Fig. 5.

Formation of H bonds linking the extracellular pathway to the chloride binding site during molecular dynamics simulations of LeuT. Data represent interactions of R30 exclusively with either Q250 (green bars) or D404 (blue bars), both residues simultaneously (orange bars), or neither (gray bars) for (A) outward-open apo (3TT1), (B) outward-occluded holo (3F48), and (C) inward-open apo (3TT3) conformations of LeuT. Panels indicate snapshots representing the most highly populated states in each conformational states of the transporter, and the colors of the borders matches that of the bars. An H bond is counted as present if the minimum distance between the H bond donor/acceptor atoms of the side chains is <3.2 Å and was computed every 100 ps. The results are averaged over three simulation repeats, each 2 µs long, and the error bars represent the SD.