Molecular dynamics simulations are used to gain insight into the binding of Na+ and leucine substrate to the bacterial amino acid transporter LeuT, focusing on the crystal structures of LeuT in the outward-open and inward-open states. For both conformations of LeuT, a third Na+ binding site involving Glu290 in addition to the two sites identified from the crystal structures is observed. Once the negative charge from Glu290 in the inward-open LeuT is removed, the ion bound to the third site is ejected from LeuT rapidly, suggesting that the protonation state of Glu290 regulates Na+ binding and release. In CL-dependent transporters where Glu290 is replaced by a neutral serine, a Cl- ion would be required to replace the role of Glu290. Thus, the simulations provide insights into understanding Na+ and substrate transport as well as Cl--independence of LeuT. (C) 2015 Elsevier Inc. All rights reserved.