Taxonomy of nuclear receptors and SERPINS by multivariate analysis of amino-acid composition

Journal of Steroid Biochemistry and Molecular Biology

Volumn 58, Issue 2, 1996, Pages 167-181

  Ojasoo, Tiiu ^a,c   Doré, Jean Christophe ^b  

^a SORBONNE UNIVERSITÉ   (France)

^b MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^c NONE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; HORMONE RECEPTOR; RETINOIC ACID RECEPTOR; SERINE PROTEINASE INHIBITOR; STEROID RECEPTOR; THYROID HORMONE RECEPTOR;

AMINO ACID ANALYSIS; ARTICLE; BARLEY; DROSOPHILA; HUMAN; MOUSE; MULTIVARIATE ANALYSIS; NONHUMAN; POXVIRUS; PROTEIN FAMILY; RAT; SHEEP; SILKWORM; SPECIES DIFFERENCE; SWINE; TAXONOMY; TECHNIQUE;

BOMBYX MORI; CELL FUSING AGENT VIRUS; HORDEUM VULGARE SUBSP. VULGARE; OVIS ARIES; POXVIRIDAE; SUS SCROFA;

EID: 0030152128     PISSN: 09600760     EISSN: None     Source Type: Journal    
DOI: 10.1016/0960-0760(96)00029-5     Document Type: Article

References (34)

