Ligand-escape pathways from the ligand-binding domain of PPARγ receptor as probed by molecular dynamics simulations

Abstract

Conformational rearrangements of peroxysome proliferator activated receptor (PPARgamma) 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. To avoid artifacts, different initial simulation conditions were used and particular attention was paid for giving time to the protein to relax during the extraction process by running 10-12 ns simulations within explicit water. Two distinct exit gates A and B were found, independently of initial conditions and method. During the exit process no interaction between GW0072 and the transactivation AF-2 helix was observed. Our results suggest that the ligand uses the intrinsic flexibility of the protein to move within the receptor. Paths A and B are very similar to those found for other nuclear receptors, suggesting that these routes are a common characteristics of nuclear receptors that are used by different kinds of ligands. Finally, the knowledge of entry/exit pathways of a receptor should be very useful in discriminating between different ligands that could have been favorably docked in the binding pocket by introducing docking along these pathways into computational drug design protocols.

A Restrained Molecular Dynamics Empirical Approach for Generating a Small Set of Structures Representative of the Internal Flexibility of a Receptor

“…It does not intend to replace traditional MD simulations for studying the actual internal dynamics of biological macromolecules since it assumes that the deformation of the receptor is articulated about cold points. This assumption is consistent with our previous study showing that the atomic fluctuation pattern observed during the extraction process of a ligand from the receptor is not very different from the pattern observed for the apo-protein [41].…”

Investigating the disorder–order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation

“…N is the number of atoms that were specified to be restrained by the external forces, while K is the force constant. After several preliminary tests and considering some other studies using TMD method (Cheng et al, 2006;Genest et al, 2008;Swift and McCammon, 2008;Warner et al, 2009), K was set to 5 kcal mol À1 Å À2 in our simulation. We made use of a steps-closer method (Mendieta et al, 2005;Liu et al, 2006), in which the RMSD between the initial structure and the targeted structure decreases by 0.5 Å in 300 ps and keeps stable in the subsequent 400 ps for each step until RMSD reaches 1.5 Å .…”

Extracting ligands from receptors by reversed targeted molecular dynamics

“…This method has also been called TMD À1 [12]. The system has a quasi-unlimited number of options to fulfil RMSD tgt , i.e., state B is a priori undefined.…”

“…For ERRc, the chosen ligand is bisphenol A (BPA) and for PPARc we opt for the partial agonist compound GW0072, also studied by Genest et al [12]. The structures are shown in Fig.…”

“…The application of steered MD or targeted MD to extract ligands from receptors has been applied to various receptor-ligand systems, providing insight in possible paths for ligands and structural adaptions of the receptor [1][2][3][4][5][6][7][8][9][10][11][12][13].…”