Unveiling hidden features of orphan nuclear receptors: The case of the small heterodimer partner (SHP)

Journal of Molecular Graphics and Modelling

Volumn 24, Issue 5, 2006, Pages 362-372

  Macchiarulo, Antonio ^a   Rizzo, Giovanni ^a   Costantino, Gabriele ^a   Fiorucci, Stefano ^a   Pellicciari, Roberto ^a  

^a UNIVERSITY OF PERUGIA   (Italy)

Author keywords

De novo modelling; Homology modelling; Orphan nuclear receptors; Protein docking; Small heterodimer partner; Structure prediction

Indexed keywords

DOCKING; GENES; MOLECULAR STRUCTURE; PROTEINS;

DE NOVO MODELING; HOMOLOGY MODELING; ORPHAN NUCLEAR RECEPTORS; PROTEIN DOCKING; SMALL HETERODIMER PARTNER; STRUCTURE PREDICTION;

DIMERS;

CELL NUCLEUS RECEPTOR; ORPHAN NUCLEAR RECEPTOR; PROTEIN; PROTEIN EID 1; RECEPTOR SUBTYPE; SMALL HETERODIMER PARTNER RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; BAY REGION BINDING SITE; BINDING COMPETITION; FUNCTIONAL PROTEOMICS; GENETIC ASSOCIATION; HIGH BIRTH WEIGHT; MOLECULAR MODEL; MUTAGENESIS; NUCLEOTIDE SEQUENCE; OBESITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEPTOR INTRINSIC ACTIVITY; STRUCTURAL PROTEOMICS; TRANSCRIPTION REGULATION;

ADENOVIRUS E1A PROTEINS; ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; ELECTROSTATICS; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CYTOPLASMIC AND NUCLEAR; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33644617967     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.09.016     Document Type: Article

References (61)

