Fig. 1

Chemical structures of the ligands used in the study. In the present study, the effect of AhR ligands (TCDD, I3C, FICZ, DIM, RES, PTL) on the protein dynamics, structure, stability and free energy landscape was examined using MDS and free energy calculations. Specifically, different conformational and ligand bound states of AhRLBD-TCDD, AhRLBD-FICZ, AhRLBD-RES, AhRLBD-PTL, AhRLBD-DIM, AhRLBD-I3C complexes were simulated to reveal the entire catalytic cycle, including the conformational change, substrate binding, protein dynamics, side chain interactions, and thermodynamics. The study provides a molecular level understanding of how the residues on AhR LBD interact with these ligands