Interactions between transmembrane helices play a key role in almost all cellular processes involving membrane proteins. We have investigated helix-helix interactions in lipid bilayers with synthetic tryptophan-flanked peptides that mimic the membrane spanning parts of membrane proteins. The peptides were functionalized with pyrene to allow the self-association of the helices to be monitored by pyrene fluorescence and Trp-pyrene fluorescence resonance energy transfer (FRET). Specific labeling of peptides at either their N or C terminus has shown that helix-helix association occurs almost exclusively between antiparallel helices. Furthermore, computer modeling suggested that antiparallel association arises primarily from the electrostatic interactions between ␣-helix backbone atoms. We propose that such interactions may provide a force for the preferentially antiparallel association of helices in polytopic membrane proteins. Helix-helix association was also found to depend on the lipid environment. In bilayers of dioleoylphosphatidylcholine, in which the hydrophobic length of the peptides approximately matched the bilayer thickness, association between the helices was found to require peptide/lipid ratios exceeding 1/25. Selfassociation of the helices was promoted by either increasing or decreasing the bilayer thickness, and by adding cholesterol. These results indicate that helix-helix association in membrane proteins can be promoted by unfavorable protein-lipid interactions.Most membrane proteins have one or more hydrophobic segments that span the membrane in an ␣-helical conformation. Interactions between these transmembrane (TM) 4 helices are important for determining the structure of multispanning membrane proteins and for assembly of membrane proteins into oligomeric structures (1-4). Several factors are thought to be responsible for the association of helices in membrane proteins, including surface complementarity, the presence of polar residues in the transmembrane region (5-7), and certain specific motifs such as the well known GXXXG pattern (8, 9). It is likely that several of these factors act in concert to determine the final folded structure, or the association of monomers to form an oligomer. In addition to helix-helix interactions, interactions between the helices and surrounding lipids also play a role in the organization and assembly of TM helices. For example, even when helices do not exhibit any tendency to undergo specific association (10 -12), helix-helix association could still occur as a result of poor packing between the lipids and helices, or from a favorable change in entropy resulting from the release of helix-bound lipids upon helix association. In these cases, helix association is primarily driven by lipid-protein interactions rather than strongly favorable protein-protein interactions. It is likely that in real membrane proteins the driving forces for folding involve both types of interaction, whether or not specific protein-protein recognition motifs are present.One property of a pr...