Mechanistic regulation of γ-secretase by their substrates

γ-Secretase (GS) is a transmembrane (TM) enzyme that plays important roles in the processing of approximately 90 substrates. The amyloid precursor protein (APP) is one of these substrates, and the peptides derived from their processing are related with the development of Alzheimer's disease. However, the mechanistic process involved in the GS substrate processing and regulation remains elusive. In this work, we employed extensive atomistic molecular dynamics simulations, reduction dimensionality, and network analysis to understand the dynamic behavior of GS in its apo form and bound to transmembrane fragments of APP-C99, APP-C83, and Notch. An evaluation of the global conformation of the enzyme revealed that GS and GS-C83 systems display extended and compact conformations. However, systems with long extracellular N-terminal substrates, such as APP-C99 and Notch, preferred compact conformations. Interestingly, our network analysis revealed that the NCT-lobule (residues 223-248) plays a crucial role in the communication and the dynamics between the extracellular and TM components of the enzyme, impacting the catalytic site. In our GS-C99 simulated system, the interaction paths of the substrate processing region encompass the ε-site and ζ-site, leading to more imprecise positioning of the catalytic residue Asp385. Conversely, our GS-C83 simulated system shows more stability at the ε-site. Our observations shed light on the important mechanics of the fascinating GS architecture and may contribute to propose new GS modulators able to impact on the Alzheimer's disease treatment.