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Temple University, Philadelphia, PA, USA.‘Flucs’ are small membrane proteins widespread in bacteria, single-celled eukaryotes, and plants. Only recently characterized, Flucs act as fluoride-specific ion channels, forming antiparallel dimers of four-helix transmembrane bundles. Little else is known about this protein family. To gain insight into the structure and function of the Flucs, we use direct-coupling analysis (DCA) and ab initio molecular modeling to generate all-atom models of the E. coli Fluc homodimer EC2. DCA uses large multiple sequence alignments to infer the interdependencies between residue positions in protein families and is robust at predicting protein contacts from sequence alone. Taking into account simple geometric considerations and strong experimental evidence for an antiparallel homodimer, we are able to parse the inter-and intra-monomeric contacts predicted by DCA. These contacts are …