A note on clustering the functionally-related paralogues and orthologues of proteins: A case of the FK506-binding proteins (FKBPs)

Computational Biology and Chemistry

Volumn 28, Issue 2, 2004, Pages 129-140

  Galat, Andrzej ^a  

^a CE Saclay ^*  (France)

Author keywords

FKBP; Multiple sequence alignment; PPIase; Sequence clusters

Indexed keywords

ALGORITHMS; AMINO ACIDS; CORRELATION METHODS; DRUG PRODUCTS; GENES; HYDROPHOBICITY; POLYPEPTIDES; PROTEINS;

FKBP; MULTIPLE SEQUENCE ALIGNMENT; PPIASE; SEQUENCE CLUSTERS;

BIOCHEMISTRY;

EUKARYOTA; MELANOGASTER; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

FK 506 BINDING PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMPARATIVE STUDY; EUKARYOTIC CELL; FACTUAL DATABASE; FUNGUS; GENETICS; GENOME; HUMAN; MOLECULAR GENETICS; PLANT; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; DATABASES, FACTUAL; EUKARYOTIC CELLS; FUNGI; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; PLANTS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TACROLIMUS BINDING PROTEINS;

EID: 2342529037     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.01.004     Document Type: Article

References (44)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A. The genome sequence of Drosophila melanogaster. Science. 287:2001;2185-2195.
2. Alnemri E.S., Fernandes-Alnemri T., Pomerenke K., Robertson N.M., Dudley K., DuBois G.C., Litwack G. FKBP46, a novel Sf9 insect cell nuclear immunophilin that forms a protein-kinase complex. J. Biol. Chem. 269:1994;30828-30834.
3. Becker J.W., Rotonda B.M., Mckeever H.K., Chan A.I., Marcy G., Wiederrecht J.D., Springer J.P. FK-506-binding protein: three-dimensional structure of the complex with the antagonist L-685818. J. Biol. Chem. 268:1993;11335-11339.
4. Blanc G., Hokamp K., Wolfe K.H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13:2003;137-144.
5. Chang J.Y., Sehgal S.N., Bansbach C.C. FK506 and rapamycin: novel pharmacological probes of the immune response. Trends Pharmacol. Sci. 12:1991;218-223.
6. Crackower M.A., Kolas N.K., Noguchi J., Sarao R., Kikuchi K., Kaneko H., Kobayashi E., Kawai Y., Kozieradzki I., Landers R., Mo R., Hui C.C., Nieves E., Cohen P.E., Osborne L.R., Wada T., Kunieda T., Moens P.B., Penninger J.M. Essential role of Fkbp6 in male fertility and homologous chromosome pairing in meiosis. Science. 300:2003;1291-1295.
7. Dornan J., Taylor P., Walkinshaw M.D. Structures of immunophilins and their ligand complexes. Curr. Top. Med. Chem. 3:2003;1392-1409.
8. Fretz H., Albers M.A., Galat A., Standaert R.F., Lane W.S., Burakoff S.J., Bierer B.E., Schreiber S.L. Rapamycin and FK506 binding proteins (immunophilins). J. Am. Chem. Soc. 113:1991;1409-1410.
9. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y., Philippsen P., Tettelin H., Oliver S.G. Life with 6000 genes. Science. 274:1996;546.
10. Galat A., Lane W.S., Standaert R.F., Schreiber S.L. A rapamycin-selective 25-kDa immunophilin. Biochemistry. 31:1992;2427-2434.
11. Galat A., Bouet F., Rivière S. Amino acid compositions of proteins and their identities. Electrophoresis. 16:1995;1095-1103.
12. Galat A., Gerbod M.C., Bouet F., Rivière S. Proteins and their amino acid compositions: uniqueness-variability-applications. Arch. Biochem. Biophys. 330:1996;229-237.
13. Galat, A., Riviere, S., 1998. Peptidyl-prolyl cis/trans isomerases. Protein Profile. Oxford University Press, Oxford, England.
14. Galat A. Sequence diversification of the FK506-binding proteins in several different genomes. Eur. J. Biochem. 267:2000;4945-4959.
15. Galat A. Peptidylprolyl cis/trans isomerases (immunophilins): biological diversity-targets-functions. Curr. Top. Med. Chem. 3:2003;1315-1347.
16. Harding M.W., Galat A., Uehling D.E., Schreiber S.L. A receptor for the immunosuppressant FK-506 is a cis-trans peptidyl-prolyl isomerase. Nature. 341:1989;761-763.
17. Harris, J.W., Stocker, H., 1998. Handbook of Mathematics and Computational Science. Springer Verlag.
