We previously raised an antibody (RA6.3) by an antiidiotypic approach which was designed to be directed against an amiloride binding domain on the epithelial Na ؉ channel (ENaC). This antibody mimicked amiloride in that it inhibited transepithelial Na ؉ transport across A6 cell monolayers. RA6.3 recognized a 72-kDa polypeptide in A6 epithelia treated with tunicamycin, consistent with the size of nonglycosylated Xenopus laevis ␣ENaC. RA6.3 specifically recognized an amiloride binding domain within the ␣-subunit of mouse and bovine ENaC. The deduced amino acid sequence of RA6.3 was used to generate a three-dimensional model structure of the antibody. The combining site of RA6.3 was epitope mapped using a novel computer-based strategy. Organic residues that potentially interact with the RA6.3 combining site were identified by data base screening using the program LUDI. Selected residues docked to the antibody in a manner corresponding to the ordered linear array of amino acid residues within an amiloride binding domain on the ␣-subunit of ENaC. A synthetic peptide spanning this domain inhibited the binding of RA6.3 to ␣ENaC. This analysis provided a novel approach to develop models of antibody-antigen interaction as well as a molecular perspective of RA6.3 binding to an amiloride binding domain within ␣ENaC.Epithelial Na ϩ channels (ENaCs) 1 are expressed in a variety of tissues, including the distal nephron of the kidney, airway and alveolar epithelia in the lung, surface cells in the distal colon, urinary bladder epithelia, skin, and ducts within salivary and sweat glands (1). These transporters facilitate the movement of Na ϩ across the apical (or luminal) plasma membrane and have a critical role in extracellular fluid volume homeostasis, control of blood pressure, fetal lung maturation, and maintenance of airway fluids (1). ENaCs consist of at least three homologous subunits, termed ␣-, -, and ␥ENaC, and are thought to form a tetrameric complex consisting of 2␣-, 1-, and 1␥-subunits (2-5), although one group has suggested a subunit stoichiometry of 3␣-, 3-, and 3␥-subunits (6). cDNAs encoding these Na ϩ channel subunits have been isolated and characterized from a variety of species. Each ENaC subunit has two predicted membrane-spanning domains. The amino-and carboxyl-terminal regions of the ENaCs are cytoplasmic, and each subunit has a large ectodomain (7-9). Domains of largely hydrophobic residues are located immediately following the putative first membrane-spanning domains and immediately preceding the second membrane-spanning domains of ␣-, -and ␥rENaC (8, 10, 11). The hydrophobic domain immediately preceding the second membrane-spanning region of ENaC (referred to as the H2 domain) may insert in the membrane and form part of the channel pore (3,7,12).The diuretic drug amiloride is a prototypic inhibitor of epithelial Na ϩ channels. Several sites have been identified within the epithelial Na ϩ channel which participate in amiloride binding. Mutagenesis studies suggest that residues preceding the second ...