Investigating Complex Formation Of C99 With Gamma-Secretase, Using Atomistic Mm-Md Simulations And Free Energy Calculations

The intramembrane aspartyl protease γ-secretase is mostly known for its assumed role in the development of familial Alzheimer's disease (FAD). Being a hetero-tetramer, it consists of four different proteins: presenilin-1 (PS1), nicastrin, APH-1 and PEN-2. The catalytic center of this complex is located deep within the hydrophobic region of presenilin where it cleaves single-pass transmembrane proteins. The most investigated substrate of γ-secretase is the C-terminal fragment of the amyloid precursor protein (APP) C99, which is cleaved at different positions by PS1. Among other peptides, C99 processing results in “amyloid beta” (Aβ) fragments of different lengths with the 40 (Aβ40) and 42 (Aβ42) amino acid long variants being the primary products. Since they are known to aggregate and form fibrillar structures (the main components of amyloid plaques, found in the brains of FAD patients) the Aβ42 peptides have been heavily implicated in Alzheimer's disease. In healthy patients, the production of Aβ40 is favored but this balance can be shifted towards Aβ42 by a large number of known PS1 mutations. The exact mechanism responsible for the formation of the different Aβ fragments is still unknown. To shed some light on the matter we conducted atomistic microsecond time-scale molecular dynamics simulations of three different C99-PS1 complexes, studying three different sites at which C99 is believed to bind to PS1 and enter its catalytically active center. We uncovered that the binding modes differ mainly in number of key protein ligand interactions (with respect to known mutation sites), active site accessibility and PS1 conformation. Based on the available data we conclude that prior to cleavage, C99 most likely binds to the cavity formed by the PS1 transmembrane domains 2 3 and 5.