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

Journal of Steroid Biochemistry and Molecular Biology

Volumn 121, Issue 1-2, 2010, Pages 124-129

  Kurcinski, Mateusz ^a   Kolinski, Andrzej ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

Flexible docking; Molecular modeling; Nuclear receptors; Protein interactions

Indexed keywords

ALITRETINOIN; AMINO ACID; RETINOIC ACID; RETINOID X RECEPTOR ALPHA; TRAP220 PROTEIN; UNCLASSIFIED DRUG; LIGAND; PEPTIDE; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR BINDING PROTEIN; PROTEIN BINDING;

ARTICLE; CRYSTALLOGRAPHY; LIGAND BINDING; METHODOLOGY; PROTEIN FOLDING; PROTEIN STRUCTURE; BINDING SITE; CELL NUCLEUS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; HUMAN; METABOLISM; PROCEDURES; PROTEIN TERTIARY STRUCTURE; THEORETICAL MODEL; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CELL NUCLEUS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HUMANS; LIGANDS; MEDIATOR COMPLEX SUBUNIT 1; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RETINOID X RECEPTOR ALPHA; TRETINOIN;

EID: 77954762639     PISSN: 09600760     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsbmb.2010.03.086     Document Type: Article

References (27)

1. Evans R.M. The steroid and thyroid hormone receptor superfamily. Science 1988, 240(4854):889-895.
2. Mangelsdorf D.J., et al. The nuclear receptor superfamily: the second decade. Cell 1995, 83(6):835-839.
3. Chawla A., et al. Nuclear receptors and lipid physiology: opening the X-files. Science 2001, 294(5548):1866-1870.
4. Mangelsdorf D.J., Evans R.M. The RXR heterodimers and orphan receptors. Cell 1995, 83(6):841-850.
5. Rotkiewicz P., et al. Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3). Proteins 2001, 44(3):188-199.
6. Sicinska W., Rotkiewicz P., DeLuca H.F. Model of three-dimensional structure of VDR bound with Vitamin D3 analogs substituted at carbon-2. J. Steroid Biochem. Mol. Biol. 2004, 89-90(1-5):107-110.
7. Sicinski R.R., et al. 2-Ethyl and 2-ethylidene analogues of 1alpha,25-dihydroxy-19-norvitamin D(3): synthesis, conformational analysis, biological activities, and docking to the modeled rVDR ligand binding domain. J. Med. Chem. 2002, 45(16):3366-3380.
8. Bourguet W., et al. Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha. Nature 1995, 375(6530):377-382.
9. Pogenberg V., et al. Characterization of the interaction between retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers and transcriptional coactivators through structural and fluorescence anisotropy studies. J. Biol. Chem. 2005, 280(2):1625-1633.
10. Kolinski A., Bujnicki J.M. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 2005, 61(Suppl. 7):84-90.
11. Kolinski A., Gront D. Comparative modeling without implicit sequence alignments. Bioinformatics 2007, 23(19):2522-2527.
12. Boniecki M., et al. Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des. 2003, 17(11):725-738.
13. Kmiecik S., Kolinski A. Characterization of protein-folding pathways by reduced-space modeling. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(30):12330-12335.
14. Kmiecik S., et al. Denatured proteins and early folding intermediates simulated in a reduced conformational space. Acta Biochim. Pol. 2006, 53(1):131-144.
15. Kmiecik S., Kolinski A. Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys. J. 2008, 94(3):726-736.
16. Kurcinski M., Kolinski A. Hierarchical modeling of protein interactions. J. Mol. Model. 2007, 13(6-7):691-698.
17. Kurcinski M., Kolinski A. Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences. J. Steroid Biochem. Mol. Biol. 2007, 103(3-5):357-360.
18. Swendsen R.H., Wang J.S. Replica Monte Carlo simulation of spin glasses. Phys. Rev. Lett. 1986, 57(21):2607-2609.
19. Gront D., Kolinski A. Utility library for structural bioinformatics. Bioinformatics 2008, 24(4):584-585.
20. Gront D., Kolinski A. BioShell-a package of tools for structural biology computations. Bioinformatics 2006, 22(5):621-622.
21. Kolinski A. Protein modeling and structure prediction with a reduced representation. Acta Biochim. Pol. 2004, 51(2):349-371.
22. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637.
23. Gront D., Kolinski A. HCPM-program for hierarchical clustering of protein models. Bioinformatics 2005, 21(14):3179-3180.
24. Gront D., Kmiecik S., Kolinski A. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chem. 2007, 28(9):1593-1597.
25. Bower M.J., Cohen F.E., Dunbrack R.L. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J. Mol. Biol. 1997, 267(5):1268-1282.
26. Sorin E.J., Pande V.S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 2005, 88(4):2472-2493.
27. Kmiecik S., Gront D., Kolinski A. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Struct. Biol. 2007, 7. p. 43.