Fluorescein isothiocyanate (FITC) was used to selectively label the rabbit intestinal brush-border imino carrier, identify the binding protein on SDS-polyacrylamide gel electrophoresis, and monitor the effect of ions on fluorescein quenching. FITC inhibits Na+-dependent L-proline transport irreversibly, but transport is protected by physiological concentrations of Na+ and L-proline. About 1 nmol of FITC/mg of protein binds specifically to the transporter, which was identified by SDS-polyacrylamide gel electrophoresis as a 100 +/- 5-kDa peptide. Na+ produced a specific, saturable quench in the fluorescence of FITC bound to the proline carrier. Both transport and FITC quenching are inhibited by n-acetylimidazole, and membranes are protected from acetylation by Na+. We conclude that Na+ binds to the proline carrier (100-kDa peptide) to produce a change in conformation that results in an increase in the affinity of the carrier for proline.