The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
Fig 10
Three representative ligands analyzed in the docking simulations.
The left panels of (A), (B) and (C) show the one dimensional projection of binding free energy landscape to RMSD with high, medium and low ISR with similar affinity as well as the corresponding structures of the different ligands, where the docked pose with the most stable affinity or the strongest binding state is chosen as the reference structure to calculate the RMSDs; the Autodock score function is used to evaluate the interaction energies between the ligand and the receptor. (high:fork structure, medium:near-linear structure, low:linear structure);the right panels of them show the corresponding binding energy spectrum for each, the sparse part of the spectrum implies there are fewer states, and dense part of the spectrum implies there are more states. (D) show the kinetic time for binding for the above three different ISRs. The upper black line represents the predicted kinetic timeoff and the under black line represents the predicted kinetic timeon. The vertical axis represents the calculated kinetic time.