APOE Genotype Difference in the Biphasic Modulation of Amyloid-β Aggregation by Direct Binding and Lowering the Nucleation Barrier

Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer’s disease (AD), while the apoE4 isoform (C112R) represents the strongest genetic risk factor. We combined binding-site mapping and discrete molecular dynamics (DMD) simulations to elucidate isoform-specific apoE-Aβ interactions. Computational peptide-array analysis identified Aβ-binding hotspots in the apoE4 N-terminal domain (NTD) around R112, conferring greater Aβ-binding propensity than apoE3. DMD simulations showed that apoE4 NTD is less stable and more solvent-exposed, resulting in stronger Aβ binding, especially near the mutation site. Upon binding apoE NTDs, Aβ exhibited an increased β-sheet content, suggesting a lowered fibril nucleation barrier. Incorporating these insights into a recently established thermodynamic–kinetic framework of amyloid aggregation rationalizes apoE’s biphasic effect on Aβ aggregation: apoE retards Aβ fibrillization at low Aβ-concentrations via monomer sequestration but accelerates the process at high concentrations by facilitating nucleation. Our findings offer mechanistic insight into the APOE genotype-dependent modulation of Aβ aggregation and may inform genotype-specific therapeutic strategies for AD.