MSITE: A new computational tool for comparison of homological proteins in holo form

Journal of Steroid Biochemistry and Molecular Biology

Volumn 121, Issue 1-2, 2010, Pages 34-42

  Sicinska, Wanda ^a   Kurcinski, Mateusz ^b  

^a INSTITUTE OF ORGANIC CHEMISTRY   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Structure comparisons; Targets for mutational analyses; Vitamin D; Vitamin D analogs; Vitamin D receptor

Indexed keywords

AMINO ACID; HETERODIMER; LIGAND; PROTEIN; VITAMIN D RECEPTOR; CALCITRIOL RECEPTOR; PROTEIN BINDING;

AMINO ACID SEQUENCE; ARTICLE; ATOM; CHEMICAL STRUCTURE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DIMERIZATION; LIGAND BINDING; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; RAT; SEQUENCE HOMOLOGY; ZEBRA FISH;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; HUMANS; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; RATS; RECEPTORS, CALCITRIOL; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; ZEBRAFISH;

EID: 77954759869     PISSN: 09600760     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsbmb.2010.04.006     Document Type: Article

References (41)

1. Rochel N., Wurtz J.M., Mitschler A., Klaholz B., Moras D. The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. Mol. Cell 2000, 5:173-179.
2. Yamada S., Shimizu M., Yamamoto K. Structure-function relationships of vitamin D including ligand recognition by the vitamin D receptor. Med. Res. Rev. 2003, 23:89-115.
3. Rochel N., Moras D. Ligand binding domain of vitamin D receptors. Curr. Top. Med. Chem. 2006, 6:1229-1241.
4. Bouillon R., Okamura W.H., Norman A.W. Structure-function relationships in the vitamin D endocrine system. Endocr. Rev. 1995, 16:200-257.
5. H.F. DeLuca, J. Wicha, 20(S)-25-hydroxy vitamin D compounds, US Patent 5,840,938 (1998).
6. 3 receptor. J. Biol. Chem. 1999, 274:16838-16845.
7. 3 with enhanced transcriptional activity. Biochem. Pharmacol. 2004, 67:1327-1336.
8. 3 are associated with enhanced activation of the vitamin D receptor. J. Biol. Chem. 1995, 270:10551-10558.
9. Binderup L., Bretting E., Calverley C., Hansen M. 20-epi-vitamin D analogues: a novel class of potent regulators of cell growth and immune responses. Biochem. Pharmacol. 1991, 42:1569-1575.
10. Tocchini-Valentini N., Rochel J.M., Wurtz D., Moras Crystal structures of the vitamin D nuclear receptor liganded with the vitamin D side chain analogues calcipotriol and seocalcitol, receptor agonists of clinical importance, Insight into a structural basis for the switching of calcipotriol to a receptor antagonist by further side chain modification. J. Med. Chem. 2004, 47:1956-1961.
11. Eelen G., Verlinden L., Camp M.V., Claessens F., De Clercq P., Vandewalle M., Bouillon R., Verstuyf A. Altered vitamin D receptor-coactivator interactions reflect superagonism of vitamin D analogs. J. Steroid Biochem. Mol. Biol. 2005, 97:65-68.
12. Eelen G., Verlinden L., Rochel N., Claessens F., De Clercq P., Vandewalle M., Tocchini-Valentini G., Moras D., Bouillon R., Verstuyf A. Superagonistic action of 14-epi-analogs of 1,25-dihydroxyvitamin D explained by vitamin D receptor coactivator interaction. Mol. Pharmacol. 2005, 67:1566-1573.
13. Hourai S., Rodrigues L.C., Antony P., Reina-San-Martin B., Ciesielski F., Magnier B.C., Schoonjans K., Mourino A., Rochel N., Moras D. Structure-based design of a superagonist ligand for the vitamin D nuclear receptor. Chem. Biol. 2008, 15:383-392.
14. 3 with selected 2α-substituted analogues. J. Med. Chem. 2006, 49:5199-5205.
15. Shulman A.I., Larson C., Mangelsdorf D.J., Ranganathan R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 2004, 116:417-429.
16. CCOMP program, http://www.icho.edu.pl/Eng/Achievements.
