Disordered versus fibril-like amyloid β (25-35) dimers in water: structure and thermodynamics.

Alzheimer's disease is associated with the precipitation of the amyloid β (Aβ) (1-40) peptide in the form of fibrils. Among the full length peptide, smaller fragments such as Aβ (25-35) which retains the toxicity of the full length peptide are also present. Aβ's toxicity is attributed to soluble oligomers which, however, are difficult to study experimentally due to their transient nature. Here we present replica exchange molecular dynamics simulations of Aβ (25-35) dimers in explicit water. Similar to a previous study, dimers are found to exist as disordered compact in equilibrium with ordered extended fibril-like conformations. In addition, our results suggest effects from slight differences in ionic conditions and yield insights on this system in unprecedented detail. In the compact state, the peptides adopt β-hairpin or unstructured U-shaped conformations with different relative orientations. In the extended state, the peptides are outstretched and form antiparallel in- or out-of-register intermolecular β-sheets. In addition to the previous study, we reveal the driving forces governing the equilibrium between the disordered and the fibril-like state. In particular, it is shown that the compact state is favored by a high entropy while the fibril-like state is lower in energy arising from favorable covalent and electrostatic interactions between and within the peptides. Our results suggest that the transition from the compact to the fibril-like state involves reptation, i.e., a change in register of an intermolecular β-sheet without dissociation of the peptides.