Figure 7.

Configuration changes of the TM3–TM6 aromatic cluster associated with the conformational transition simulated in the 660 ns MD trajectory. The starting conformation was the LeuT crystal structure⁶, in which the Leu molecule found in the S1 site (PDB 2A65) was removed (a) and (b) are the crystal structures with substrate (Leu)⁶ or inhibitor (Trp)⁷ bound in the S1 site, respectively. Y107 and Y108 from TM3, and F252 and F253 from TM6 are rendered in sticks. The ligands are in space-filling representation. (c) The outward movement of TM6 (with Na⁺ only bound) indicated by a white arrow, overlaps the one evident in the LeuT-Trp structure (PDB 3F3A)⁷, which has been proposed to represent the ‘open-to-out’ conformation. (d) Superimposed view of the aromatic cluster in the context of the Na1 site. The side chains are colored corresponding to the backbone colors in a–c. The overlap between F253 (in the Na-only simulation) and the Trp in the extracellular vestibule of the Trp-bound crystal structure (Trp602 of PDB 3F3A), is indicated by a dotted circle. Only the ligand and Na⁺ ions from the Trp-bound structure are shown. (e) Changes in Χ¹ rotamer values for the aromatic cluster residues along the MD trajectory.