Atomic-level characterization of conformational transition and substrate binding of xCT transporter

xCT is a component of heterodimeric amino acids transporter system Xc- that has been known to work at the cross-roads of maintaining neurological processes and regulating antioxidant defense. xCT is a sodium-independent amino acid antiporter, that imports L-cystine and exports L-glutamate in a 1:1 ratio. The transporter has 12 transmembrane domains with intracellular N- and C-termini, which can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward facing occluded state and outward facing open state. We investigated the conformational transitions within these two states by employing series of targeted molecular dynamics simulations. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. Further, we analyzed the ligand binding within the intermediate conformations obtained from the transition simulations. We docked anionic L-cystine and L-glutamate within the cavities alone or in combination to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligand and xCT and observed that ligands bind to similar residues within the channel, and these residues are essential for substrate binding/permeation. In addition, we analyzed the correlations between ligand binding and conformational transition and observed conformations that are representatives for intermediate ligand bound states. The results presented in the study provide insights into the interplay of conformational transition and ligand binding as xCT goes from one probable conformation to another while transporting the ligand. And the data thus adds to the existing evidence of alternating access mechanism pertaining to the functioning of transporters.