Folding Landscapes of the Alzheimer Amyloid-β(12-28) Peptide

The energy landscape for folding of the 12-28 fragment of the Alzheimer amyloid β (Aβ) peptide is characterized using replica-exchange molecular dynamics simulations with an all-atom peptide model and explicit solvent. At physiological temperatures, the peptide exists mostly as a collapsed random coil, populating a small fraction (less than 10%) of hairpins with a β-turn at position V18F19, with another 10% of hairpin-like conformations possessing a bend rather than a turn in the central VFFA positions. A small fraction of the populated states, ∼14%, adopt polyproline II (PPII) conformations. Folding of the structured hairpin states proceeds through the assembly of two locally stable segments, VFFAE and EDVGS. The interactions stabilizing these locally folded structural motifs are in conflict with those stabilizing the global fold of A12-28, a signature of underlying residual frustration in this peptide. At increased temperature, the population of both β-strand and PPII conformations diminishes in favor of β-turn and random-coil states. On the basis of the conformational preferences of Aβ 12-28 monomers, two models for the molecular structure of amyloid fibrils formed by this peptide are proposed.