Mitochondria-mediated apoptosis is regulated by proteins of the Bcl-2 superfamily, most of which contain a C-terminal hydrophobic domain that plays a role in membrane targeting. Experiments with BNIP3 have implicated the transmembrane (TM) domain in its proapoptotic function, homodimerization, and interactions with Bcl-2 and Bcl-x L . We show that the BNIP3 TM domain self-associates strongly in Escherichia coli cell membranes and causes reversible dimerization of a soluble protein in the detergent SDS when expressed as an in-frame fusion. Limited mutational analysis identifies specific residues that are critical for BNIP3 TM selfassociation in membranes, and these residues are also important for dimerization in SDS micelles, suggesting that the self-association observed in membranes is preserved in detergent. The effects of sequence changes at positions Ala 176 and Gly 180 suggest that the BNIP3 TM domain associates using a variant of the GXXXG motif previously shown to be important in the dimerization of glycophorin A. The importance of residue His 173 in BNIP3 TM domain dimerization indicates that polar residues, which have been implicated in self-association of model TM peptides, can act in concert with the AXXXG motif to stabilize TM domain interactions. Our results demonstrate that the hydrophobic C-terminal TM domain of the pro-apoptotic BNIP3 protein dimerizes tightly in lipidic environments, and that this association has a strong sequence dependence but is independent of the identity of flanking regions. Thus, the transmembrane domain represents another region of the Bcl-2 superfamily of proteins that is capable of mediating strong and specific protein-protein interactions.The Bcl-2 superfamily of proteins plays a central role in regulating mitochondria-mediated apoptosis; the Bax subfamily promotes apoptosis, whereas the Bcl-2 subfamily protects against apoptosis (reviewed in Ref. 1). Protein-protein interactions between Bax and Bcl-2 subfamily members help determine cell fate (2, 3) and have accordingly been the subject of intensive study. Four regions of sequence homology, the BH1 through BH4 domains, contribute to the structure and function of these proteins, and the BH3 domain is particularly implicated in heterodimerization events (4 -9). Peptide and small molecule inhibitors of these protein-protein interactions can modulate apoptosis, further demonstrating the functional and pharmaceutical importance of these contacts (10 -13).Differentiation and development in metazoans requires celland signal-specific inputs to a functional Bcl-2/Bax checkpoint. The pro-apoptotic "BH3-only" proteins, which show homology to the Bcl-2 superfamily through the BH3 domain alone (14), are expressed or activated in specific tissues and in response to certain stimuli, making them candidates for connecting diverse signaling pathways to the ubiquitous apoptosis effector machinery (15, 16). BNIP3 (Bcl-2/19-kDa interacting protein 3) is a BH3-only protein whose expression and pro-apoptotic activity is induced following hyp...