Replica-permutation molecular dynamics simulations of an amyloid-β(16–22) peptide and polyphenols

Abstract

Aggregates of amyloid-β (Aβ) peptides, such as oligomers and amyloid fibrils, are related to Alzheimer’s disease. Polyphenols are known to inhibit the aggregation of Aβ peptides. We performed all-atom replica-permutation molecular dynamics simulations of an Aβ fragment, Aβ16–22, and two kinds of polyphenols, myricetin and rosmarinic acid in explicit water solvent. We found that glutamic acid E22 of the Aβ16–22 peptide has the highest probability to bind to the polyphenols and specified the hydroxyl groups and carboxyl groups of polyphenols that contribute to the binding.