Mechanism and Energetics of Ligand Release in the Aspartate Transporter Glt(Ph)

The bacterial aspartate transporter Glt(Ph) cotransports three Na+ ions with the substrate. The mechanism and energetics of ligand binding have previously been studied using molecular dynamics simulations on the crystal structure of Glt(Ph) captured in the outward-facing state. Here we use the recent crystal structure of the inward-facing state of Glt(Ph) to study the reverse process of unbinding of ligands. Gating behavior is studied in the presence of different ligands. A detailed characterization of the intracellular gate is given, pointing out the differences from the extracellular gate. We then perform free energy simulations to calculate the binding affinities of all the ligands in different combinations, from which the unbinding order is determined as Na2, (gate opens), Asp, Na1, and Na3. The strong coupling between Asp and Na1 is quantified from several free energy calculations. Na3 has the largest affinity to Glt(Ph), and therefore, its unbinding is proposed as the rate-limiting step in the transport cycle. The release time of Na3, estimated from Kramers' rate theory, is shown to be consistent with the experimental turnover rate of the transporter.