Conformational mapping of the cytosolic linker between domains III and IV of the cardiac Na+ channel protein and binding studies with a site-directed channel modifying antibody.

By combining antibody binding studies with conformational mapping using synthetic peptides, the structure of the cytosolic linker between domains III and IV of the cardiac Na+ channel alpha-subunit was analyzed. Inside-out patch clamp experiments with isolated cardiac Na+ channels from neonatal rat cardiocytes confirmed that a polyclonal antibody against amino acids 1490-1507 of the cardiac Na+ channel recognizes the linker in situ since Na+ inactivation became significantly retarded. Epitope fine mapping with a series of overlapping peptides identified the sequence YYNAMKKLG (corresponding to amino acids 1496-1504 of the cardiac sodium channel alpha-subunit) as the binding locus of the site directed antibody, an interesting result with respect to structure-function relationships because the functionally important hydrophobic amino-acid cluster in position 1487-1489 is not included. Circular dichroism measurements of synthetic 20-mer peptides in hydrophilic and lipophilic environments provided indications for a notable alpha-helical content only for segment GGQDIFMTEEQKKYYNAMKK. This sequence corresponds to amino acids 1483-1502 in the linker and adopts a highly ordered pattern of charge distribution due to this helical conformation. Ordered structure and helix dipole moment represent physical properties which may be important in a refined model for explaining the function of the linker in terminating the open channel configuration.