Figure 1.
Left: Schematic view of the overall structure of a G protein-coupled receptor (GPCR), with depiction of the connectivity of the intracellular (IL) and extracellular (EL) loops between helices (H).
Right: 3D structure of the reconstructed µOR structure (see “Methods”). Color codes of ILs, ELs, and Hs are identical in both left and right pictures.
Figure 2.
Radius of gyration of the µOR structure along the 0.5 µs all-atom MD simulation.
Figure 3.
Identification of the secondary structure elements of the µOR structure during the 0.5 µs all-atom MD simulation.
Secondary structures are classified according to the color code illustrated below. The regions for the different helices, ILs and ELs, with respect to the µOR structure are depicted on the right side.
Figure 4.
Standard deviation of the mean dihedral angles calculated from the 0.5 µs all-atom MD production between four consecutives Cα atoms along the µOR backbone.
Table 1.
Standard deviation (SD) of the mean dihedral angles computed from sequences of four consecutives Cα atoms along the µOR backbone from the 0.5 µs all-atom MD simulation.
Figure 5.
Root Mean Square Fluctuation (RMSF) of the Cα atoms along the µOR structure computed during the 0.5 µs all-atom MD production.
Color codes of ILs, ELs, and Hs are the same as in Figure 1.
Table 2.
Mean Root Mean Square Fluctuation (RMSF) computed for the Cα atoms of the µOR backbone from the 0.5 µs all-atom MD simulation.
Table 3.
Minimum, maximum, mean, and standard deviation (SD) values of the maximum helix angle value observed using the BENDIX representation for to the different helices of the µOR structure from the 0.5 µs all-atom MD simulation.
Figure 6.
POCASA binding site volume measured every 5 ns of the 0.5 µs all-atom MD simulation of the µOR structure.
Figure 7.
Superimposition of the binding site conformations observed at the 270th (green) and 375th (blue) ns frames, i.e., the frames of the minimum and maximum POCASA volume, respectively, as deserved during the 0.5 µs all-atom MD simulation of the µOR structure.
The three residues labelled, i.e., F153, W293, and Y326, are the only ones located in the minimum volume pocket. The corresponding residues of the binding site conformation related to the maximum POCASA volume are presented in red.
Figure 8.
Representation of the pocket binding site as detected with the POCASA software.
The shape comes from the gathering of the positions of the POCASA probe sphere explored every 100th ns frame of the 0.5 µs all-atom MD simulation of the µOR structure. The five pockets illustrate the variation of the binding site shape during the simulation.
Figure 9.
Domain subdivisions of the µOR structure as obtained using the GeoStaS algorithm applied to the 0.5 µs all-atom MD simulation.
The seven resulting domains are D1 (red), D2 (green), D3 (blue), D4 (cyan), D5 (pink), D6 (yellow), and D7 (black).
Table 4.
Numbers of residues in the helices (H1–H8), ILs, and ELs composing the different domains, i.e., D1 to D7, as determined with the GeoStaS algorithm applied to the 0.5 µs all-atom µOR MD simulation.
Table 5.
Number of edges and its mean value per residue in the residue-residue interaction network determined from the all-atom 0.5 µs MD simulation for the helices, ILs, and ELs of the µOR structure.
Figure 10.
Modularization of the µOR structure as obtained through the network approach applied to the 0.5 µs MD simulation.
The twelve resulting modules are M1 (blue), M2 (red), M3 (gray black), M4 (orange), M5 (yellow), M6 (brown), M7 (gray), M8 (green), M9 (white), M10 (pink), M11 (cyan), and M12 (purple).
Table 6.
Composition in terms of helices (H1–H8), ILs, and ELs of the different modules, i.e., M1 to M12, as determined through the network modularization of the all-atom 0.5 µs MD simulation. Numbers between brackets correspond to the total number of residues gathered in each of the modules of the µOR structure.
Figure 11.
Vector field representation of the three first principal modes obtained from the 0.5 µs all-atom MD simulation of the µOR structure.