Fig 1.
A. Simulation boxes for the FSHR and LHCGR (orange and lavender structures, respectively). The leucine rich region (LRR), hinge region (HR) and transmembrane (TM) domain are indicated. The SDPC bilayer is depicted with the lipid tails as white spheres, and the phosphorus atoms of the lipid heads as olive spheres. Solvent water molecules are depicted as small spheres in blue-gray. Side chains of cysteine residues are depicted in licorice, green for the FSHR and yellow for the LHCGR. Disulfide bonds are identified for C292-C338 and C276-C356 in the FSHR structure, and C279-C336 in that of the LHCGR. The bond C292-C338 at the HR of FSHR was not defined between C336 and C304, which are the homologous positions in the LHCGR. B. Structural alignment of the FSHR model (orange cartoons) and its corresponding cryo-EM structure (cyan cartoons) bound to its cognate agonist (not shown) and the Gs-protein. In the background as context, lipid tails are depicted as white sticks; phosphate atoms, as olive spheres; and cysteine atoms in licorice lavender and blue for FSHR and 8I2G structures, respectively. The conformation of both structures corresponds to the active conformation [21].
Table 1.
Relative distances among the LRR, HR, and TM domains of the receptors’ structures and the FSHR AF model.
Fig 2.
Distances among structural domains of the FSHR.
(A) Distance LRR-HR vs LRR -TM. (B) Distance LRR-HR vs TM-HR. (C) Distance LRR-TM vs TM-HR. Numbers in parenthesis indicate the correlation coefficients for every pair of distances. Color code: R1-blue, R2-magenta, and R3-gray.
Fig 3.
Distances between structural domains of the LHCGR.
(A) Distance LRR-HR vs LRR -TM. (B) Distance LRR-HR vs TM-HR. (C) Distance LRR-TM vs TM-HR. Numbers in parenthesis are the correlation coefficients for every pair of distances. Color code: R1 gray, R2 magenta, and R3 blue, POPC carbon gray.
Fig 4.
RMSD matrix analysis (gray scale) for the TM helices of LHCGR.
(A) replicate R1, (B) replicate R2, (C) replicate R3, and (D) trajectory in POPC. Red solid lines along the diagonal were drawn for visual identification of self-similar groups. The cluster analysis is shown in the insets. Conformations in clusters include structures within 0.5 Å of RMSD among each other. The cluster number is identified in the vertical axis. Horizontal segments along the curve identify the time frames forming a given cluster.
Fig 5.
Principal component analysis for the LHCGR.
PC1 and PC2 (A-C) and PC3-PC4 (D-F) of trajectories R1-3 (blue dots). Projections for cluster 6383 of R1 (A, D), 4193 of R2 (B,E) and 2964 of R3 (C,F; black dots); clusters 2595 of R2 (B,E), and 1404 of R3 (C,F; lavender dots). TM domain conformations in clusters were identified with a 0.5 Å RMSD cutoff, ie. a structure was included whenever its RMSD was lower than 0.5 Å from any of the members in that cluster.
Fig 6.
Distributions of the trajectory projections on the first four eigenvectors for the LHCGR in replicates R1 (brown), R2 (orange), and R3 (brown-orange). PC1 (A), PC2 (B), PC3 (C), and PC4 (D).
Fig 7.
RMSD matrix analysis (gray scale) for the TM helices of the FSHR.
A. replicate R1; B. replicate R2; and C. replicate R3. The corresponding cluster analyses are shown in the insets. Conformations in clusters include structures within 0.5 Å of RMSD among each other. The cluster number is identified in the vertical axis. Horizontal segments along the curve identify the time frames forming a given cluster.
Fig 8.
Principal component (PC) analysis in the FSHR.
Projections on PC1-PC2 (A-C) and PC3-PC4 (D-F) of trajectories R1-3 (blue dots). Projections for clusters 3405 in R1, 1171 in R2, and 0733 in R3 are included (black dots). Clusters include conformations whose RMSD difference is lower than 0.5 Å in the TM domain region.
Fig 9.
Distributions of the trajectory projections on the first four eigenvectors for the FSHR in replicates R1 (orange), R2 (brown-orange), and R3 (brown).
PC1 (A), PC2 (B), PC3 (C), and PC4 (D).
Fig 10.
Projection of the first principal component (PC1) on the 3D structure of the gonadotropin receptors.
A. FSHR (orange structure) with arrows on Cα atoms that represent the amplitude and directions of the motion of PC1. B. LHCGR (orange structure) with arrows on Cα atoms that represent the amplitude and directions of the motion of PC1. Color code for arrows: yellow-R1, white-R2, and lavender-R3. Motion of the extracellular regions dominated the dynamics of the receptors. The LHCGR showed divergent motions in replicates R1 to R3 as trajectories started from configurations, respectively, at 0 ns,100 ns, and 180 ns of the POPC run.
Fig 11.
Distances among the LRR, HR and TM domain in the LHCGR (Å) in R1 (upper plots), R2 (middle plots) and R3 (lower plots). Analysis for clusters 6383 of R1; 1129, 2596, and 4193 of R2; and 1404, 2407, and 2964 of R3.
Fig 12.
Distances among LRR, HR and TM domains of the FSHR (Å). Blue dots, group 3406 of R1; magenta dots, group 1171 of R2; and black dots, group 0733 of R3.