External loop 5 (EL5) of serotonin transporter was analyzed by mutating each of the residues from Thr-480 to Ala-511, one at a time, with cysteine. Cysteine was well-tolerated at most positions, although G485C, Y495C, and E508C had low transport activities. Replacement with cysteine rendered mutants G484C-P499C sensitive to partial or complete inactivation by [2-(trimethylammonium)ethyl] methanethiosulfonate and (2-sulfonatoethyl) methanethiosulfonate. Within this sensitive region, the rates of reaction varied by over 2 orders of magnitude. Rates of inactivation were not significantly affected by removal of Na(+) or by addition of cocaine or serotonin. These results suggest that modification of EL5 interferes with the transport process but is not sensitive to substrate and ion binding.

Intramembrane proteolysis is a new and rapidly growing field. In vitro assays utilizing recombinant substrates for γ-secretase, an intramembrane-cleaving enzyme, are critically important in order to characterize the biochemical properties of this unusual enzyme. Several recombinant Notch proteins of varying length are commonly used as in vitro substrates for CHAPSO-solubilized γ-secretase. Here we report that several recombinant Notch construct undergo limited or no proteolysis in vitro. Instead, upon incubation with or without γ-secretase, variants of the intact protein migrate during SDS-PAGE at the location expected for the γ-secretase specific cleavage products. In addition, we show that addition of aspartyl-and γ-secretase specific protease inhibitors are able to retard the formation of these variants independent of γ-secretase, which could lead to the erroneous conclusion that Notch cleavage by solubilized γ-secretase was achieved in vitro even when no proteolysis occurred. In contrast, substrates produced in mammalian or insect cells are cleaved efficiently in vitro. These observations suggest that in vitro studies reliant on recombinant, bacterially produced Notch TMD should be performed with the inclusion of additional controls able to differentiate between actual cleavage and this potential artifact.γ-Secretase, a multi-protein enzymatic complex with aspartyl-protease activity, is a member of a unique class of proteases classified as Intramembrane Cleavage Proteases (I-CliPs), which catalyze cleavage of substrate proteins within the hydrophobic lipid bilayer (1,2). Clinical † PKC and RK are supported by Washington University and the national institutes of health grant P50 AG05681 *Author for correspondence: Kopan@wustl.edu, (3,4). γ-Secretase is also responsible for the cleavage of many other proteins, most notably Notch, which is critical not only for early embryonic development and adult immune system function, but is involved in stem cell maintenance and in several diseases including cancer, stroke, and multiple sclerosis (5,6,7,8,9,10). Lastly, despite an intense interest in this enzyme as a therapeutic target (9-14), γ-secretase remains a member of a novel class of proteases whose catalytic properties are largely unknown (15) and thus an increasing number of laboratories will join in the effort to characterize this activity.Several groups have developed in vitro cleavage assays whereby the ability of partially purified γ-secretase, in CHAPSO-solubilized membrane extracts, to cleave recombinant Notch proteins is measured (16). While there are several variations reported for how to enrich membrane fractions with γ-secretase (17,18), the size and complexity of this enzyme may preclude the determination of its high-resolution structure using current techniques. Nonetheless, a structural study of γ-secretase substrates would shed considerable light on the mechanism of cleavage until structural information for the entire enzyme becomes available. It has been established that truncated substrate...