Ligand-specific structural changes in the vitamin D receptor in solution

Biochemistry

Volumn 50, Issue 51, 2011, Pages 11025-11033

  Singarapu, Kiran K ^a   Zhu, Jinge ^a   Tonelli, Marco ^a   Rao, Hongyu ^a   Assadi Porter, Fariba M ^a   Westler, William M ^a   Deluca, Hector F ^a   Markley, John L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2-METHYLENE; BINDING POCKETS; BIOLOGICAL ACTIVITIES; COACTIVATORS; CRYSTALLOGRAPHIC STRUCTURE; LIGAND BINDING DOMAIN; LIGAND-BINDING SITES; MOLECULAR MECHANISM; NATURAL HORMONE; NUCLEAR HORMONE RECEPTOR; PROTEIN CONFORMATION; SELECTIVE RECRUITMENT; STRUCTURAL CHANGE; TRANSACTIVATION DOMAIN; VITAMIN D RECEPTOR; VITAMIN-D;

BINDING SITES; CHEMICAL SHIFT;

LIGANDS;

2 METHYLENE 19 NOR 1,25 DIHYDROXYVITAMIN D3; 2 METHYLENE 25 CAROBOBUTOXY 26,27 CYCLO 22 DEHYDRO 1ALPHA,24 DIHYDROXY 19 NORVITAMIN D3; CALCITRIOL; UNCLASSIFIED DRUG; VITAMIN D RECEPTOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HORMONE RECEPTOR INTERACTION; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; RAT; SIGNAL TRANSDUCTION; TRANSACTIVATION;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; BONE DENSITY CONSERVATION AGENTS; CALCITRIOL; DATABASES, PROTEIN; LIGANDS; MEDIATOR COMPLEX SUBUNIT 1; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, SECONDARY; RATS; RECEPTORS, CALCITRIOL; RECOMBINANT FUSION PROTEINS; SOLUBILITY;

EID: 84055184366     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201637p     Document Type: Article

References (35)

