; Amyloid beta-Peptides; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Physical Sciences; Chemical Sciences; Engineering; Arctic
• Online Access: https://escholarship.org/uc/item/0jg6p377

The amyloid β-protein (Aβ), 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 Aβ(21-30) decapeptide region is a critical step in the aggregation of Aβ. We report results of constant temperature all-atom molecular dynamics simulations in explicit water of the dynamics of monomeric Aβ(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 β-hairpin structures with the highest probability in the Iowa mutant. At least three β-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 β-hairpin lifetime (≥500 ns), closely followed by the Iowa mutant (≈500 ns). Aβ(21-30) and the Arctic mutant had significantly lower lifetimes (≈200 ns). Hydrophobic packing of side chains was responsible for enhanced β-hairpin lifetimes in the Dutch and Iowa mutants, whereas lifetimes in Aβ(21-30) and its Arctic mutant were influenced by the backbone hydrogen bonding. The data suggest that prolonged β-hairpin lifetimes may impact peptide pathogenicity in vivo.