The crystal structure of Na+-coupled galactose symporter (vSGLT) reports the transporter in its substrate-bound state, with a Na+ ion modeled in a binding site corresponding to that of a homologous protein, leucine transporter (LeuT). In repeated molecular dynamics simulations, however, we find the Na+ ion instable, invariably and spontaneously diffusing out of the transporter through a pathway lined by D189, which appears to facilitate the diffusion of the ion toward the cytoplasm. Further analysis of the trajectories and close structural examination, in particular, comparison of the Na+-binding sites of vSGLT and LeuT, strongly indicates that the crystal structure of vSGLT actually represents an ion-releasing state of the transporter. The observed dynamics of the Na+ ion, in contrast to the substrate, also suggests that the cytoplasmic release of the Na+ ion precedes that of the substrate, thus shedding light on a key step in the transport cycle of this secondary transporter.
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