1. Mangelsdorf, D. J., Thummel, C., Beato, M., Herrlich, P., Schutz, G., Umesono, K., Blumberg, B., Kastner, P., Mark, M., Chambon, P., and Evans, R. M. (1995) The nuclear receptor superfamily: the second decade Cell 83, 835-839
2. DeLuca, H. F. (2008) Evolution of our understanding of vitamin D Nutr. Rev. 66, S73-S87
3. Holick, M. F. (2008) The vitamin D deficiency pandemic and consequences for non-skeletal health: Mechanism of action Mol. Aspects Med. 29, 361-368
4. Bikle, D. (2009) Nonclassic Actions of Vitamin D J. Clin. Endocrinol. Metab. 94, 26-34
5. Ramagopalan, S. V., Heger, A., Berlanga, A. J., Maugeri, N. J., Lincoln, M. R., Burrell, A., Handunnetthi, L., Handel, A. E., Disanto, G., Orton, S. M., Watson, C. T., Morahan, J. M., Giovannoni, G., Ponting, C. P., Ebers, G. C., and Knight, J. C. (2010) A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution Genome Res. 20, 1352-1360
6. Brown, A. J. and Slatopolsky, E. (2008) Vitamin D analogs: Therapeutic applications and mechanisms for selectivity Mol. Aspects Med. 29, 433-452
7. Wurtz, J. M., Bourguet, W., Renaud, J. P., Vivat, V., Chambon, P., Moras, D., and Gronemeyer, H. (1996) A canonical structure for the ligand-binding domain of nuclear receptors Nat. Struct. Biol. 3, 87-94
8. Lu, J. Y., Cistola, D. P., and Li, E. (2006) Analysis of ligand binding and protein dynamics of human retinoid X receptor alpha ligand-binding domain by nuclear magnetic resonance Biochemistry 45, 1629-1639 (Pubitemid 43222107)
9. Johnson, B. A., Wilson, E. M., Li, Y., Moller, D. E., Smith, R. G., and Zhou, G. C. (2000) Ligand-induced stabilization of PPAR gamma monitored by NMR spectroscopy: Implications for nuclear receptor activation J. Mol. Biol. 298, 187-194
10. MacDonald, P. and Dowd, D. R. (2011) Vitamin D, in Vitamin D (Feldman, D., Pike, J. W., and Adams, J. S., Eds.) 3 rd ed., pp 193-209, Elsevier, London.
11. Nolte, R. T., Wisely, G. B., Westin, S., Cobb, J. E., Lambert, M. H., Kurokawa, R., Rosenfeld, M. G., Willson, T. M., Glass, C. K., and Milburn, M. V. (1998) Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma Nature 395, 137-143 (Pubitemid 28425645)
12. Bourguet, W., Ruff, M., Chambon, P., Gronemeyer, H., and Moras, D. (1995) Crystal Structure of the Ligand-Binding Domain of the Human Nuclear Receptor RXR-alpha Nature 375, 377-382
13. Huang, P. X., Chandra, V., and Rastinejad, F. (2010) Structural Overview of the Nuclear Receptor Superfamily: Insights into Physiology and Therapeutics Annu. Rev. Physiol. 72, 247-272
14. Moras, D. and Gronemeyer, H. (1998) The nuclear receptor ligand-binding domain: structure and function Curr. Opin. Cell Biol. 10, 384-391 (Pubitemid 28287050)
15. Shiau, A. K., Barstad, D., Loria, P. M., Cheng, L., Kushner, P. J., Agard, D. A., and Greene, G. L. (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen Cell 95, 927-937 (Pubitemid 29019045)
16. Brzozowski, A. M., Pike, A. C., Dauter, Z., Hubbard, R. E., Bonn, T., Engstrom, O., Ohman, L., Greene, G. L., Gustafsson, J. A., and Carlquist, M. (1997) Molecular basis of agonism and antagonism in the oestrogen receptor Nature 389, 753-758 (Pubitemid 27458965)
17. Vanhooke, J. L., Benning, M. M., Bauer, C. B., Pike, J. W., and DeLuca, H. F. (2004) Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D-3 hormone analogues and a LXXLL-containing coactivator peptide Biochemistry 43, 4101-4110 (Pubitemid 38445629)
18. Vanhooke, J. L., Tadi, B. P., Benning, M. M., Plum, L. A., and DeLuca, H. F. (2007) New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D-3 with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations Arch. Biochem. Biophys. 460, 161-165 (Pubitemid 46589395)
19. Tocchini-Valentini, G., Rochel, N., Wurtz, J. M., Mitschler, A., and Moras, D. (2001) Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands Proc. Natl. Acad. Sci. U. S. A. 98, 5491-5496 (Pubitemid 32435669)
20. Klaholz, B. P., Mitschler, A., Belema, M., Zusi, C., and Moras, D. (2000) Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRAR gamma Proc. Natl. Acad. Sci. U. S. A. 97, 6322-6327 (Pubitemid 30412712)
21. Klaholz, B. P., Renaud, J. P., Mitschler, A., Zusi, C., Chambon, P., Gronemeyer, H., and Moras, D. (1998) Conformational adaptation of agonists to the human nuclear receptor RAR gamma Nat. Struct. Biol. 5, 199-202 (Pubitemid 28113751)
22. Shevde, N. K., Plum, L. A., Clagett-Dame, M., Yamamoto, H., Pike, J. W., and DeLuca, H. F. (2002) A potent analog of 1 alpha,25-dihydroxyvitamin D-3 selectively induces bone formation Proc. Natl. Acad. Sci. U. S. A. 99, 13487-13491 (Pubitemid 35215408)
23. Glebocka, A., Sicinski, R. R., Plum, L. A., Clagett-Dame, M., and DeLuca, H. F. (2006) New 2-alkylidene 1 alpha,25-dihydroxy-19-norvitamin D-3 analogues of high intestinal activity: Synthesis and biological evaluation of 2-(3 '-alkoxypropylidene) and 2-(3-hydroxypropylidene) derivatives J. Med. Chem. 49, 2909-2920
24. Pellecchia, M., Sebbel, P., Hermanns, U., Wuthrich, K., and Glockshuber, R. (1999) Pilus chaperone FimC-adhesin FimH interactions mapped by TROSY- NMR Nat. Struct. Biol. 6, 336-339 (Pubitemid 29166481)
25. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPIPE-A Multidimensional Spectral Processing System Based on UNIX Pipes J. Biomol. NMR 6, 277-293
26. Bartels, C., Xia, T. H., Billeter, M., Güntert, P., and Wüthrich, K. (1995) The Program XEASY for Computer-Supported NMR Spectral-Analysis of Biological Macromolecules J. Biomol. NMR 5, 1-10
27. Eghbalnia, H. R., Wang, L., Bahrami, A., Assadi, A., and Markley, J. L. (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements J. Biomol. NMR 32, 71-81 (Pubitemid 41086469)
28. Shen, Y., Delaglio, F., Cornilescu, G., and Bax, A. (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44, 213-223
29. 13C Chemical Shifts J. Biomol. NMR 4, 171-180
30. Farmer, B. T., II (1996) Localizing The NADP + Binding Site on the Murb Enzyme by NMR Nat. Struct. Biol. 3, 995-997 (Pubitemid 27014626)
31. DeLano, W. L. and Lam, J. W. (2005) PyMOL: A communications tool for computational models Abstr. Pap. Am. Chem. Soc. 230, U1371-U1372
32. Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y. E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C. F., Tolmie, D. E., Kent Wenger, R., Yao, H., and Markley, J. L. (2008) BioMagResBank Nucleic Acids Res. 36, D402-408
33. Heery, D. M., Kalkhoven, E., Hoare, S., and Parker, M. G. (1997) A signature motif in transcriptional co-activators mediates binding to nuclear receptor Nature 387, 733-736 (Pubitemid 27270617)
34. Le, H. and Oldfield, E. (1994) Correlation between 15N NMR chemical shifts in proteins and secondary structure J. Biomol. NMR 4, 341-348
35. Güntert, P. (2004) Automated NMR structure calculation with CYANA Methods Mol. Biol. 278, 353-378