Induced fit in liver X receptor beta: a molecular dynamics-based investigation.
Identifieur interne : 000048 ( Ncbi/Checkpoint ); précédent : 000047; suivant : 000049Induced fit in liver X receptor beta: a molecular dynamics-based investigation.
Auteurs : Alexandre Beautrait [France] ; Arnaud S. Karaboga ; Michel Souchet ; Bernard MaigretSource :
- Proteins [ 1097-0134 ] ; 2008.
Descripteurs français
- KwdFr :
- Cristallographie aux rayons X, Ligands, Modèles moléculaires, Protons, Protéines de liaison à l'ADN (), Protéines de liaison à l'ADN (métabolisme), Récepteurs cytoplasmiques et nucléaires (), Récepteurs cytoplasmiques et nucléaires (métabolisme), Récepteurs nucléaires orphelins, Simulation numérique, Structure secondaire des protéines, Structure tertiaire des protéines.
- MESH :
- métabolisme : Protéines de liaison à l'ADN, Récepteurs cytoplasmiques et nucléaires.
- Cristallographie aux rayons X, Ligands, Modèles moléculaires, Protons, Protéines de liaison à l'ADN, Récepteurs cytoplasmiques et nucléaires, Récepteurs nucléaires orphelins, Simulation numérique, Structure secondaire des protéines, Structure tertiaire des protéines.
English descriptors
- KwdEn :
- Computer Simulation, Crystallography, X-Ray, DNA-Binding Proteins (chemistry), DNA-Binding Proteins (metabolism), Ligands, Models, Molecular, Orphan Nuclear Receptors, Protein Structure, Secondary, Protein Structure, Tertiary, Protons, Receptors, Cytoplasmic and Nuclear (chemistry), Receptors, Cytoplasmic and Nuclear (metabolism).
- MESH :
- chemical , chemistry : DNA-Binding Proteins, Receptors, Cytoplasmic and Nuclear.
- chemical , metabolism : DNA-Binding Proteins, Receptors, Cytoplasmic and Nuclear.
- Computer Simulation, Crystallography, X-Ray, Ligands, Models, Molecular, Orphan Nuclear Receptors, Protein Structure, Secondary, Protein Structure, Tertiary, Protons.
Abstract
Ligand induced fit phenomenon occurring at the ligand binding domain of the liver X receptor beta (LXRbeta) was investigated by means of molecular dynamics. Reliability of a 4-ns trajectory was tested from two distinct LXRbeta 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 LXRbeta 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 LXRbeta-related induced fit process. This protocol could therefore be used for refining ligand docking solutions of a structure-based design strategy.
DOI: 10.1002/prot.21977
PubMed: 18275080
Affiliations:
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Karaboga</name></author><author><name sortKey="Souchet, Michel" sort="Souchet, Michel" uniqKey="Souchet M" first="Michel" last="Souchet">Michel Souchet</name></author><author><name sortKey="Maigret, Bernard" sort="Maigret, Bernard" uniqKey="Maigret B" first="Bernard" last="Maigret">Bernard Maigret</name></author></analytic><series><title level="j">Proteins</title><idno type="eISSN">1097-0134</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation</term><term>Crystallography, X-Ray</term><term>DNA-Binding Proteins (chemistry)</term><term>DNA-Binding Proteins (metabolism)</term><term>Ligands</term><term>Models, Molecular</term><term>Orphan Nuclear Receptors</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term><term>Protons</term><term>Receptors, Cytoplasmic and Nuclear (chemistry)</term><term>Receptors, Cytoplasmic and Nuclear (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cristallographie aux rayons X</term><term>Ligands</term><term>Modèles moléculaires</term><term>Protons</term><term>Protéines de liaison à l'ADN ()</term><term>Protéines de liaison à l'ADN (métabolisme)</term><term>Récepteurs cytoplasmiques et nucléaires ()</term><term>Récepteurs cytoplasmiques et nucléaires (métabolisme)</term><term>Récepteurs nucléaires orphelins</term><term>Simulation numérique</term><term>Structure secondaire des protéines</term><term>Structure tertiaire des protéines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA-Binding Proteins</term><term>Receptors, Cytoplasmic and Nuclear</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA-Binding Proteins</term><term>Receptors, Cytoplasmic and Nuclear</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines de liaison à l'ADN</term><term>Récepteurs cytoplasmiques et nucléaires</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Crystallography, X-Ray</term><term>Ligands</term><term>Models, Molecular</term><term>Orphan Nuclear Receptors</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term><term>Protons</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cristallographie aux rayons X</term><term>Ligands</term><term>Modèles moléculaires</term><term>Protons</term><term>Protéines de liaison à l'ADN</term><term>Récepteurs cytoplasmiques et nucléaires</term><term>Récepteurs nucléaires orphelins</term><term>Simulation numérique</term><term>Structure secondaire des protéines</term><term>Structure tertiaire des protéines</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ligand induced fit phenomenon occurring at the ligand binding domain of the liver X receptor beta (LXRbeta) was investigated by means of molecular dynamics. Reliability of a 4-ns trajectory was tested from two distinct LXRbeta 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 LXRbeta 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 LXRbeta-related induced fit process. This protocol could therefore be used for refining ligand docking solutions of a structure-based design strategy.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Vandœuvre-lès-Nancy</li></settlement><orgName><li>Nancy-Université</li></orgName></list><tree><noCountry><name sortKey="Karaboga, Arnaud S" sort="Karaboga, Arnaud S" uniqKey="Karaboga A" first="Arnaud S" last="Karaboga">Arnaud S. Karaboga</name><name sortKey="Maigret, Bernard" sort="Maigret, Bernard" uniqKey="Maigret B" first="Bernard" last="Maigret">Bernard Maigret</name><name sortKey="Souchet, Michel" sort="Souchet, Michel" uniqKey="Souchet M" first="Michel" last="Souchet">Michel Souchet</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Beautrait, Alexandre" sort="Beautrait, Alexandre" uniqKey="Beautrait A" first="Alexandre" last="Beautrait">Alexandre Beautrait</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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