The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor α ligand-binding domain

Molecular Endocrinology

Volumn 21, Issue 1, 2007, Pages 30-48

  Folkertsma, Simon ^a,b   Van Noort, Paula I ^b   De Heer, Arnold ^b   Carati, Peter ^b   Brandt, Ralph ^b   Visser, Arie ^b   Vriend, Gerrit ^b   De Vlieg, Jacob ^a,b  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b NV ORGANON   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

6 [1 (5,6,7,8 TETRAHYDRO 3,5,5,8,8 PENTAMETHYL 2 NAPHTHYL)CYCLOPROPYL]NICOTINIC ACID; BEXAROTENE; METHOPRENE; RETINOID X RECEPTOR ALPHA;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER MODEL; CONFORMATIONAL TRANSITION; FLUORESCENCE RESONANCE ENERGY TRANSFER; IN VITRO STUDY; LIGAND BINDING; MOLECULAR DOCKING; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN MOTIF; SIMULATION;

AMINO ACID SEQUENCE; CLUSTER ANALYSIS; DIMERIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; KINETICS; LIGANDS; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RETINOID X RECEPTOR ALPHA; RETINOIDS; SEQUENCE HOMOLOGY, AMINO ACID; TETRAHYDRONAPHTHALENES;

EID: 33845966382     PISSN: 08888809     EISSN: None     Source Type: Journal    
DOI: 10.1210/me.2006-0072     Document Type: Article

References (64)

1. Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, Umesono K, Blumberg B, Kastner P, Mark M, Chambon P, Evans RM 1995 The nuclear receptor superfamily: the second decade. Cell 83:835-839
2. Giguere V 1999 Orphan nuclear receptors: from gene to function. Endocr Rev 20:689-725
3. Kliewer SA, Lehmann JM, Willson TM 1999 Orphan nuclear receptors: shifting endocrinology into reverse. Science 284:757-760
4. Renaud JP, Rochel N, Ruff M, Vivat V, Chambon P, Gronemeyer H, Moras D 1995 Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid. Nature 378:681-689
5. Renaud JP, Moras D 2000 Structural studies on nuclear receptors. Cell Mol Life Sci 57:1748-1769
6. Egea PF, Mitschler A, Rochel N, Ruff M, Chambon P, Moras D 2000 Crystal structure of the human RXRα ligand-binding domain bound to its natural ligand: 9-cis retinoic acid. EMBO J 19:2592-2601
7. Darimont BD, Wagner RL, Apriletti JW, Stallcup MR, Kushner PJ, Baxter JD, Fletterick RJ, Yamamoto KR 1998 Structure and specificity of nuclear receptor-coactivator interactions. Genes Dev 12:3343-3356
8. Nolte RT, Wisely GB, Westin S, Cobb JE, Lambert MH, Kurokawa R, Rosenfeld MG, Willson TM, Glass CK, Milburn MV 1998 Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-γ. Nature 395:137-143
9. Ding XF, Anderson CM, Ma H, Hong H, Uht RM, Kushner PJ, Stallcup MR 1998 Nuclear receptor-binding sites of coactivators glucocorticoid receptor interacting protein 1 (GRIP1) and steroid receptor coactivator 1 (SRC-1): multiple motifs with different binding specificities. Mol Endocrinol 12:302-313
10. Xu HE, Stanley TB, Montana VG, Lambert MH, Shearer BG, Cobb JE, McKee DD, Galardi CM, Plunket KD, Nolte RT, Parks DJ, Moore JT, Kliewer SA, Willson TM, Stimmel JB 2002 Structural basis for antagonist-mediated recruitment of nuclear co-repressors by PPARα. Nature 415:813-817
11. Perissi V, Staszewski LM, McInerney EM, Kurokawa R, Krones A, Rose DW, Lambert MH, Milburn MV, Glass CK, Rosenfeld MG 1999 Molecular determinants of nuclear receptor-corepressor interaction. Genes Dev 13:3198-3208
12. Hu X, Lazar MA 1999 The CoRNR motif controls the recruitment of corepressors by nuclear hormone receptors. Nature 402:93-96
13. Iannone MA, Simmons CA, Kadwell SH, Svoboda DL, Vanderwall DE, Deng SJ, Consler TG, Shearin J, Gray JG, Pearce KH 2004 Correlation between in vitro peptide binding profiles and cellular activities for estrogen receptor-modulating compounds. Mol Endocrinol 18:1064-1081
14. Downes M, Verdecia MA, Roecker AJ, Hughes R, Hogenesch JB, Kast-Woelbern HR, Bowman ME, Ferrer JL, Anisfeld AM, Edwards PA, Rosenfeld JM, Alvarez JG, Noel JP, Nicolaou KC, Evans RM 2003 A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Mol Cell 11:1079-1092
15. Lee G, Elwood F, McNally J, Weiszmann J, Lindstrom M, Amaral K, Nakamura M, Miao S, Cao P, Learned RM, Chen JL, Li Y 2002 T0070907, a selective ligand for peroxisome proliferator-activated receptor γ, functions as an antagonist of biochemical and cellular activities. J Biol Chem 277:19649-19657
16. Chambon P 1996 A decade of molecular biology of retinoic acid receptors. FASEB J 10:940-954
17. Horton C, Maden M 1995 Endogenous distribution of retinoids during normal development and teratogenesis in the mouse embryo. Dev Dyn 202:312-323
18. Heyman RA, Mangelsdorf DJ, Dyck JA, Stein RB, Eichele G, Evans RM, Thaller C 1992 9-cis Retinoic acid is a high affinity ligand for the retinoid X receptor. Cell 68:397-406
19. Lengqvist J, Mata De Urquiza A, Bergman AC, Willson TM, Sjovall J, Perlmann T, Griffiths WJ 2004 Polyunsaturated fatty acids including docosahexaenoic and arachidonic acid bind to the retinoid X receptor α ligand-binding domain. Mol Cell Proteomics 3:692-703
20. de Urquiza AM, Liu S, Sjoberg M, Zetterstrom RH, Griffiths W, Sjovall J, Perlmann T 2000 Docosahexaenoic acid, a ligand for the retinoid X receptor in mouse brain. Science 290:2140-2144
21. Lemotte PK, Keidel S, Apfel CM 1996 Phytanic acid is a retinoid X receptor ligand. Eur J Biochem 236:328-333
22. Dawson MI 2004 Synthetic retinoids and their nuclear receptors. Curr Med Chem Anti-Canc Agents 4:199-230
