Integrative modeling of diverse protein-peptide systems using CABS-dock
Fig 7
Correlation between substrate binding and movement of the flaps of HIV-1 protease observed during a docking simulation.
Ligand binding is characterized by the distance between the carbonyl oxygen atom of the substrate’s 5th peptide bond and the center of the enzyme’s active site (x-axis on the plot). Flap movement is monitored as the distance between the Cα atoms of two GLY:52 residues located in chains A and B of HIV-1 protease (y-axis on the plot). The left panel shows HIV-1 protease with a bound substrate and closed flaps. The right panel shows the enzyme without a bound substrate and with open flaps. The enzyme and substrate are presented in a trace representation for clarity. Two HIV-1 protease domains are shown in blue and green. The substrate is marked in red. Two catalytic aspartic acid residues, showing the center of the enzyme’s active site, are marked with yellow spheres.
doi: https://doi.org/10.1371/journal.pcbi.1011275.g007