Effects of familial Alzheimer's disease mutations on gamma-secretase activation for cleavage of amyloid precursor protein

Gamma-secretase, the “proteasome of the membrane”, cleaves within the membrane of 150+ peptide substrates with central roles in biology and medicine, including amyloid precursor protein (APP). Presenilin-1 (PS1) is the catalytic subunit of gamma-secretase and its mutations cause early-onset familial Alzheimer's disease (FAD). However, the exact pathogenic mechanism of FAD remains elusive. Here, we have combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations on the enzyme-substrate interactions between gamma-secretase and APP. Biochemical experiments showed that all six FAD mutations rendered gamma-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant gamma-secretase. The PS1 FAD mutants were found to reduce gamma-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our complementary experimental and simulation findings provide important mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of gamma-secretase and APP.