Modulation Mechanisms of Transmembrane Domain Flexibilityin Amyloid Precursor Protein and Notch: A Coarse-Grained SimulationStudy on the Impact of Upper and Lower Leaflet Composition in Liquid-Orderedand Liquid-Disordered Ternary Bilayer Membranes

Abstract Alzheimer’s disease (AD) and Notch-related pathologies are linked to dysregulated γ-secretase cleavage of amyloid precursor protein (APP) and Notch transmembrane domains (TMDs). However, γ-secretase inhibitors for AD often disrupt Notch signaling, necessitating strategies to selectively modulate substrate cleavage. This study employs coarse-grained molecular dynamics simulations to investigate how lipid bilayer composition─specifically liquid-ordered (Lo) and liquid-disordered (Ld) phases with varying cholesterol (Chol), palmitoyl-sphingomyelin, and 1,2-dioleoyl-sn-phosphatidylcholine ratios─impacts the flexibility and stability of APP and Notch TMDs. Our key findings reveal that Chol-rich Lo phases enhance APP TMD flexibility, promoting γ-secretase cleavage and Aβ production, while Notch TMD stability is largely unaffected by Chol, favoring Ld phases, replicating perfectly the existing experimental observations and resolving several conflicting perspectives. A critical innovation lies in identifying asymmetric lipid compositions (e.g., Chol-enriched lower leaflets) as regulators of APP–Notch selectivity. These results highlight membrane microenvironment engineering as a promising therapeutic avenue to decouple APP and Notch processing. Future work should validate these findings experimentally and explore lipid-based modulators for AD treatment with reduced side effects.