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Literature DB >> 20398753

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. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

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Year: 2010 PMID： 20398753 PMCID： PMC2906686 DOI： 10.1016/j.jsbmb.2010.03.086

Source DB: PubMed Journal: J Steroid Biochem Mol Biol ISSN： 0960-0760 Impact factor: 4.292

27 in total

Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid.

1. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations.

2. HCPM--program for hierarchical clustering of protein models.

3. BioShell--a package of tools for structural biology computations.

4. Folding pathway of the b1 domain of protein G explored by multiscale modeling.

5. Utility library for structural bioinformatics.

6. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.

Review 7. Nuclear receptors and lipid physiology: opening the X-files.

Review 8. The RXR heterodimers and orphan receptors.

9. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Review 10. The steroid and thyroid hormone receptor superfamily.

Review 1. The retinoid X receptors and their ligands.

2. CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

3. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.

4. Structure prediction of the second extracellular loop in G-protein-coupled receptors.