Panel 1 shows a diagram of protein conformational change upon ligand binding, where interaction with key residues shifts the structure from unbound to bound state. Panel 2 shows a diagram of simulation-based force application on critical residues to reproduce the bound conformation using linear response principles. Panel 3 shows a diagram of directional force probing, where forces applied in multiple directions identify those that drive conformational change toward or away from the bound state.
Principle of LRT. (i) Sketch of experimental structure of a protein in ligand-free (left) and -bound (right) conformation in which ligand (blue) interacts with two critical residues (yellow). (ii) LRT simulation of ligand binding. Forces (black arrows) are applied to critical residues to obtain holo-form of binding site. The predicted conformation of the binding site from the simulation should mimic the experimental holo structure. (iii) In the null LRT model forces are applied in all possible directions to a critical residue (purple) distant from the ligand-free binding site. The conformational change from different force directions are then compared with experimental structures. In that case, the red vector shifts the conformation of the binding site toward its holo-form, while the blue vector initiates a shift in the opposite direction. Hence, ligand binding will presumably exert a force on the critical residue in the direction of the red vector.