Figure 7.

Molecular dynamics ensembles of the Ex4-related polypeptide ligands bound to GLP-1R. Molecular dynamics simulations were started from a model built from the cryo-EM structure of the human GLP-1/GLP-1R complex (PDB code 6X18) (for further details, see the Experimental Section). (a) Structural representation of Ex4-Tc5b variants with a tightening Tc fold. (b) Distance distribution of the centroids of residues W25 (ligand side) and W214^GLP-1R (of the ECL1 loop of the GLP-1R receptor) and (c) distribution of the χ₁ dihedral angle of W214^GLP-1R in the simulated complexes and in experimentally determined structures of the human GLP-1R complexes (see data availability). Most abundant (d–g) gauche(−) orientation of W214^GLP-1R corresponding to an arrangement where W214^GLP-1R (green) and W39^GLP-1R (blue) of the receptor enclose the F/Y-X-X-W-L motif of the ligand and (h,i) antiperiplanar orientation of W214^GLP-1R in which the two receptor Trp-s are positioned near each other, leaving the ligand core exposed. (j) RBS analysis of the trajectories. Independently moving segments are colored differently. Gray coloring indicates regions that were not resolved into any of the rigid segments and, thus, move completely freely. The number of structures shown for each complex corresponds to the number of clusters needed to represent at least 95% of the snapshots, reflecting the structural heterogeneity of the systems. The TM6 segments of the ligand variants, whose dynamic properties most significantly influence signal transduction, are highlighted by a red circle.