Membrane topology of I-CLiPs and their substrates. (A) Presenilin is processes into two pieces, an N-terminal fragment (NTF, dark portion) and a C-terminal fragment (CTF, light portion) that remain associated. Each fragment donates one aspartate essential for g-secretase activity. APP and other substrates are first cleaved in the extracellular domain (APP by b-secretase, Notch by a metalloprotease), and the remnant is cleaved twice within the membrane by g-secretase to produce the Ab peptide of Alzheimer’s disease (secreted) and the intracellular domain (freed into the cytosol). Inset: Presenilin interacts with three other membrane proteins, nicastrin, Aph-1, and Pen-2 to form active g-secretase. (B) SPP, like presenilin, contains two aspartates essential for protease activity in opposite orientation. Signal peptides are removed from membrane proteins via signal peptidase, and these peptides are released from the membrane by SPP-mediated intramembrane proteolysis. (C) ) S2P contains conserved HEXXH and LDG motifs found in metalloproteases. SREBP is first cleaved by S1P in the luminal loop. The regulatory domain (Reg) interacts with the cholesterol-sensing SCAP to ensure that S1P proteolysis only occurs when cholesterol levels are low. Subsequent intramembrane proteolysis releases this transcription factor for expression of genes essential to cholesterol and fatty acid synthesis. (D) Rhomboids contain a conserved serine, histidine, and asparagines which comprise a putative catalytic triad of a serine protease. Rhomboid-1 cleaves within the transmembrane region of the Drosophila EGF-like growth factor Spitz.