Stable conformation of full-length amyloid-β (1–42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1–42) is more prone to aggregation than Aβ(1–40). We here search stable conformations of solvated Aβ(1–42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1–42) contributing to the stabilization of the monomer are highlighted.