Single Point Mutation Alters the Microstate Dynamics of Amyloid β‑Protein Aβ42 as Revealed by Dihedral Dynamics Analyses

The aggregation of amyloid β-protein (Aβ) has been associated with the pathogenesis of Alzheimer’s disease. A number of single point mutations at residues A21, E22, D23, and M35 have been identified to show increased or decreased aggregation tendency. Although the effects of point mutations on the structural properties of Aβ peptides have been intensively studied, how single point mutation affects the kinetics of Aβ remains unknown. In this work, dihedral dynamics analyses, which combine dihedral principle component analysis (dPCA), potential of mean force (PMF) calculations, and Markov state models (MSMs), were proposed to elucidate the different global free energy landscapes (FELs), the PMF of individual dihedral angle, and microstates/macrostates for a number of Aβ42 mutants (Flemish A21G, Arctic E22G, Italian E22K, Dutch E22Q, Iowa D23N, Japanese E22Δ, and M35 oxidation Met35OX). Our simulation results show that one point mutation is sufficient to change the rugged FEL of Aβ42 by altering the energy barriers around basins. This alteration was also observed in the potential of each dihedral angle to varying degrees, although most minima of PMF do not shift. MSMs further reveal that E22 mutants (E22Δ, E22G, E22K, and E22Q) and D23N generate more hub-like microstates than wild type Aβ42, thus creating diverse alternative pathways for conformational transitions and increasing subsequent aggregation. In contrast, transitions are more preferred within the same microstate of A21G and Met35OX. Mapping MSM to FEL suggests that transitions between different sets of microstates are kinetically feasible but thermodynamically difficult.