Fig 1.
Notations of the 7 transmembrane helices (H1 to H7) and the intracellular helix H8. (A) Ribbon representation. (B) Bendix representation, ranging from blue (no helix tilt) to red (maximum helix tilt).
Fig 2.
Superimposition of the heavy atoms and MARTINI beads of lipid.
(A) POPC, (B) DPPC, and (C) POPE.
Table 1.
Protocol of the coarse-grained MD simulations.
Table 2.
RMSD comparison for each μOR helix embedded in POPC membrane.
Table 3.
Tilt angle, using Bendix, for μOR embedded in POPC membrane.
Table 4.
Tilt angle of H5, with standard deviations for the μOR embedded in POPC membrane.
Table 5.
Maximum tilt angles, with standard deviations, of each helix of μOR.
Table 6.
Tilt angle of the two part of helix H5 with standard deviation.
Fig 3.
Number of contacts between each protein bead and each lipid bead type.
(A) POPC, (B) DPPC, and (C) POPE, as obtained from the 15 μs CG MD runs at P = 1.01325 bar and T = 310 K. The D3B bead in POPC and POPE is replaced by a C3B in DPPC. Lines between the points are present to guide the reading of the graphs.
Fig 4.
Primary structure of μOR in (A) POPC, (B) DPPC, and (C) POPE membrane.
Each AA of μOR is colored as a function of its contact frequency with the lipids, as obtained from the 15 μs CG MD runs at P = 1.01325 bar and T = 310 K, ranging from yellow (0%) to red (100%).
Fig 5.
Network graph of lipid movements around μOR.
Network graph obtained using Gephi as determined from the three 15 μs CG MD runs at P = 1.01325 bar and T = 310 K of (A) POPC, (B) DPPC, and (C) POPE interacting with μOR for the external and internal membrane layers. Each circle represents a site of μOR, according to helix label. As an example, 167 stands for helices H1, H6, and H7. The more often a site is visited by lipids, the larger the circle. In the same way, a connection between two nodes is thicker when the lipid transfer frequency between two protein sites is higher. In each network, the node color shade is a function of the clustering results, as described in Materials and Methods.