Fig. 5: High level of structural adaptation at the designed receptor–peptide binding interface.
From: Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis
a WT CXCR4 ligand-binding cavity with depths marked for N-terminal residues P3, P5, and P7. b Cross-sectional area across cluster centers from molecular dynamics simulations. (mean ± s.d.) c 3D map of structure-function relationship. Activity shifts from WT of individual receptor–peptide pairs (z-axis for potency and bars colored according to maximal activity) are plotted as a function of conformational shifts of the peptide (y-axis: calculated by Principal Component Analysis on bound peptide ensembles (see Methods)) and conformational shifts of the receptor binding pocket (x-axis: calculated by cross-sectional area at the P5 depth, 10.25 Å (see Methods)) for the center of the largest cluster of conformations.
