Substrate Binding By Gamma-Secretase: Conformational Dynamics Of The Enzyme Active Site And Substrate Recognition With An Example Of The Amyloid Precursor Protein

γ-secretase is a multimeric membrane-embedded aspartyl protease that mediates regulated intramembrane proteolysis of type I transmembrane proteins. The enzyme complex consists of nicastrin, anterior pharynx defective 1, presenilin enhancer 2 and presenilin, with the latter bearing the catalytic aspartates. Aberrant activity of this enzyme against amyloid precursor protein results in overproduction of β-amyloid polypeptides, what eventually leads to development of Alzheimer's Disease, while abnormal Notch processing is linked to a several types of cancer. Although the enzyme has been extensively studied, the actual localization of the binding site still remains controversial. Recent experimental results suggest that the access to the binding site is governed by the cleft either between the helices 2 and 6 or helices 6 and 9 of presenilin. The mechanism of the substrate recognition is also unclear, as γ-secretase is known to cleave at least 90 different substrates and, so far, has been linked to the presence of cholesterol. In this work we use Molecular Dynamics simulations to investigate the substrate binding mechanism of γ-secretase with an example of βCTF protein, which is the direct precursor of β-amyloid polypeptides. We characterize the conformational changes that are proposed to govern the access to the binding site, showing that the actual binding site is located between helices 6 and 9 of presenilin. The presented results also suggest that the substrate binds to the active site of γ-secretase according to induced fit rather than conformational selection model. We also show that initial substrate binding of γ-secretase is driven by hydrophobic mismatch.