Molecular Dynamics Simulations On The AhR-Ligand Binding Modes

The aryl hydrocarbon receptor(AhR)is a ligand-dependent transcription factor belonging to the basic Helix-Loop-Helix Per-Arnt-Sim(bHLH/PAS)family.They are able to activate gene expressions of downstream factors in an AhR-dependent manner,leading to carcinogenic,teratogenic effects,biotransformation and so on.The ligands of AhR can be classified into two types synthetic ligands and natural ligands.The synthetic AhR ligands includes the halogenated aromatic hydrocarbons(HAHs),the non-halogenated polycyclic aromatic hydrocarbons(PAHs),and the derivatives of PAHs,such as the polychlorinated dibenzo-p-dioxins(PCDDs),the polychlorinated dibenzofurans(PCDFs),2,3,7,8-tetrachlor-odibenzo-p-dioxin(TCDD,dioxin)etc.Several studies have demonstrated that the AhR contributes to the regulation of autoimmune responses,cancer progression,inflammation,cell migration,cell growth,and apoptosis.In this study,the four mutation models(WT,Phe289A1a,Tyr316A1a,Ile319Ala)were performed using the amber99sb force field of GROMACS software package.The complex stability,protein conformational change,active site volume and binding free energy of the binary complex were analysized by "gatekeeper" residues function.Via molecular dynamics(MD)simulation,the effects of different ligands on AhR ligand binding domain(LBD)were comprehensively analyzed by four distinct aspects including protein-ligand binding mode,binding free energy,changes of protein conformation and changes of the binding pocket.The results indicated that mutagenesis will reduce the stablility of AhR ligand binding domain(LBD)environment,and Phe289,Tyr316 and Ile319 play "gatekeeper" roles through hydrophobic interaction.The whole structure analysis demonstrates that mutagenesis comes from the pockets,which will destabilize cavity environment,causing obvious fluctuations and leading to low ligand-affinity and ligand escape.Via the interaction of AhR with different ligands,it is indicated various ligands have dissimilar binding sites in the LBD pocket.Moreover,some key amino acid residues,e.g.Phe289,Phe318,Gln377 etc.,are in presence in diverse AhR-ligand binding modes,conferring AhR adaptability to different ligands in space through their own structural fine control.We also found amino acid residues as Phe289,Ile619,and Met342 were highly accountable to the binding free energies.Our observations highlighted a kind of adapting process by which AhR could adjust its own conformation and shape to accommodate different ligands.The main conformational adjustments occurred in the A-B-loop and E-alpha.These simulation results interpret some experimental phenomena and provide further structural informations that are useful in drug design based on AhR.