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A hallmark of AD is the presence of plaques found between neurons in the brain. These mainly consist of insoluble β-amyloid protein fragments and are thought to be cytotoxic when aggregated. This can lead to neuron death and subsequent loss of memory and perception. The β-amyloid peptide has 40~42 residues and comes from the transmembrane (TM) segment of amyloid precursor protein (APP), which has a large extracellular domain (ECD) and a small intracellular domain (ICD). APP can be processed by two different pathways. It can be cleaved by α-secretase to release the APP ECD. This cleavage blocks production of β-amyloid and reduces plaque buildup. In the second pathway, APP is first cleaved by β-secretase at the extracellular side near the TM segment, and then by γ-secretase within the TM segment. This releases β-amyloid peptides with lengths of 37–43 residues. The two major forms of β-amyloid peptides have 40 (Aβ-40) and 42 residues (Aβ-42) and contain most of the TM segment. These peptides, especially the longer Aβ-42, are hydrophobic and can easily aggregate into large oligomers.

The cryo-electron microscopy structure of γ-secretase: towards complex assembly, substrate recognition and a catalytic mechanism