17. 3: an insight from a computational analysis. J. Steroid Biochem. Mol. Biol. 2009, 113:253-258.
18. Feng W., Ribeiro R.C.J., Wagner R.L., Nguyen H., Apriletti J.W., Fletteric R.J., Baxter J.D., Kushner P.J., West B.L. Hormone-dependent co-activator binding to a hydrophobic cleft on nuclear receptors. Science 1998, 280:1747-1749.
19. 3 hormone analogues and a LXXLL-containing co-activator peptide. Biochemistry 2004, 43:4101-4110.
20. 3 receptor preferentially recruits the coactivator SRC-1 during up-regulation of the osteocalcin gene. J. Steroid Biochem. Mol. Biol. 2007, 103:420-424.
21. Vaisanen S., Ryhanen S., Saarela J.T.A., Perakyla M., Andresin T., Maenpaa P.H. Structurally and functionally important amino acids of the agonistic conformation of the human vitamin D receptor. Mol. Pharmacol. 2004, 62:788-794.
22. Yamada S., Yamamoto K. Ligand recognition by vitamin D receptor: total alanine scanning mutational analysis of the residues lining binding pocket of vitamin D receptor. Curr. Top. Med. Chem. 2006, 6:1255-1265.
23. Dunbrack R.L. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 2002, 12:431-440.
24. Lovell S.C., Word J.M., Richardson J.S., Richardson D.C. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:400-405.
25. http://www.usm.maine.edu/~rhodes/SPVTut/text/STut09aTN.html.
26. W. Kabsh, C. Sander, DSSP, updated CMBI version by ElmK, 1982.
27. Chothia C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 1976, 105:1-14.
28. Bourguet W., Vivat V., Wurtz J.M., Chambon P., Gronemeyer H., Moras D. Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Mol. Cell 2000, 5:289-298.
29. Gampe R.T., Montana V.G., Lambert M.H., Miller A.B., Bledsoe R.K., Milburn M.V., Kliewer S.A., Wilson T.M., Xu H.E. Asymmetry in the PPARγ/RXRα crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Mol. Cell 2000, 5:545-555.
30. Germain P., Staels B., Dacquet C., Spedding M., Laudet V. International Union of Pharmacology. LXIII. Retinoid X Receptors. Pharmacol. Rev. 2006, 58:685-704.
31. 3-dependent transcription by synthetic LXXLL peptide antagonists that target the activation domains of the vitamin D and retinoid X receptors. J. Bone Miner. Res. 2002, 17:2196-2205.
32. Jin C.H., Kerner S.A., Hong M.H., Pike J.W. Transcriptional activation and dimerization functions in the human vitamin D receptor. Mol. Endocrinol. 1996, 10:945-957.
33. Atschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
34. Sanchez-Martinez R., Castillo A.I., Steinmeyer A., Aranda A. The retinoid X receptor ligand restores defective signaling by the vitamin D receptor. EMBO Rep. 2006, 7:1030-1034.
35. 3 receptor: a network of co-activator interactions. Gene 2000, 246:9-21.
36. Barry J.B., Leongs G.M., Church W.B., Issa L.L., Eisman J.A. Interactions of SKIP/NCoA-62, TFIIB, and Retinoid X Receptor with vitamin D receptor helix H10 residues. J. Biol. Chem. 2003, 278:8224-8228.
37. Darimont B.D., Wagner R.L., Apriletti J.W., Stallcup M.R., Kushner P.J., Baxter J.D., Fletterick R.J., Yamamoto K.R. Structure and specificity of nuclear receptor-co-activator interactions. Genes Dev. 1998, 12:3343-3356.
38. Lee W., Noy N. Interaction of RXR with co-activators are differentially mediated by helix 11 of the receptor's ligand binding domain. Biochemistry 2004, 41:2500-2508.
39. Tocchini-Valentini G.D., Rochel N., Wurtz J.M., Mitschler A., Moras D. Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:5491-5496.
40. Ciesielski F., Rochel N., Moras D. Adaptability of the vitamin D nuclear receptor to the synthetic ligand Gemini: remodeling the LBP with one side chain rotation. J. Steroid Biochem. Mol. Biol. 2007, 103:235-242.
41. 3 receptor permits sensitive interaction with agonists. Mol. Pharmacol. 2000, 57:1206-1217.