Abstractγ-Secretase is a founding member of membrane-embedded aspartyl proteases that cleave substrates within transmembrane domains, and this enzyme is an important target for the development of therapeutics for Alzheimer's disease. The structure of γ-secretase and its precise catalytic mechanism still remain largely unknown. γ-Secretase is a complex of four integral membrane proteins, with presenilin (PS) as the catalytic component. To gain structural and functional information about the 9-transmembrane domain (TMD) presenilin, we employed a cysteine mutagenesis/disulfidecrosslinking approach. Here we report that native Cys92 is close to both Cys410 and Cys419, strongly implying that TMD1 and TMD8 are adjacent to each other. This structural arrangement also suggests that TMD8 is distorted from an ideal helix. Importantly, binding of an active-site directed inhibitor, but not a docking-site directed inhibitor, reduces the ability of the native cysteine pairs of PS1 to crosslink upon oxidation. These findings suggest that the conserved cysteines of TMD1 and TMD8 contribute to or allosterically interact with the active site of γ-secretase.Accumulation of the amyloid β-protein (Aβ) is one of the defining pathological features of Alzheimer's disease. Aβ is produced from the amyloid β-protein precursor (APP) as a result of sequential proteolytic cleavages first by β-secretase (1) and then by γ-secretase (2). γ-Secretase is an aspartyl transmembrane protease that cleaves a number of type I membrane protein substrates, including APP and Notch, in the middle of their transmembrane domains in a poorly understood process of hydrolysis within a hydrophobic environment (3). γ-Secretase is composed of four transmembrane proteins, Aph-1, Pen-2, Nicastrin (NCT) (4-10) and presenilin (PS), which is ostensibly the catalytic component of an unusual aspartyl protease (3,11,12). Despite substantial progress in establishing the full identity of γ-secretase (7-9,13, 14) and the step-wise assembly of the γ-secretase complex (7,15,16), the molecular structure of the protease complex or even any of its individual components remains unknown. PS, as the catalytic component, is of major interest, but only some indirect evidence about its structural arrangement has been reported to date. Indeed, it has only very recently been established that PS1 is a 9-TMD protein (17,18). PS is endoproteolytically processed into an N-terminal fragment (NTF) and C-terminal fragment (CTF) (19). These fragments are metabolically stable, remain associated, and their formation is tightly regulated (20). Also, it is widely † This work was supported by grants to M.S.W. from the National Institutes of Health (NS41355 and AG17574) and the Alzheimer's Association (IIRG-02-4047) and a fellowship to H. L. (Wenner-Gren Foundation in Sweden). An understanding of the mechanism of γ-secretase proteolysis requires a detailed description of the three-dimensional organization of its transmembrane domains. In light of inherent difficulties in obtaining a structure of γ-secr...