23. Li Y, Choi M, Suino K, Kovach A, Daugherty J, Kliewer SA, Xu HE 2005 Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner. Proc Natl Acad Sci USA 102:9505-9510
24. Sablin EP, Krylova IN, Fletterick RJ, Ingraham HA 2003 Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1. Mol Cell 11:1575-1585
25. Watkins RE, Wisely GB, Moore LB, Collins JL, Lambert MH, Williams SP, Willson TM, Kliewer SA, Redinbo MR 2001 The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity. Science 292:2329-2333
26. Uppenberg J, Svensson C, Jaki M, Bertilsson G, Jendeberg L, Berkenstam A 1998 Crystal structure of the ligand binding domain of the human nuclear receptor PPARγ. J Biol Chem 273:31108-31112
27. Xu HE, Lambert MH, Montana VG, Parks DJ, Blanchard SG, Brown PJ, Sternbach DD, Lehmann JM, Wisely GB, Willson TM, Kliewer SA, Milburn MV 1999 Molecular recognition of fatty acids by peroxisome proliferator-activated receptors. Mol Cell 3:397-403
28. Hsu CL, Chen YL, Yeh S, Ting HJ, Hu YC, Lin H, Wang X, Chang C 2003 The use of phage display technique for the isolation of androgen receptor interacting peptides with (F/W)XXL(F/W) and FXXLY new signature motifs. J Biol Chem 278:23691-23698
29. Dubbink HJ, Hersmus R, Verma CS, van der Korput HA, Berrevoets CA, van Tol J, Ziel-van der Made AC, Brinkmann AO, Pike AC, Trapman J 2004 Distinct recognition modes of FXXLF and LXXLL motifs by the androgen receptor. Mol Endocrinol 18:2132-2150
30. He B, Minges JT, Lee LW, Wilson EM 2002 The FXXLF motif mediates androgen receptor-specific interactions with coregulators. J Biol Chem 277:10226-10235
31. Northrop JP, Nguyen D, Piplani S, Olivan SE, Kwan ST, Go NF, Hart CP, Schatz PJ 2000 Selection of estrogen receptor β- and thyroid hormone receptor β-specific coactivator-mimetic peptides using recombinant peptide libraries. Mol Endocrinol 14:605-622
32. Heery DM, Hoare S, Hussain S, Parker MG, Sheppard H 2001 Core LXXLL motif sequences in CREB-binding protein, SRC1, and RIP140 define affinity and selectivity for steroid and retinoid receptors. J Biol Chem 276:6695-6702
33. Pogenberg V, Guichou JF, Vivat-Hannah V, Kammerer S, Perez E, Germain P, de Lera AR, Gronemeyer H, Royer CA, Bourguet W 2005 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 280:1625-1633
34. Farooqui M, Franco PJ, Thompson J, Kagechika H, Chandraratna RA, Banaszak L, Wei LN 2003 Effects of retinoid ligands on RIP140: molecular interaction with retinoid receptors and biological activity. Biochemistry 42:971-979
35. Seol W, Chung M, Moore DD 1997 Novel receptor interaction and repression domains in the orphan receptor SHP. Mol Cell Biol 17:7126-7131
36. Ghosh JC, Yang X, Zhang A, Lambert MH, Li H, Xu HE, Chen JD 2002 Interactions that determine the assembly of a retinoid X receptor/corepressor complex. Proc Natl Acad Sci USA 99:5842-5847
37. Love JD, Gooch JT, Benko S, Li C, Nagy L, Chatterjee VK, Evans RM, Schwabe JW 2002 The structural basis for the specificity of retinoid-X receptor-selective agonists: new insights into the role of helix H12. J Biol Chem 277:11385-11391
38. Stanley TB, Leesnitzer LM, Montana VG, Galardi CM, Lambert MH, Holt JA, Xu HE, Moore LB, Blanchard SG, Stimmel JB 2003 Subtype specific effects of peroxisome proliferator-activated receptor ligands on corepressor affinity. Biochemistry 42:9278-9287
39. Gampe RT, Jr., Montana VG, Lambert MH, Miller AB, Bledsoe RK, Milburn MV, Kliewer SA, Willson TM, Xu HE 2000 Asymmetry in the PPARγ/RXRα crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Mol Cell 5:545-555
40. Suino K, Peng L, Reynolds R, Li Y, Cha JY, Repa JJ, Kliewer SA, Xu HE 2004 The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and heterodimerization. Mol Cell 16:893-905
41. Xu HE, Lambert MH, Montana VG, Plunket KD, Moore LB, Collins JL, Oplinger JA, Kliewer SA, Gampe Jr RT, McKee DD, Moore JT, Willson TM 2001 Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors. Proc Natl Acad Sci USA 98:13919-13924
42. Levin AA, Sturzenbecker LJ, Kazmer S, Bosakowski T, Huselton C, Allenby G, Speck J, Ratzeisen C, Rosenberger M, Lovey A, Grippo JF 1992 9-cis Retinoic acid stereoisomer binds and activates the nuclear receptor RXRα. Nature 355:359-361
