Epitopes for monoclonal antibodies directed against the purified adult rat skeletal muscle sodium channel (rSkM1) were localized using channel proteolysis and fusion proteins. The interactions between these and other monoclonal antibodies with site-specific polyclonal antibodies were used to investigate the spatial relationships among rSkM1 cytoplasmic segments. Competition between antibodies for binding was performed using a solution-phase assay in which solubilized channel protein retains many of the biophysical characteristics of the rSkM1 protein in vivo. Our results support a model in which: 1) the amino terminus assumes a rigid structure having a fixed orientation with respect to other intracellular segments; 2) the interdomain 2-3 region is centrally located on the cytoplasmic surface of the channel, extends farther into the cytoplasm, and has an intermediate degree of flexibility; 3) the beginning of the amino terminus and end of the carboxyl terminus specifically interact with each other; and 4) domains 1 and 4 are adjacent. The sequences responsible for the interaction of the amino and carboxyl termini were identified by demonstrating the specific binding of a synthetic peptide encompassing the first 30 residues of the rSkM1 amino terminus to a fusion protein containing the rSkM1 carboxyl terminus.In studies of voltage-dependent ion channels, a major goal is to correlate specific aspects of protein structure with channel function. In order to attain this goal, an accurate model of channel tertiary structure is required. Sequence information for a variety of voltage-dependent sodium channels is now available, providing the basis for several models of channel tertiary structure (1-5). All current models postulate the presence of four membrane-embedded homologous domains joined by cytoplasmic linking and terminal sequences. Although the models were initially based largely on theoretical considerations, various aspects have been tested using a variety of molecular, biochemical, and immunological techniques, and their general features have been validated.In previous studies, we used a combination of limited proteolysis and antibody binding to provide experimental support for the presence of four compact repeat domains in the skeletal muscle sodium channel, to identify the topography of the regions that join and flank these domains, and to probe the relative orientation of the large extramembrane cytoplasmic elements (6 -11). This work also allowed us to map the location of epitopes for monoclonal antibodies we had previously generated against purified sodium channel protein. Our binding studies divided these antibodies into two large groups based on mutually exclusive competition (11). While epitopes in each group were typically clustered in similar regions of the channel sequence, in several cases we found monoclonals in the same group that recognized epitopes widely separated in the primary sequence but presumably brought together in the native protein by folding of the polypeptide backbone (6, 12). Ident...