Vesicle fusion in eukaryotes is thought to involve the assembly of a highly conserved family of proteins termed soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) into a highly stable parallel four-helix bundle. We have used intermolecular single-molecule fluorescence resonance energy transfer to characterize preassembled neuronal SNARE complexes consisting of syntaxin, synaptobrevin, and synaptosome-associated protein of 25 kDa on deposited lipid bilayers. Surprisingly, we found a mixture of parallel as well as antiparallel configurations involving the SNARE motifs of syntaxin and synaptobrevin as well as those of syntaxin and synaptosome-associated protein of 25 kDa. The subpopulation with the parallel four-helix bundle configuration could be greatly enriched by an additional purification step in the presence of denaturant, indicating that the parallel configuration is the energetically most favorable state. Interconversion between the configurations was not observed. From this observation, we infer the conversion rate to be <1.5 h ؊1 . The existence of antiparallel configurations suggests a regulatory role of chaperones, such as N-ethylmaleimide-sensitive factor, or the membrane environment during SNARE complex assembly in vivo, and it could be a partial explanation for the relatively slow rates of vesicle fusion observed by reconstituted fusion experiments in vitro.A ll membrane fusion events in eukaryotes are thought to involve a highly conserved family of proteins termed soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) (1, 2). The neuronal SNAREs syntaxin, synaptosome-associated protein of 25 kDa (SNAP-25), and synaptobrevin are involved in the Ca 2ϩ -dependent fusion of synaptic vesicles with the presynaptic plasma membrane (3). Before synaptic vesicle docking, the individual SNAREs, syntaxin and SNAP-25, are primarily found on the plasma membrane, where they may exist as unfolded monomers, preformed binary complexes, or in complex with chaperones. At some point during docking and fusion of synaptic vesicles, heterotrimeric SNARE complexes form between syntaxin, SNAP-25, and the synaptic vesicle SNARE, synaptobrevin. SNARE complex formation is thought to occur first in trans with proteins on opposite membranes, and end with formation of a cis complex with proteins residing in the same membrane. Thus, SNARE complex crystal structures (4-7) probably represent the state of the SNARE complex at the endpoint of the fusion reaction (8).The inhibition of neurotransmitter release after the specific cleavage of any one of the SNAREs by clostridial neurotoxin proteases supports the fundamental role of the SNARE proteins in synaptic vesicle fusion (9, 10). However, whereas high concentrations of SNAREs have been shown to be sufficient to fuse synthetic liposomes in vitro (11), the molecular relationship between SNARE complex formation and Ca 2ϩ -triggered vesicle-membrane fusion in vivo remains unclear (12).Syntaxin, SNAP-25, and synaptobrevin have been the...