Retinoic acid receptor: A simulation analysis of retinoic acid binding and the resulting conformational changes

Journal of Molecular Biology

Volumn 291, Issue 1, 1999, Pages 101-115

  Blondel, Arnaud ^a,d   Renaud, Jean Paul ^b   Fischer, Stefan ^a   Moras, Dino ^b   Karplus, Martin ^a,c  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^c HARVARD UNIVERSITY   (United States)

^d CNRS   (France)

Author keywords

Diffusion; Nuclear receptors; Path calculation; Retinoic acid; X ray structures

Indexed keywords

CELL NUCLEUS RECEPTOR; HELIX LOOP HELIX PROTEIN; MUTANT PROTEIN; RETINOIC ACID; RETINOIC ACID RECEPTOR;

ARTICLE; BIOENERGY; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; DYNAMICS; LIGAND BINDING; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; RECEPTOR BINDING;

EID: 0344931796     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2879     Document Type: Article

References (32)

1. Allenby G., Bocquel M. T., Saunders M., Kazmer S., Speck J., Rosenberger M., Lovey A., Kastner P., Grippo J. F., Chambon P., Levin A. A. Retinoic acid receptors and retinoid X receptors: interactions with endogenous retinoic acids. Proc. Natl Acad. Sci. USA. 90:1993;30-34.
2. Bourguet W., Ruff M., Chambon P., Gronemeyer H., Moras D. Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-α Nature. 375:1995;377-382.
3. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:1983;187-217.
4. Brzozowski A. M., Pike A. C. W., Dauter Z., Hubbard R. E., Bonn T., Engström O., Öhman L., Greene G. L., Gustafsonn J.-Å., Carlquist M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature. 389:1997;753-758.
5. Carlson M. L., Regan R., Elber R., Li H., Phillips G. N. Jr., Olson J. S., Gibson Q. H. Nitric oxide recombination to double mutants of myoglobin: role of ligand diffusion in a fluctuating heme pocket. Biochemistry. 33:1994;10597-10606.
6. Case D. A., Karplus M. Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132:1979;343-368.
7. De Luca L. M. Retinoids and their receptors in differentiation, embryogenesis, and neoplasia. FASEB J. 5:1991;2924-2933.
8. Durand B., Saunders M., Gaudon C., Roy B., Losson R., Chambon P. Activation function 2 (AF-2) of retinoic acid receptor and 9-cis retinoic acid receptor: presence of a conserved autonomous constitutive activating domain and influence of the nature of the response element on AF-2 activity. EMBO J. 13:1994;5370-5382.
9. Elber R., Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion though myoglobin. J. Am. Chem. Soc. 112:1990;9161-9175.
10. Evans S. V. SETOR: hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph. 11:1993;134-138.
11. Fetrow J. S. Omega loops: non-regular secondary structures significant in protein function and stability. FASEB J. 9:1995;708-717.
12. Fischer S., Karplus M. Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom. Chem. Phys. Letters. 194:1992;252-261.
13. Gibson Q. H., Regan R., Elber R., Olson J. S., Carver T. E. Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants. J. Biol. Chem. 267:1992;22022-22034.
14. Hörlein A. J., Näär A. M., Heinzel T., Torchia J., Gloss B., Kurokawa R., Ryan A., Kamei Y., Söderström M., Glass C. K., Rosenfeld M. G. Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature. 377:1995;397-404.
15. Klaholz B. P., Renaud J. P., Mitschler A., Zusi C., Chambon P., Gronemeyer H., Moras D. Conformational adaptation of agonists to the human nuclear receptor RAR-gamma. Nature Struct. Biol. 5:1998;199-202.
16. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
17. Krust A., Green S., Argos P., Kumar V., Walter P., Bornert J. M., Chambon P. The chicken oestrogen receptor sequence: homology with v-erbA and the human oestrogen and glucocorticoid receptors. EMBO J. 5:1986;891-897.
18. Kurokawa R., Söderström M., Hörlein A., Halachmi S., Brown M., Rosenfeld M. G., Glass C. K. Polarity-specific activities of retinoic acid receptors determined by a co-repressor. Nature. 377:1995;451-454.
19. Leid M. Ligand-induced alteration of the protease sensitivity of retinoid X receptor alpha. J. Biol. Chem. 269:1994;14175-14181.
20. Leid M., Kastner P., Chambon P. Multiplicity generates diversity in the retinoic acid signaling pathways. Trends Biochem. Sci. 7:1992;427-433.
21. Leng X., Blanco J., Tsai S. Y., Ozato K., O'Malley B. W., Tsai M. J. Mouse retinoid X receptor contains a separable ligand-binding and transactivation domain in its E region. Mol. Cell. Biol. 15:1995;255-263.
22. Leszczynski J. F., Rose G. D. Loops in globular proteins: a novel category of secondary structure. Science. 234:1986;849-855.
23. Lin B. C., Hong S. H., Krig S., Yoh S. M., Privalsky M. L. A conformational switch in nuclear hormone receptors is involved in coupling hormone binding to corepressor release. Mol. Cell. Biol. 17:1997;6131-6138.
24. Mangelsdorf D. J., Thummel C., Beato M., Herrlich P., Schutz G., Umesono K., Blumberg B., Kastner P., Mark M., Chambon P., Evans R. M. The nuclear receptor superfamily: the second decade. Cell. 83:1995;835-839.
25. Merritt E. A., Murphy M. E. P. Raster3D version 2.0, a program for photorealistic molecular graphics. Acta Crystallog. sect. D. 50:1994;869-873.
26. Renaud J-P., Rochel N., Ruff M., Vivat V., Chambon P., Gronemeyer H., Moras D. Crystal structure of the RAR-γ ligand-binding domain bound to all- trans retinoic acid. Nature. 378:1995;681-689.
27. Saitou M., Narumiya S., Kakizuka A. Alteration of a single amino acid residue in retinoic acid receptor causes dominant-negative phenotype. J. Biol. Chem. 269:1994;19101-19107.
28. Šali A., Blundell T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815.
29. Straub J. E., Karplus M. Energy equipartitioning in the classical time-dependent hartree approximation. J. Chem. Phys. 94:1991;6737-6739.
30. Voegel J. J., Heine M. J. S., Zechel C., Chambon P., Gronemeyer H. TIF2, a 160 kDa transcriptional mediator for the ligand-dependent activation function AF-2 of nuclear receptors. EMBO J. 15:1996;3667-3675.
31. Wagner R. L., Apriletti J. W., McGrath M. E., West B. L., Baxter J. D., Fletterick R. J. A structural role for hormone binding in the thyroid hormone receptor. Nature. 378:1995;690-697.
32. Wurtz J. M., Bourguet W., Renaud J. P., Vivat V., Chambon P., Moras D., Gronemeyer H. A canonical structure for the ligand-binding domain of nuclear receptors. Nature Struct. Biol. 3:1996;87-94.