1. J.M. Maglich, A. Sluder, X. Guan, Y. Shi, and D.D. McKee Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes Genome Biol. 2 2001 RESEARCH0029
2. R. Mohan, and R.A. Heyman Orphan nuclear receptor modulators Curr. Top. Med. Chem. 3 2003 1637 1647
3. T.M. Willson, and J.T. Moore Genomics versus orphan nuclear receptors-a half-time report Mol. Endocrinol. 16 2002 1135 1144
4. D.J. Mangelsdorf, C. Thummel, M. Beato, P. Herrlich, and G. Schutz The nuclear receptor superfamily: the second decade Cell 83 1995 835 839
5. A. Aranda, and A. Pascual Nuclear hormone receptors and gene expression Physiol. Rev. 81 2001 1269 1304
6. V. Giguere Orphan nuclear receptors: from gene to function Endocrinol. Rev. 20 1999 689 725
7. P. Chambon A decade of molecular biology of retinoic acid receptors FASEB J. 10 1996 940 954
8. C.K. Glass, D.W. Rose, and M.G. Rosenfeld Nuclear receptor coactivators Curr. Opin. Cell Biol. 9 1997 222 232
9. L. Xu, C.K. Glass, and M.G. Rosenfeld Coactivator and corepressor complexes in nuclear receptor function Curr. Opin. Genet. Dev. 9 1999 140 147
10. J.M. Wurtz, W. Bourguet, J.P. Renaud, V. Vivat, and P. Chambon A canonical structure for the ligand-binding domain of nuclear receptors Nat. Struct. Biol. 3 1996 87 94
11. A.M. Brzozowski, A.C. Pike, Z. Dauter, R.E. Hubbard, and T. Bonn Molecular basis of agonism and antagonism in the oestrogen receptor Nature 389 1997 753 758
12. W. Seol, H.S. Choi, and D.D. Moore An orphan nuclear hormone receptor that lacks a DNA binding domain and heterodimerizes with other receptors Science 272 1996 1336 1339
13. H.K. Lee, Y.K. Lee, S.H. Park, Y.S. Kim, and J.W. Lee Structure and expression of the orphan nuclear receptor SHP gene J. Biol. Chem. 273 1998 14398 14402
14. W. Chen, E. Owsley, Y. Yang, D. Stroup, and J.Y. Chiang Nuclear receptor-mediated repression of human cholesterol 7alpha-hydroxylase gene transcription by bile acids J. Lipid Res. 42 2001 1402 1412
15. S. Sanyal, J.Y. Kim, H.J. Kim, J. Takeda, and Y.K. Lee Differential regulation of the orphan nuclear receptor small heterodimer partner (SHP) gene promoter by orphan nuclear receptor ERR isoforms J. Biol. Chem. 277 2002 1739 1748
16. T.T. Lu, M. Makishima, J.J. Repa, K. Schoonjans, and T.A. Kerr Molecular basis for feedback regulation of bile acid synthesis by nuclear receptors Mol. Cell 6 2000 507 515
17. Y.K. Lee, K.L. Parker, H.S. Choi, and D.D. Moore Activation of the promoter of the orphan receptor SHP by orphan receptors that bind DNA as monomers J. Biol. Chem. 274 1999 20869 20873
18. S. Gupta, R.T. Stravitz, P. Dent, and P.B. Hylemon Down-regulation of cholesterol 7alpha-hydroxylase (CYP7A1) gene expression by bile acids in primary rat hepatocytes is mediated by the c-Jun N-terminal kinase pathway J. Biol. Chem. 276 2001 15816 15822
19. B. Goodwin, S.A. Jones, R.R. Price, M.A. Watson, and D.D. McKee A regulatory cascade of the nuclear receptors FXR, SHP-1, and LRH-1 represses bile acid biosynthesis Mol. Cell 6 2000 517 526
20. C.C. Hung, I.S. Farooqi, K. Ong, J. Luan, and J.M. Keogh Contribution of variants in the small heterodimer partner gene to birthweight, adiposity, and insulin levels: mutational analysis and association studies in multiple populations Diabetes 52 2003 1288 1291
21. H. Nishigori, H. Tomura, N. Tonooka, M. Kanamori, and S. Yamada Mutations in the small heterodimer partner gene are associated with mild obesity in Japanese subjects Proc. Natl. Acad. Sci. U.S.A. 98 2001 575 580
22. Y.K. Lee, and D.D. Moore Dual mechanisms for repression of the monomeric orphan receptor liver receptor homologous protein-1 by the orphan small heterodimer partner J. Biol. Chem. 277 2002 2463 2467
23. Y.K. Lee, H. Dell, D.H. Dowhan, M. Hadzopoulou-Cladaras, and D.D. Moore The orphan nuclear receptor SHP inhibits hepatocyte nuclear factor 4 and retinoid X receptor transactivation: two mechanisms for repression Mol. Cell Biol. 20 2000 187 195
24. L. Johansson, J.S. Thomsen, A.E. Damdimopoulos, G. Spyrou, and J.A. Gustafsson The orphan nuclear receptor SHP inhibits agonist-dependent transcriptional activity of estrogen receptors ERalpha and ERbeta J. Biol. Chem. 274 1999 345 353
25. J. Gobinet, G. Auzou, J.C. Nicolas, C. Sultan, and S. Jalaguier Characterization of the interaction between androgen receptor and a new transcriptional inhibitor, SHP Biochemistry 40 2001 15369 15377
26. L.J. Borgius, K.R. Steffensen, J.A. Gustafsson, and E. Treuter Glucocorticoid signaling is perturbed by the atypical orphan receptor and corepressor SHP J. Biol. Chem. 277 2002 49761 49766
27. C. Brendel, K. Schoonjans, O.A. Botrugno, E. Treuter, and J. Auwerx The small heterodimer partner interacts with the liver X receptor alpha and represses its transcriptional activity Mol. Endocrinol. 16 2002 2065 2076
28. H. Nishizawa, K. Yamagata, I. Shimomura, M. Takahashi, and H. Kuriyama Small heterodimer partner, an orphan nuclear receptor, augments peroxisome proliferator-activated receptor gamma transactivation J. Biol. Chem. 277 2002 1586 1592
