title: Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid.
abstract: Study on molecular mechanism of conformational reorientation of RXR-alpha ligand binding domain is presented. We employed CABS--a reduced model of protein dynamics to model folding pathways of binding 9-cis retinoic acid to apo-RXR molecule and TRAP220 peptide fragment to the holo form. Based on obtained results we also propose a sequential model of RXR activation by 9-cis retinoic acid and TRAP220 coactivator. Methodology presented here may be used for investigation of binding pathways of other NR/hormone/cofactor sets.
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. mkurc@chem.uw.edu.pl
authors.forename: Mateusz
authors.initials: M
authors.lastname: Kurcinski
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
mesh_terms: D000077556:Alitretinoin; D001665:Binding Sites; D002467:Cell Nucleus / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D006801:Humans; D008024:Ligands; D056913:Mediator Complex Subunit 1 / Q000378:metabolism*; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D047490:Retinoid X Receptor alpha / Q000378:metabolism*; D014212:Tretinoin / Q000378:metabolism*
chemical_list: D008024:Ligands; D056913:Mediator Complex Subunit 1; D010455:Peptides; D047490:Retinoid X Receptor alpha; D000077556:Alitretinoin; D014212:Tretinoin
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