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Ligand entry pathways in the ligand binding domain of PPARγ receptor
Author(s) -
Aci-Sèche Samia,
Genest Monique,
Garnier Norbert
Publication year - 2011
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2011.07.014
Subject(s) - ligand (biochemistry) , docking (animal) , chemistry , in silico , biophysics , receptor , nuclear receptor , molecular dynamics , stereochemistry , computational biology , biochemistry , biology , computational chemistry , transcription factor , medicine , nursing , gene
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.