Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
Figure 2
Gate interactions and intracellular pathway.
Transition to the inward-facing conformation causes disruption of the intracellular gate but not the extracellular gate, and solvation of the cytoplasmic pathway to the substrate site occurs. A. The extracellular gate interactions remain stable throughout simulation as illustrated by the depicted shortest distance between the carboxylate oxygen atoms of Glu493 and guanidinium nitrogen atoms of Arg104. B. Arg104 and Glu493 form an ionic interaction and contribute to the extracellular gate. Tyr176 and Phe335 form an aromatic lid on top of the central binding pocket lined by TM1 (red), TM3 (blue), TM6 (green), and TM8 (yellow). Protein side chains are shown in gray, and the 5-HT substrate is colored by atom type with carbons in purple. C. The shortest distance between Asp452 carboxylate oxygen atoms and Arg79 guadinium nitrogen atoms in the intracellular gate are seen. D. In the intracellular gate, Arg79 and Asp452 form an ionic interaction, and Tyr350 and Glu444 interacts via a hydrogen bond. The N-terminal is shown in red, TM6 in green and TM8 in yellow. Protein side chains are shown in gray sticks. E. Calculated SASAs of the proposed cytoplasmic pathway residues (Phe88, Ser91, Gly94, Gly273, Ser277, Val281, Thr284, Phe347, Ala441, Glu444, and Thr448) are shown. The SASA of Sim8 (light blue line) increases from around 200 Å2 to 400 Å2 after 35 ns of simulation. F. Position of cytoplasmic pathway residues in hSERT. TM1, TM5, TM6 and TM8 are shown in light salmon. The remaining TMs are shown in beige. The residues found experimentally to line the cytoplasmic pathway [24], [32]–[34] are displayed in sticks surrounded by transparent surfaces and colored with those from TM1 in red, TM5 in orange, TM6 in green and TM8 in yellow. The POPC bilayer is shown in spheres and colored by atom type with light blue carbons.