Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
Figure 5
The transition to the inward-facing conformation opens up a pathway towards the cytoplasm for the Na2-ion lined by TM1 (red), TM5 (orange), TM6 (green), and TM8 (yellow). The 5-HT substrate is shown in spheres and colored by atom type, with carbons in purple. Protein residues are shown in gray sticks, and the Na2-ion is shown as a cyan sphere with the initial position of the Na2-ion indicated as a transparent light blue sphere. Water molecules found in the intracellular cavity is indicated by light gray sticks and a transparent surface. A. The snapshot after 33.9 ns molecular dynamics simulation in Sim8 where the Na2-ion is located just below the initial binding pocket formed by Ser438, Leu434, Val97, Gly94, and Asp437. The only coordination partners remaining are Asp437 and Gly94, which are located in the bottom of the ion binding site. B. Molecular dynamics snapshot after 75.4 ns (33.9 ns snapshot from Sim8 and additional 41.5 ns in Sim8b). The Na2-ion is partly transported and located between the two aromatic residues Phe347 and Phe440 and coordinated by the acidic residue Glu444. C. The Na2-ion is completely transported after 80.4 ns (33.9 ns in Sim8 and additional 46.5 ns in Sim8b) and is fully solvated by water and does not possess any interactions with the protein. D. The monitored positions of the Na2-ion in Sim8b are displayed as cyan spheres during the additional 50 ns of simulation started from the Sim8 snapshot. The spheres indicate the transport pathway of the Na2-ion from the central ion binding site to the cytoplasm. It can be observed that TM1, TM5, TM6, and TM8 are lining the transport pathway.