43. Boehm MF, Zhang L, Zhi L, McClurg MR, Berger E, Wagoner M, Mais DE, Suto CM, Davies JA, Heyman RA, Nadzam AM 1995 Design and synthesis of potent retinoid X receptor selective ligands that induce apoptosis in leukemia cells. J Med Chem 38:3146-3155
44. Harmon MA, Boehm MF, Heyman RA, Mangelsdorf DJ 1995 Activation of mammalian retinoid X receptors by the insect growth regulator methoprene. Proc Natl Acad Sci USA 92:6157-6160
45. Xu RX, Lambert MH, Wisely BB, Warren EN, Weinert EE, Waitt GM, Williams JD, Collins JL, Moore LB, Willson TM, Moore JT 2004 A structural basis for constitutive activity in the human CAR/RXRα heterodimer. Mol Cell 16:919-928
46. Gampe Jr RT, Montana VG, Lambert MH, Wisely GB, Milburn MV, Xu HE 2000 Structural basis for autorepression of retinoid X receptor by tetramer formation and the AF-2 helix. Genes Dev 14:2229-2241
47. Egea PF, Mitschler A, Moras D 2002 Molecular recognition of agonist ligands by RXRs. Mol Endocrinol 16:987-997
48. Haffner CD, Lenhard JM, Miller AB, McDougald DL, Dwornik K, Ittoop OR, Gampe Jr RT, Xu HE, Blanchard S, Montana VG, Consler TG, Bledsoe RK, Ayscue A, Croom D 2004 Structure-based design of potent retinoid X receptor α agonists. J Med Chem 47:2010-2029
49. Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G 2004 A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain. J Mol Biol 341:321-335
50. Folkertsma S, van Noort PI, Brandt RF, Bettler E, Vriend G, de Vlieg J 2005 The nuclear receptor ligand-binding domain: a family-based structure analysis. Curr Med Chem 12:1001-1016
51. Otero MP, Torrado A, Pazos Y, Sussman F, De Lera AR 2002 Stereoselective synthesis of annular 9-cis-retinoids and binding characterization to the retinoid X receptor. J Org Chem 67:5876-5882
52. Smith CL, O'Malley BW 2004 Coregulator function: a key to understanding tissue specificity of selective receptor modulators. Endocr Rev 25:45-71
53. Gronemeyer H, Gustafsson JA, Laudet V 2004 Principles for modulation of the nuclear receptor superfamily. Nat Rev Drug Discov 3:950-964
54. Lala DS, Mukherjee R, Schulman IG, Koch SS, Dardashti LJ, Nadzan AM, Croston GE, Evans RM, Heyman RA 1996 Activation of specific RXR heterodimers by an antagonist of RXR homodimers. Nature 383:450-453
55. Canan Koch SS, Dardashti LJ, Hebert JJ, White SK, Croston GE, Flatten KS, Heyman RA, Nadzan AM 1996 Identification of the first retinoid X, receptor homodimer antagonist. J Med Chem 39:3229-3234
56. Mi LZ, Devarakonda S, Harp JM, Han Q, Pellicciari R, Willson TM, Khorasanizadeh S, Rastinejad F 2003 Structural basis for bile acid binding and activation of the nuclear receptor FXR. Mol Cell 11:1093-1100
57. Kong EH, Heldring N, Gustafsson JA, Treuter E, Hubbard RE, Pike AC 2005 Delineation of a unique protein-protein interaction site on the surface of the estrogen receptor. Proc Natl Acad Sci USA 102:3593-3598
58. Codina A, Benoit G, Gooch JT, Neuhaus D, Perlmann T, Schwabe JW 2004 Identification of a novel co-regulator interaction surface on the ligand binding domain of Nurr1 using NMR footprinting. J Biol Chem 279:53338-53345
59. Muller JM, Isele U, Metzger E, Rempel A, Moser M, Pscherer A, Breyer T, Holubarsch C, Buettner R, Schule R 2000 FHL2, a novel tissue-specific coactivator of the androgen receptor. EMBO J 19:359-369
60. Tzameli I, Chua SS, Cheskis B, Moore DD 2003 Complex effects of rexinoids on ligand dependent activation or inhibition of the xenobiotic receptor, CAR. Nucl Recept 1:2
61. Shiau AK, Barstad D, Radek JT, Meyers MJ, Nettles KW, Katzenellenbogen BS, Katzenellenbogen JA, Agard DA, Greene GL 2002 Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Nat Struct Biol 9:359-364
62. Huang HJ, Norris JD, McDonnell DP 2002 Identification of a negative regulatory surface within estrogen receptor α provides evidence in support of a role for corepressors in regulating cellular responses to agonists and antagonists. Mol Endocrinol 16:1778-1792
63. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M 1983 CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217
64. Kouwijzer ML, Mestres J 2002 Molecular docking and dynamics simulations in the ligand binding domain of steroid hormone receptors. Trends Drug Res III:57-66