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Cluster Induced fit in liver X receptor beta: a molecular dynamics-based investigation

Alexandre Beautrait 1 Arnaud S. Karaboga Michel Souchet Bernard Maigret 1
1 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : Ligand induced fit phenomenon occurring at the ligand binding domain of the liver X receptor beta (LXR) was investigated by means of molecular dynamics. Reliability of a 4-ns trajectory was tested from two distinct LXR crystal complexes 1PQ6B/GW and 1PQ9B/T09 characterized by an open and a closed state of the pocket, respectively. Crossed complexes 1PQ6B/T09 and 1PQ9B/GW were then submitted to the same molecular dynamic conditions, which were able to recover LXR conformations similar to the original crystallography data. Analysis of open to closed and closed to open conformational transitions pointed out the dynamic role of critical residues lining the ligand binding pocket involved in the local remodeling upon ligand binding (e.g., Phe271, Phe329, Phe340, Arg319, Glu281). Altogether, the present study indicates that the molecular dynamic protocol is a consistent approach for managing LXR-related induced fit process. This protocol could therefore be used for refining ligand docking solutions of a structure-based design strategy.
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Submitted on : Sunday, November 16, 2008 - 10:07:41 PM
Last modification on : Friday, February 26, 2021 - 3:28:05 PM


  • HAL Id : inria-00339117, version 1



Alexandre Beautrait, Arnaud S. Karaboga, Michel Souchet, Bernard Maigret. Cluster Induced fit in liver X receptor beta: a molecular dynamics-based investigation. Proteins - Structure, Function and Bioinformatics, Wiley, 2008, 72 (3), pp.873-882. ⟨inria-00339117⟩



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