Understanding the mechanism of ion-coupled transport requires investigation of both the structural rearrangements necessary for moving substrates and ions across the membrane and also the interactions between ligands and their binding sites that determine when these rearrangements take place. We have studied the conformational changes that occur in neurotransmitter transporters and their bacterial homologues and examined the way that ion and substrate binding regulate these changes. In this family of neurotransmitter-sodium symporters (NSS) the transport mechanism involves two ligand-dependent conformational changes. Sodium binding stabilizes these proteins in an outward-facing conformation and subsequent binding of substrate overcomes the conformational restriction imposed by sodium to allow conversion of the transporter to an inward-facing state from which substrates and sodium can be released to the cytoplasm. Networks of ionic and hydrophobic interactions are responsible for these actions of sodium and substrate. These studies, together with recent structural discoveries, have required re-evaluation of the transport stoichiometry for biogenic amines such as serotonin, dopamine or norepinephrine.