Figure 1.
Binding of ligands in S1P1 extracellular pocket.
(A) Ligand structures after equilibration: antagonist (yellow) and agonist (purple). Helices represent the crystal structure; (B) The structures of ligand-receptor complexes after 700 ns MD simulations. The antagonist-receptor structure colored in blue, while agonist-receptor structure in yellow.
Figure 2.
Rotamer switches at S1P1 extracellular region.
(A) Apo S1P1, the χ1 angle of Y982.57 changed at 100 ns while W2696.48 and F2656.44 were stable during the whole simulation; (B, B′) antagonist ML056/S1P1, the χ1 angle of Y982.57 changed at 550 ns (or 300 ns in 2nd simulation); the χ2 of W2696.48 fluctuated in the initial 500 ns of simulation and it was stable in 2nd simulation; F2656.44 was stable in both simulation with antagonist; (C, C′) agonist S1P/S1P1, the χ1 angle of Y982.57 was relatively stable while both the χ2 angle of W2696.48 and χ1 of F2656.44 fluctuated considerably during the simulations. Internal water molecules are shown as pink dots. The initial structures of complexes after equilibration are shown in grey, while the final structures are shown in color. Blue dashed ellipse indicates lack of a flip of residue Y982.57 in case of complex with agonist.
Figure 3.
Water molecules in vicinity of residue D912.50 in agonist-bound receptor during MD simulation.
(A) 0 ns; (B) 100 ns; (C) 700 ns. Only water molecules within 4 Å of residue D912.50 are shown.
Figure 4.
Water molecules at the intracellular side.
(A, A′) Number of water molecules within 4 Å of the NPxxY motif at TM7. Apo S1P1 in black, complex with antagonist in green, and complex with agonist in red. (B) The final structures including water molecules near NPxxY motif in Apo (on left) and agonist-bound receptor (on right). Antagonist-bound structure is similar to the Apo S1P1.
Figure 5.
Movement of intracellular part of TM7 in agonist-bound receptor structure.
(A) The superimposed initial (grey) and final (yellow) agonist-bound structures. (B) Plot of the kink angle in TM7 with a pivot point at P3087.50 for both simulations with agonist. During the simulation TM7 is gradually bending and the kink angle is changing from 155° to 130°.
Figure 6.
Movements of transmembrane helices in S1P1 receptor.
(A) RMSD of S1P1 TM regions during MD simulations. Apo S1P1 in black, ML056/S1P1 in green and cyan, and S1P/S1P1 in red and blue. (B) Different states of agonist-bound receptor structure during MD simulation. The 3D plot shows distances between cytoplasmic ends of TM helices: TM7-TM3, TM3-TM6 and TM6-TM7. The central structures from each cluster are shown. The “intermediate” and “active” conformations are superimposed on the “inactive” one (in grey).
Figure 7.
Proposition of activation mechanism of S1P1.
Binding of agonist (S1P) can lead to conformational changes of highly conserved residues W2696.48 and F2656.44 (step 1 and 2) forming a core of a transmission switch. Afterwards, rearrangement of centrally located residues facilitate the redirected flow of water molecules inside a receptor (step 3) which is a prerequisite for a larger motion of cytoplasmic parts of transmembrane helices (step 4).