Figure 5.

Molecular dynamics simulations of sphingosine-1-phosphate receptors. (A) Detailed view of the narrow channel of S1P₁ where the alkyl tail of S1P (in orange) must expand. The end of the channel is delimited by the amino acids at positions 4.56, 5.42 and 5.46. The structure depicts the final conformation at 0.2 μs. (B) Same as in panel A but rotated 180°. (C) Volume of the channel in S1P₁ (black), S1P₂ (red), S1P₄ (blue) and S1P₅ (green) along the MD trajectories with the natural S1P agonist as calculated with POVME⁴⁹. (D) Sequence alignment, among sphingosine receptors, of the amino acids forming this channel. (E) The final conformation, at 0.2 μs, obtained in the MD simulations of S1P₄ in complex with C16 (in green) and S1P₅ in complex with C20 (in orange).