Cooperative Roles of Hydrophilic Loop 1 and the C-Terminus of Presenilin 1 in the Substrate-Gating Mechanism of γ-Secretase

Abstract

␥-Secretase is a multisubunit protease complex that is responsible for generating amyloid-␤ peptides, which are associated with Alzheimer disease. The catalytic subunit of ␥-secretase is presenilin 1 (PS1), which contains an initial substrate-binding site that is distinct from the catalytic site. Processive cleavage is suggested in the intramembrane-cleaving mechanism of ␥-secretase. However, it largely remains unknown as to how ␥-secretase recognizes its substrate during proteolysis. Here, we identified that the ␣-helical structural region of hydrophilic loop 1 (HL1) and the C-terminal region of human PS1 are distinct substrate-binding sites. Mutational analyses revealed that substrate binding to the HL1 region is critical for both -and ␥-cleavage, whereas binding to the C-terminal region hampers ␥-cleavage. Moreover, we propose that substrate binding triggers conformational changes in PS1, rendering it suitable for catalysis. Our data provide new insights into the complicated catalytic mechanism of PS1.

Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production

“…interacted with the TM of C99 and displayed high flexibility during the MD simulations indicating a role in substrate recognition. This corroborates earlier studies by Tomita et al [68] and is also partly evident from the cryo-EM structure of PS1-γ-secretase with C83 [19], although the thermal motions are expected top be much smaller at cryo temperature and thus possibly lead to only one bound conformation state.…”

Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

“…Subsequently performed post‐processing free energy calculations using molecular mechanics Poisson–Boltzmann surface area (MMPBSA) method (Genheden & Ryde, ) indicated that hNCT‐E242 indeed stabilizes GSEC‐APP/Aβ interactions by 2.90 ± 0.13 kcal/mol (mean ± SEM, with N = 1,500). Furthermore, the simulations supported the importance of the interactions between APP ectodomain and the first extracellular loop of PSEN1 (residues 109–118), a region reported previously to be involved in the substrate recognition (Takagi‐Niidome et al , ) and mutated in FAD.…”

Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1

“…Substrate binding to HL1 is indispensable for both 3and g-cleavage, whereas binding to the C-terminal of PS1 hampers cleavage. 98 During the simulations, the RMSF of the catalytic aspartates is 0.17-0.28 nm (average 0.22 nm) and 0.12-0.15 nm (average 0.14 nm), respectively, for the Asp-263 and Asp-366, suggesting that the latter catalytic aspartate is much more restricted in its movement, which could be of catalytic relevance.…”