Aß Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization using a Combined MD/NMR Approach

Abstract

Amyloid s (As) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease. However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of As monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of As aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the µs/replica timescale are used to characterize the structural ensembles of As42, As40, and M35-oxidized As42, three physiologically prevalent isoforms with substantially different aggregation properties, the latter of which has hitherto not been investigated with computational techniques. Further, comparisons of J coupling data calculated from the REMD trajectories with their corresponding experimental values are used to validate these simulations and monitor equilibration. Our analysis indicates that all simulations converge on the 100 ns/replica timescale toward ensembles that yield good agreement with experimental J couplings. Here, we describe As monomers that are far more structured than other computational studies that rely on characterizations made on smaller timescales. Prominent in the C-terminus are antiparallel s-hairpin topologies between L17-A21, A30-L36, and V39-A41, reminiscent of oligomer and fibril models, that expose the composite hydrophobic side chains to solvent and may serve as hotspots for self-association. A persistent V24-K28 bend motif is observed in all three species that is stabilized by buried backbone to side chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the side chain identities of the FAD-linked E22 and D23 residues in As monomer structure. These characterizations help illustrate the conformational landscapes of As monomers at atomic resolution and provide insight into the early stages of As aggregation pathways.