Atomic-level description of amyloid β-dimer formation

All-atom simulations have been carried out on a monomer and dimer of the aggregation-prone fragment (16-22) of amyloid β peptide, which is implicated in Alzheimer's disease. The replica exchange molecular dynamics method, which has been successfully applied to peptide folding, is utilized as a means to sample the configurational space with proper Boltzmann weighting so that the structural, motional, and thermodynamic description of self-assembly can be obtained. The free energy landscape showing the delicate balance between different monomer and dimer conformations is mapped along carefully chosen reaction coordinates. The canonical ensembles at 38 different temperatures are used to describe the thermodynamics and the relative stabilities of at least six different dimer conformations including that of parallel and antiparallel orientations. We also delineate the nature of the molecular forces that activate and stabilize these different dimer conformations as a function of temperature, especially as related to secondary structural propensity of monomer. We identify parallel loop dimer conformations that are stabilized due to specific interactions with water molecules.