1. 1. Nishikawa K., Kubota Y. and Ooi T.: Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution. J. Biochem. 94 (1983) 981-995.
2. 2. Sheridan R. P., Dixon J. S., Venkataghavan R., Kuntz I. D. and Scott K. P.: Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures. Biopolymers 24 (1985) 1995-2023.
3. 3. Klein P. and Delisi C.: Prediction of protein structural class from the amino-acid sequence. Biopolymers 25 (1986) 1659-1672.
4. 4. Nakashima H., Nishikawa K. and Ooi T.: The folding type of a protein is relevant to the amino acid composition. J. Biochem. (Tokyo) 99 (1986) 153-162.
5. 5. Dubchak I., Holbrook S. R. and Kim S. H.: Prediction of protein folding class from amino-acid composition. Proteins: Struct. Funct. Genet. 16 (1993) 79-91.
6. 6. Metfessel B. A., Saurugger P. N., Connelly D. P. and Rich S. S.: Cross-validation of protein structural class prediction using statistical clustering and neural networks. Protein Sci. 2 (1993) 1171-1182.
7. 7. Boberg J., Salakoski T. and Vihinen M.: Accurate prediction of protein secondary class with fuzzy structural vectors. Protein Eng. 8 (1995) 505-512.
8. 8. Chou K. C.: A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Struct. Funct. Genet. 21 (1995) 319-344.
9. 9. Zhang C. T., Chou K. C. and Maggiora G. M.: Predicting protein structural classes from amino-acid composition: application of fuzzy clustering. Protein Eng. 8 (1995) 425-435.
10. 10. Gower J. C. and Ross G. J. S.: Minimum spanning trees and single linkage cluster analysis. Appl. Statist. 18 (1969) 54-64.
11. 11. Benzécri J. P.: L'Analyse des Données: II. L'Analyse des Correspondances. Vol. 2. Dunod, Paris (1983).
12. 12. Greenacre M. J.: Theory and Application of Correspondence Analysis. Academic Press, New York (1983).
13. 13. Jambu M.: Exploratory and Multivariate Data Analysis. Academic Press, New York (1991).
14. 14. Fichant G. and Gautier C.: Statistical method for predicting protein coding regions in nucleic acid sequences. CABIOS 3 (1987) 287-295.
15. 15. Doré J. C. and Ojasoo T.: Molecular taxonomy by Correspondence Factorial Analysis (CFA) In: Advanced Computer-assisted Techniques in Drug discovery Vol. 3 (Edited by H. van de Waterbeemd). (Methods and principles in medicinal chemistry) VCH, Weinheim (1994) pp. 190-227.
16. 16. Ojasoo T., Raynaud J. P. and Doré J. C.: Affiliations among steroid receptors as revealed by multivariate analysis of steroid binding data. J. Steroid Biochem. Molec. Biol. 48 (1994) 31-36.
17. 17. Ojasoo T., Raynaud J. P. and Doré J. C.: Correspondence factor analysis of steroid libraries. Steroids 60 (1995) 458-469.
18. 18. Nakai K., Kidera A. and Kanehisa M.: Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2 (1988) 93-100.
19. 19. Laudet V., Hänni C., Coll J., Catzeflis F. and Stéhelin D.: Evolution of the nuclear receptor gene superfamily. EMBO J. 11 (1992) 1003-1013.
20. 20. Amero S. A., Kretsinger R. H., Moncrief N. D., Yamamoto K. R. and Pearson W. R.: The origin of nuclear receptor proteins: a single precursor distinct from other transcriptional factors. Molec. Endocr. 6 (1992) 3-7.
21. 21. O'Malley B. W. and Tsai M.-J.: Overview of the steroid receptor superfamily of gene regulatory proteins. In: Steroid Hormone Action (Edited by M. G. Parker). IRL Press, Oxford (1993) pp. 45-63.
22. 22. Gaboriaud C., Bissery V., Benchetrit T. and Mornon J. P.: Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 224 (1987) 149-155.
23. 23. Lemesle-Varloot L., Henrissat B., Gaboriaud C., Bissery V., Morgat A. and Mornon J. P.: Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72 (1990) 555-574.
24. 24. Raynaud J. P., Bissery V., Gaboriaud C., Ojasoo T., Teutsch G. and Mornon J. P.: An analysis of the steroid binding domains of receptors and of ligand structure and binding affinity. In Steroid/Thyroid Hormone Receptor Family and Gene Regulation (Edited by J. Carlstedt-Duke, H. Eriksson and J. Å. Gustafsson). Birkhäuser Verlag, Basel (1989) pp. 337-366.
25. 25. Mornon J. P., Bissery V., Gaboriaud C., Thomas A., Ojasoo T. and Raynaud J. P.: Hydrophobic Cluster Analysis (HCA) of the hormone-binding domain of receptor proteins. J. Steroid Biochem. 34 (1989) 355-361.
26. 26. Lemesle-Varloot L., Ojasoo T., Mornon J. P. and Raynaud J. P.: A model for the determination of the 3D-spatial distribution of the functions of the hormone binding domain of receptors that bind 3-keto-4-ene steroids. J. Steroid Biochem. Molec. Biol. 41 (1992) 369-388.
27. 27. Bourguet W., Ruff M., Chambon P., Gronemeyer H. and Moras D.: Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-α. Nature 375 (1995) 377-382.
28. 28. Bairoch A. and Boeckmann B.: The SWISS-PROT protein sequence data bank: current status. Nucl. Acids Res. 22 (1994) 3578-3580.
29. 29. Mornon J. P., Thoreau E., Rowlands D., Callebaut I. and Moreau G.: Putative dimeric organization of nuclear receptor hormone-binding domains deduced from hydrophobic cluster analysis. Comptes. R. Acad. Sci. Paris 317 (1994) 597-606.
30. 30. Prim R. C.: Shortest connection networks and some generalisations. Bell Syst. Technol. J. 36 (1957) 1389-1401.
31. 31. Lance G. N. and Williams W. T.: Computer programs for hierarchical polymeric classification ("similarity analyses"). Comp. J. 9 (1966) 60-64.
32. 32. Giguère V.: Retinoic acid receptors and cellular retinoid binding proteins: complex interplay in retinoid signaling. Endocr. Rev. 15 (1994) 61-79.
33. 33. Mocz G.: Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins. Protein Sci. 4 (1995) 1178-1187.
34. 34. Wright H. T.: Introns and higher-order structure in the evolution of serpins. J. Molec. Biol. 36 (1993) 136-143.