Computational analysis of the structural basis of ligand binding to the crustacean retinoid X receptor

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 5, Issue 4, 2010, Pages 317-324

  Purna Chandra Nagaraju, G ^a   Prasad, G L V ^b   Taliaferro Smith, L ^a   Aruna, B V ^c   Naik, B Reddya ^b   Sekhar, Y Nataraja ^d  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b OSMANIA UNIVERSITY   (India)

^c Heerskink School of Medicine   (United States)

^d UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Docking; Homology; Ligands; Naloxone; Neurotransmitters; RXR

Indexed keywords

DOPAMINE; NALOXONE; NEUROTRANSMITTER; RETINOID X RECEPTOR; RETINOID X RECEPTOR ALPHA; SEROTONIN;

ARTICLE; CELUCA PUGILATOR; CRUSTACEA; DNA TEMPLATE; GENE FUNCTION; LIGAND BINDING; MOLECULAR DOCKING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

CELUCA PUGILATOR; CRUSTACEA; HEXAPODA; VERTEBRATA;

EID: 78649905839     PISSN: 1744117X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbd.2010.09.002     Document Type: Article

References (50)

1. H. Asazuma, S. Nagata, M. Kono, and H. Nagasawa Molecular cloning and expression analysis of ecdysone receptor and retinoid X receptor from the kuruma prawn, Marsupenaeus japonicus Comp. Biochem. Physiol. B 148 2007 139 150
2. 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
3. M. Bomirsky, E. Arenderczyk, L. Kawinska, and H. Kleinholz Partial characterization of crustacean gonad-inhibiting hormone Int. J. Invertbr. Reprod. 3 1981 213 219
4. J.A. Carmichael, M.C. Lawrence, L.D. Graham, P.A. Pilling, V.C. Epa, L. Noyce, G. Lovrecz, D.A. Winkler, A. Pawlak-Skrzecz, R.E. Eaton, G.N. Hannan, and R.J. Hill The X-ray structure of a hemipteran ecdysone receptor ligand-binding domain: comparison with a lepidopteran ecdysone receptor ligand-binding domain and implications for insecticide design J. Biol. Chem. 280 2005 22258 22269
5. R. Chenna, H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D. Higgins, G. Thompson, and D. Julie Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res. 31 2003 3497 3500 (Pubitemid 37442184)
6. A.C. Chung, D.S. Durica, S.W. Clifton, B.A. Roe, and P.M. Hopkins Cloning of crustacean ecdysteroid receptor and retinoid-X receptor gene homologs and elevation of retinoid-X receptor mRNA by retinoic acid J. Mol. Cell. Endocrinol. 139 1998 209 227
7. A. Cravchik, and P.V. Gejman Functional analysis of the human D5 dopamine receptor missense and nonsense variants: differences in dopamine binding affinities Pharmacogenetics 9 1999 199 206 (Pubitemid 29359002)
8. A.M. de Urquiza, S. Liu, M. Sjoberg, R.H. Zetterstrom, W. Griffiths, J. Sjovall, and T. Perlmann Docosahexaenoic acid, a ligand for the retinoid X receptor in mouse brain Science 290 2000 2140 2144
9. D.S. Durica, and P.M. Hopkins Expression of the genes encoding the ecdysteroid and retinoid receptors in regenerating limb tissues from the fiddler crab, Uca pugilator Gene 171 1996 237 241
10. S. Eastman-Reks, and M. Fingerman Effects of neuroendocrine tissue and cyclic AMP on ovarian growth in vivo and in vitro in the fiddler crab, Uca pugilator Comp. Biochem. Physiol. 79A 1984 679 684
11. P.F. Egea, B.P. Klaholz, and D. Moras Ligand-protein interactions in nuclear receptors of hormones FEBS J. 476 2000 62 67
12. R.M. Evans The steroid and thyroid hormone receptor super family Science 240 1988 889 895
13. J. Felsenstein PHYLIP-Phylogeny Inference Package (Version 3.2) Cladistics 5 1989 164 166
