Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein

Alzheimer's disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1-40 and Aβ1-42, other C-terminally truncated Aβ peptides, including Aβ1-38 and Aβ1-43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aβ1-38, Aβ1-40, Aβ1-42, and Aβ1-43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aβ1-38 and Aβ1-40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aβ1-42 and Aβ1-43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aβ1-42) or octamers and pentadecamers (for Aβ1-43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aβ1-42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure-function paradigm governing oligomers formed by various Aβ isoforms.