Fig. 4: Molecular dynamics simulations investigate the CLR binding pocket stability.
From: Structural basis for lipid-mediated activation of G protein-coupled receptor GPR55
a, b Averaged CLR mass density plot generated from martini coarse-grained simulations for (a) martini system 1 (CLR is placed in the structure pose) and (b) for martini system 2 (CLR was removed), the yellow circle highlights the CLR density in both figures. c Superimposition of final structures from all-atom system 1 (shown in cyan) containing CLR and ML184 with system 4 (shown in yellow) where ML184 and CLR were removed shows that significant changes in the protein conformation is observed (black arrow) when the CLR molecule was removed from the binding site. The structural CLR molecule is shown in green and ML184 is shown in orange. d Enlarged view of the CLR binding pocket and (e) surface representation show that CLR binding site is occluded significantly. The all-atom simulation without ML184 and CLR also has an impact on the ligand binding pocket as shown in (f, g). h Overview of four simulated all-atom systems with the RMSD of the ML184 binding pocket calculated from the representative structure of the most populated cluster, compared to system 1. n.a.: not applicable.