29. L. Johansson, A. Båvner, J.S. Thomsen, M. Farnegardh, and J.A. Gustafsson The orphan nuclear receptor SHP utilizes conserved LXXLL-related motifs for interactions with ligand-activated estrogen receptors Mol. Cell Biol. 20 2000 1124 1133
30. A. Båvner, L. Johansson, G. Toresson, J.A. Gustafsson, and E. Treuter A transcriptional inhibitor targeted by the atypical orphan nuclear receptor SHP EMBO Rep. 3 2002 478 484
31. W.R. MacLellan, G. Xiao, M. Abdellatif, and M.D. Schneider A novel Rb- and p300-binding protein inhibits transactivation by MyoD Mol. Cell Biol. 20 2000 8903 8915
32. S. Miyake, W.R. Sellers, M. Safran, X. Li, and W. Zhao Cells degrade a novel inhibitor of differentiation with E1A-like properties upon exiting the cell cycle Mol. Cell Biol. 20 2000 8889 8902
33. Accelrys Insight-II: San Diego, CA.
34. PHD Predict Protein Server at http://cubic.bioc.columbia.edu/ predictprotein/:San Diego, CA.
35. A. Fiser, and A. Sali Modeller: generation and refinement of homology-based protein structure models Methods Enzymol. 374 2003 461 491
36. D.E. Kim, D. Chivian, and D. Baker Protein structure prediction and analysis using the Robetta server Nucleic Acids Res. 32 2004 W526 W531
37. B.N. Dominy, and C.L. Brooks Development of a generalized born model parametrization for proteins and nucleic acids J. Phys Chem. B 103 1999 3765 3773
38. R. Luthy, J.U. Bowie, and D. Eisenberg Assessment of protein models with three-dimensional profiles Nature 356 1992 83 85
39. A.L. Morris, M.W. MacArthur, E.G. Hutchinson, and J.M. Thornton Stereochemical quality of protein structure coordinates Proteins 12 1992 345 364
40. G. Moont, H.A. Gabb, and M.J. Sternberg Use of pair potentials across protein interfaces in screening predicted docked complexes Proteins 35 1999 364 373
41. I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification Proteins 1 1986 47 59
42. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, and W.E. Hart Automated docking using lamarckian genetic algorithm and empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662
43. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, and Z. Zhang Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
44. WU-BLAST http://www.ebi.ac.uk/blast2/: San Diego, CA.
45. S.F. Altschul, and E.V. Koonin Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases Trends Biochem. Sci. 23 1998 444 447
46. I.M. Billas, L. Moulinier, N. Rochel, and D. Moras Crystal structure of the ligand-binding domain of the ultraspiracle protein USP, the ortholog of retinoid X receptors in insects J. Biol. Chem. 276 2001 7465 7474
47. G.M. Clayton, S.Y. Peak-Chew, R.M. Evans, and J.W. Schwabe The structure of the ultraspiracle ligand-binding domain reveals a nuclear receptor locked in an inactive conformation Proc. Natl. Acad. Sci. U.S.A. 98 2001 1549 1554
48. S. Przibilla, W.W. Hitchcock, M. Szecsi, M. Grebe, and J. Beatty Functional studies on the ligand-binding domain of Ultraspiracle from Drosophila melanogaster Biol. Chem. 385 2004 21 30
49. Y.Y. Park, H.J. Kim, J.Y. Kim, M.Y. Kim, and K.H. Song Differential role of the loop region between helices H6 and H7 within the orphan nuclear receptors small heterodimer partner and DAX-1 Mol. Endocrinol. 18 2004 1082 1095
50. W. Seol, M. Chung, and D.D. Moore Novel receptor interaction and repression domains in the orphan receptor SHP Mol. Cell Biol. 17 1997 7126 7131
51. E.A. Ortlund, Y. Lee, I.H. Solomon, J.M. Hager, and R. Safi Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP Nat. Struct. Mol. Biol. 12 2005 357 363
52. L.A. Kelley, R.M. MacCallum, and M.J. Sternberg Enhanced genome annotation using structural profiles in the program 3D-PSSM J. Mol. Biol. 299 2000 499 520
53. L. Rychlewski, L. Jaroszewski, W. Li, and A. Godzik Comparison of sequence profiles. Strategies for structural predictions using sequence information Protein Sci. 9 2000 232 241
54. J. Shi, T.L. Blundell, and K. Mizuguchi FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties J. Mol. Biol. 310 2001 243 257
55. D. Fischer 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor Proteins 51 2003 434 441
56. L.J. McGuffin, and D.T. Jones Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 19 2003 874 881
57. J. Gough, K. Karplus, R. Hughey, and C. Chothia Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure J. Mol. Biol. 313 2001 903 919
58. K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski 3D-Jury: a simple approach to improve protein structure predictions Bioinformatics 19 2003 1015 1018
59. D. Chivian, D.E. Kim, L. Malmstrom, P. Bradley, and T. Robertson Automated prediction of CASP-5 structures using the Robetta server Proteins 53 Suppl. 6 2003 524 533
60. N. Potier, I.M. Billas, A. Steinmetz, C. Schaeffer, and A. van Dorsselaer Using nondenaturing mass spectrometry to detect fortuitous ligands in orphan nuclear receptors Protein Sci. 12 2003 725 733
61. S.M. Echwald, K.L. Andersen, T.I. Sorensen, L.H. Larsen, and T. Andersen Mutation analysis of NR0B2 among 1545 Danish men identifies a novel c.278G>A (p.G93D) variant with reduced functional activity Hum. Mutat. 24 2004 381 387