14. M. Fingerman Crustacean endocrinology: a retrospective, prospective, and introspective analysis Physiol. Zool. 70 1997 257 269
15. J. Gasteiger, and M. Marsilli Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
16. F. Grun, H. Watanabe, Z. Zamanian, L. Maeda, K. Arima, R. Cubacha, D.M. Gardiner, J. Kanno, T. Iguchi, and B. Blumberg Endocrine-disrupting organotin compounds are potent inducers of adipogenesis in vertebrates Mol. Endocrinol. 20 2006 2141 2155
17. M.A. Harmon, M.F. Boehm, R.A. Heyman, and D.J. Mangelsdorf Activation of mammalian retinoid X receptors by the insect growth regulator methoprene Proc. Nat. Acad. Sci. U.S.A. 92 1995 6157 6160
18. R.A. Heyman, D.J. Mangelsdorf, J.A. Dyck, R.B. Stein, G. Eichele, R.M. Evans, and C. Thaller 9-cis retinoic acid is a high affinity ligand for the retinoid X receptor Cell 68 1992 397 406
19. P.M. Hopkins, D. Durica, and W. Tracy RXR isoforms and endogenous retinoids in the fiddler crab, Uca pugilator Comp. Biochem. Physiol. 151A 2008 602 614
20. G. Jones, and P.A. Sharp Ultraspiracle: an invertebrate nuclear receptor for juvenile hormones Proc. Natl Acad. Sci. USA 94 1997 13499 13503
21. G. Jones, D. Jones, P. Teal, A. Sapa, and M. Wozniak The retinoid-X receptor ortholog, ultraspiracle, binds with nanomolar affinity to an endogenous morphogenetic ligand FEBS J. 273 2006 1 14
22. H.-W. Kim, S.G. Lee, and D.L. Mykles Ecdysteroid-responsive genes, RXR and E75, in the tropical land crab, Becarcinus lateralis: differential tissue expression of multiple RXR isoforms generated at three alternative splicing sites in the hinge and ligand-binding domains Mol. Cell. Endocrinol. 242 2005 80 95
23. Z. Kostrouch, M. Kostrouchova, W. Love, E. Jannini, J. Piatigorsky, and J.E. Rall Retinoid acid X receptor in the diploblast, Tripedalia cystophora Proc. Natl Acad. Sci. USA 95 1998 13442 13447
24. A.A. Levin, L.J. Sturzenbecker, S. Kazmer, T. Bosakowski, C. Huselton, G. Allenby, J. Speck, C. Kratzeisen, M. Rosenberger, and A. Lovey 9-cis retinoic acid stereoisomer binds and activates the nuclear receptor RXR alpha Nature 355 1992 359 361
25. S. Lorenzon, P. Pasqual, and E.A. Ferrero Biogenic amines control blood glucose level in the shrimp Palaemon elegans F.B. Schram, The Biodiversity Crisis and Crustacea: Crustacean Issues vol. 12 1999 Rotterdam Balkema 471 480
26. S. Lorenzon, P. Edomi, P.G. Giulianini, R. Mettulio, and E.A. Ferrero Variation of crustacean hyperglycemic hormone (cHH) level in the eyestalk and hemolymph of the shrimp Palaemon elegans following stress J. Exp. Biol. 207 2004 4205 4213
27. S. Lorenzon, P. Edomi, P.G. Giulianini, R. Mettulio, and E.A. Ferrero Role of biogenic amines and CHH in the crustacean hyperglycemic stress Response J. Exp. Biol. 208 2005 3341 3347
28. R. Lüthy, J.U. Bowie, and D. Eisenberg Assessment of protein models with three-dimensional profiles Nature 356 1992 83 85
29. M. Mark, and P. Chambon Functions of RARs and RXRs in vivo: genetic dissection of the retinoid signaling pathway Pure Appl. Chem. 75 2003 1709 1732
30. M. Mark, N.B. Ghyselinck, and P. Chambon Function of retinoid nuclear receptors: lessons from genetic and pharmacological dissections of the retinoic acid signaling pathway during mouse embryogenesis Ann. Rev. Pharmacol. Toxicol. 46 2006 451 480
31. T. Masuko, I. Suzuki, Y. Kizawa, K. Kusama-Eguchi, K. Watanabe, and K. Kashiwagi Monoamines directly inhibit N-methyl-D-aspartate receptors expressed in Xenopus oocytes in a voltage-dependent manner Neurosci. Lett. 371 2004 30 33
32. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662
33. G.P.C. Nagaraju, and P.S. Reddy On the mode of action of Methionine-enkephalin in inducing hyperglycemia in the fiddler crab Uca lactea annulipes Bull. Mar. Sci. 70 2002 107 111
34. G.P.C. Nagaraju, N. Siva Kumari, G.L.V. Prasad, B. Rajitha, M. Madan, Rao M. Sreenivasa, and B. Reddya Naik Computational analysis and structural prediction of VIH-related peptides from selected crustacean species Bioinformation 4 2009 6 11
35. J.-I. Nishikawa, S. Mamiya, T. Kanayama, T. Nishikawa, F. Shiraishi, and T. Horiguchi Involvement of the retinoid X receptor in the development of imposex caused by organotins in gastropods Environ. Sci. Technol. 38 2004 6271 6276
36. K.A. Olszewski, L. Yan, and D. Edwards SeqFold-fully automated fold recognition and modeling software-validation and application Theor. Chem. Acc. 11 1999 57
37. A.E. Oro, E.S. Ong, J.S. Margolis, J.W. Posakony, M. McKeown, and R.M. Evans The Drosophila gene knirps-related is a member of the steroid-receptor gene super family Nature 336 1988 493 496
38. T. Otsu Bihormonal control of sexual cycle in the fresh water crab, Potamon dehaani Embryologia 8 1963 1 20
39. T.A.J. Priya, F. Li, J. Zhang, B. Wang, C. Zhao, and J. Xiang Molecular characterization and effect of RNA interference of retinoid X receptor (RXR) on E75 and chitinase gene expression in Chinese shrimp Fenneropenaeus chinensis Comp. Biochem. Physiol. 153B 2009 121 129
40. A. Sali, and T.L. Blundell Comparative protein modeling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
41. R. Sarojini, R. Nagabhushanam, and M. Fingerman Dopaminergic and enkephalinergic involvement in the regulation of blood glucose in the red swamp crayfish, Procambarus clarkii Gen. Comp. Endocrinol. 97 1995 160 170
42. R. Sarojini, R. Nagabhushanam, and M. Fingerman In vivo effects of dopamine and dopaminergic antagonists on testicular maturation in the red swamp crayfish, Procambarus clarkii Biol. Bull. 189 1995 340 346
43. R. Sarojini, R. Nagabhushanam, and M. Fingerman An in vitro study of the inhibitory action of methionine enkephalin on ovarian maturation in the red swamp crayfish Procambarus clarkii Comp. Biochem. Physiol. 117C 1997 207 210
44. J.L. Sobell, T.J. Lind, and D.C. Sigurdson The D5 dopamine receptor gene in schizophrenia: identification of a nonsense change and multiple missense changes but lack of association with disease Hum. Mol. Genet. 4 1995 507 514
45. C.D. Wang, T.K. Gallaher, and J.C. Shih Site-directed mutagenesis of the serotonin 5-hydroxytrypamine2 receptor: identification of amino acids necessary for ligand binding and receptor activation Mol. Pharmacol. 43 1993 931 940
46. Y.H. Wang, G. Wang, and G.A. LeBlanc Cloning and characterization of the retinoid X receptor from a primitive crustacean Daphnia magna Gen. Comp. Endocrinol. 150 2007 309 318
47. S.J. Weiner, P.A. Kollman, and D.A. Case New force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 106 1984 765 784
48. S.J. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case An all atom force field for simulations of proteins and nucleic acids J. Comput. Chem. 7 1986 230 252
49. M. Wiens, R. Batel, M. Korzhev, and W.E.G. Muller Retinoid X receptor and retinoic acid response in the marine sponge Suberites domuncula J. Exp. Biol. 206 2003 3261 3271
50. G. Wolf Is 9-cis-retinoic acid the endogenous ligand for the retinoic acid-X receptor? Nutr. Rev. 64 2006 532 538