title: Ligand entry pathways in the ligand binding domain of PPARγ receptor.
abstract: To address the question of ligand entry process, we report targeted molecular dynamics simulations of the entry of the flexible ionic ligand GW0072 in the ligand binding domain of the nuclear receptor PPARγ. Starting with the ligand outside the receptor the simulations led to a ligand docked inside the binding pocket resulting in a structure very close to the holo-form of the complex. The results showed that entry process is guided by hydrophobic interactions and that entry pathways are very similar to exit pathways. We suggest that TMD method may help in discriminating between ligands generated by in silico docking.
authors.affiliation: Centre de Biophysique Moléculaire, UPR 4301-Affiliated to the University of Orléans, CNRS, Orléans, France. samia.aci@cnrs-orleans.fr
authors.forename: Samia
authors.initials: S
authors.lastname: Aci-Sèche
authors.forename: Monique
authors.initials: M
authors.lastname: Genest
authors.forename: Norbert
authors.initials: N
authors.lastname: Garnier
mesh_terms: D008024:Ligands; D056004:Molecular Dynamics Simulation; D047495:PPAR gamma / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D008024:Ligands; D047495:PPAR gamma