SecA protein of Escherichia coli, when added externally to the vesicles composed of phosphatidylethanolamine, dioleoylphosphatidylglycerol and cardiolipin, was found to be fragmented by trypsin encapsulated within the vesicles. In the presence of ATP or its non-hydrolyzing analogue, ATP-gamma S, the number of fragments and extent of hydrolysis occurred much less than in the absence of these compounds. When ADP was added, however, the hydrolysis products were similar to those when no nucleotide was present. Quenching of SecA fluorescence by vesicle-entrapped iodide corroborated the digestion results. These experiments demonstrated that the SecA protein traverses the lipid bilayer and its membrane topology depends on the kind of nucleotide present. (C) 1994 Academic Press, Inc.