Figure 1.
Molecular Mechanics/Coarse-grained system set-up.
A) Schematic representation of the regions defined in the MM/CG model. The MM, I and CG regions are colored in green, orange, light blue, respectively. B) MM/CG representation of the hTAS2R38 receptor in complex with PTC. Water molecules and residues belonging to the MM and I regions are represented as lines. The agonist atoms are represented as orange spheres. The protein Cα atoms are represented in violet.
Figure 2.
β2 AR in complex with the S-Car ligand.
A) S-Car binding site of the central structure of the only cluster of the MM/CG simulations. This cluster represent 100% of the conformations of the adduct. B) RMSD of the Cα atoms plotted as a function of time in the MM/CG simulations. C–D) Distribution of agonist-protein H-bonds in the MM/CG simulations of the β2 AR/S-Car complex based on the X-ray structure [14] (black line) and on an homology model (violet line, this work).
Figure 3.
Central structures of PTC/A - PROP/A and PTC/B - PROP/B main clusters emerging from our MM/CG simulations.
Residues forming mostly or exclusively hydrophobic contacts with the agonists (Met100, Phe264, Phe197, Trp99, Trp201, Tyr193) are colored in green, pink, orange, light violet, purple, yellow, respectively. The agonists are shown in ball-and-sticks representation and they are colored by atom type. The ECL2 loop interacts with the binding site only in the A complexes. It is shown in red cartoon. Selected distances for Asn179, Thr180, Arg181 and Asn183 residues in the ECL2 loop are shown for PTC/A and PROP/A.
Figure 4.
Dose-response curves of TAS2R38 wild type and mutants after stimulation with increasing PTC and PROP concentrations (0 to 1000 µM). Each point corresponds to the mean ± standard deviation. The mean is calculated from at least three independent experiments. A–C) PTC application, D–F) PROP application.
Table 1.
Selected MM/CG distances (in Angstrom) in the central structure of the main clusters of the PTC/B and PROP/B adducts.
Table 2.
Experimental EC50 and maximum activity values towards PTC and PROP obtained for WT TAS2R38 and selected mutants.
Figure 5.
Dose-response curves of TAS2R38 wild type and mutants after stimulation with increasing PTC and PROP concentrations (0 to 1000 µM). Each point corresponds to the mean ± standard deviation. The mean is calculated from at least three independent experiments. A–D) PTC application, E–H) PROP application.
Figure 6.
Dose-response curves of TAS2R38 wild type and mutants after stimulation with increasing PTC and PROP concentrations (0 to 1000 µM). Each point corresponds to the mean ± standard deviation. The mean is calculated from at least three independent experiments. A-E) PTC application, F-J) PROP application.
Figure 7.
Binding of PTC and PROP to the TAS2R38 bitter receptor as emerging from MM/CG simulations and experiments. Residues forming hydrophobic interactions and H-bonds with the agonists are indicated in blue and red, respectively. Residues shaping the cavities are in black color. The ECL2 loop does not interact directly with the agonists.
Table 3.
Analysis of the positions mutated in this work that were also mutated in other members of the bitter receptors family.