18. Harris T.W., Lee R., Schwarz E., Bradman K., Lawson D., Chen W., Blaiser D., et al. WormBase: a cross-species database for comparative genomics. Nucl. Acids Res. 31:2003;133-137.
19. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation matrices from protein sequences. CABIOS. 8:1992;275-282.
20. Kondrashov F.A., Rogozin I.B., Wolf Y.I., Koonin E.V. Selection in the evolution of gene duplications. Genome Biol. 3:2002;1-9.
21. Kraulis P.J. Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:1991;946-950.
22. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132.
23. Lander E.S., Lintoin L.M., Birren B., Nusbaum C. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
24. Liang, J., Hung, D.T., Schreiber, S.L.S., Clardy, J., 1995. X-ray fragment of hFKBP-25 (residues 116 to 224) (pdb1pbk.ent), PDB Brookhaven.
25. Meyer B.K., Pray-Grant M.G., Vanden-Heuvel J.P., Perdew G.H. Hepatitis B virus X-associated protein 2 is a subunit of the unliganded aryl hydrocarbon receptor core complex and exhibits transcriptional enhancer activity. Mol. Cell. Biol. 18:1998;978-988.
26. Otto S.P., Yong P. The evolution of gene duplicates. Adv. Genet. 46:2002;451-483.
27. Patterson C.E., Gao J., Rooney A.P., Davis E.C. Genomic organization of mouse and human 65 kDa FK506-binding protein genes and evolution of the FKBP multigene family. Genomics. 79:2002;881-889.
28. Rhee S.Y., Beavis W., Berardini T.Z., Chen G., Dixon D., Doyle M., et al. The Arabidopsis Information Resource (TAIR): a model organisms database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucl. Acids Res. 31:2003;224-228.
29. Rivière S., Menez A., Galat A. On the localization of FKBP25 in T-lymphocytes. FEBS Lett. 315:1993;247-251.
30. Rosner M., Hofer K., Kubista M., Hengstschlager M. Cell size regulation by the human TSC tumor suppressor proteins depends on PI3K and FKBP38. Oncogene. 22:2003;4786-4798.
31. Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., et al. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature. 408:2000;820-822.
32. Schreiber S.L. Chemistry and biology of the immunophilins and their immunosuppressive ligands. Science. 251:1991;283-287.
33. Schultz L.W., Martin P.K., Liang J., Schreiber S.L., Clardy J. Atomic structure of the immunophilin FKBP13-FK506 complex: insights into the composite binding surface for calcineurin. J. Am. Chem. Soc. 116:1994;3129-3130.
34. Shirane M., Nakayama K.I. Inherent calcineurin inhibitor FKBP38 targets Bcl-2 to mitochondria and inhibits apoptosis. Nat. Cell Biol. 5:2003;28-37.
35. Siekerka J.J., Hung S.H.Y., Poe M., Lin S.C., Sigal N.H. A cytosolic binding protein for the immunosuppressant FK506 has peptidyl-prolyl isomerase activity but is distinct from cyclophilin. Nature. 341:1989;755-757.
36. The FlyBase Consortium. 2003. The FlyBase database of the Drosophila genome projects and community literature. Nucl. Acids Res. 31, 171-175.
37. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
38. Tsai J., Taylor R., Chothia C., Gerstein M. The packing density in proteins: standard radii and volumes. J. Mol. Biol. 290:1999;253-266.
39. van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L.S., Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229:1993;105-124.
40. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J. The sequence of the human genome. Science. 291:2001;1304-1351.
41. Wheeler D.L., Church D.M., Federhen S., Lash A.E., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E., Tatusova T.A., Wagner L. Database resources of National Center for Biotechnology. Nucl. Acids Res. 31:2003;28-33.
42. Wilson R.K. How the worm was won. The C. elegans genome sequencing project. Trends Genet. 15:1999;51-58.
43. Wood V., Gwilliam R., Rajandream M.A., Lyne M., Lyne R., Stewart A., Sgouros J., Peat N., Hayles J., et al. The genome sequence of Schizosaccharomyces pombe. Nature. 415:2002;871-880.
44. Wu C.H., Yeh L.S.L., Huang H., Arminski L., Castro-Alvear K., Chen Y., Hu Z., Kourtesis P., Ledley R.S., Suzek B.E., Vinayaka C.R., Zhang J., Barker W. The protein information resource (PIR). Nucl. Acids Res. 31:2003;345-347.