Genest, D ; Garnier, N ; Arrault, A ; Marot, C ; Morin-Allory, L ; Genest, M
European Biophysics Journal 37 (4) 369-379
publié le , mis à jour le
Conformational rearrangements of peroxysome proliferator activated receptor (PPAR ?) ligand-binding domain (LBD) that accompany the release and binding of ligands are not well understood. To determine the major events associated with the escape of the partial agonist GW0072, molecular dynamic (MD) simulations were performed using two different methods : reversed targeted molecular dynamics (TMD-1) and time-dependent distance restraints (TDR) using as restraints either the root mean square deviation from a reference structure (TMD-1) or the distance between the geometrical centers of the binding pocket and of the ligand (TDR). Both methods do not assume any a priori route for ligand extraction.