Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern

Computational Biology and Chemistry

Volumn 28, Issue 1, 2004, Pages 39-49

  Inoue, Yasuhito ^a   Ikeda, Masami ^a,b   Shimizu, Toshio ^a  

^a HIROSAKI UNIVERSITY   (Japan)

^b IWATE UNIVERSITY   (Japan)

Author keywords

Binary topology pattern; Functional identification; G protein coupled receptor; Length of loop domain; Transmembrane topology

Indexed keywords

AMINO ACIDS; BIOCHEMISTRY; BIOLOGICAL MEMBRANES; CLASSIFICATION (OF INFORMATION); GENETIC ENGINEERING; MARKOV PROCESSES; TOPOLOGY;

BINARY TOPOLOGY PATTERN (BTP); FUNCTIONAL IDENTIFICATION; G PROTEIN COUPLED RECEPTORS (GPCR); LENGTH OF LOOP DOMAIN; TRANSMEMBRANE (TM) TOPOLOGY;

PROTEINS;

EUKARYOTA; MAMMALIA; MELANOGASTER; MUSCULUS; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

G PROTEIN COUPLED RECEPTOR; PROTEOME;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; GENOME; HUMAN; MAMMAL; METABOLISM; OLFACTORY RECEPTOR; PHYLOGENY; PROTEIN TRANSPORT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL ANALYSIS;

ANIMALS; DATA INTERPRETATION, STATISTICAL; GENOME; HUMANS; MAMMALS; PHYLOGENY; PROTEIN TRANSPORT; PROTEOME; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, ODORANT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

EID: 0842286957     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2003.11.003     Document Type: Article

References (32)

1. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science. 287:2000;2185-2195.
2. Altschul 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. 25:1997;3389-3402.
3. Aparicio S., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:2002;1301-1310.
4. Bateman A., et al. The Pfam protein families database. Nucleic. Acids Res. 30:2002;276-280.
5. Boeckmann B., et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:2003;365-370.
6. Clements J.D., Martin R.E. Identification of novel membrane proteins by searching for patterns in hydropathy profiles. Eur. J. Biochem. 269:2002;2101-2107.
7. Clyne P.J., Warr C.G., Freeman M.R., Lessing D., Kim J., Carlson J.R. A novel family of divergent seven-transmembrane proteins: candidate odorant receptors in Drosophila. Neuron. 22:1999;327-338.
8. Dehal P., et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 298:2002;2157-2167.
9. Gardner M.J., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419:2002;498-511.
10. Hirokawa T., Boon-Chieng S., Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 14:1998;378-379.
11. Holt R.A., et al. The genome sequence of the malaria mosquito Anapheles gambiae. Science. 298:2002;129-149.
12. Horn F., Bettler E., Oliveira L., Campagne F., Cohen F.E., Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 31:2003;294-297.
13. Karchin R., Karplus K., Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 18:2002;147-159.
14. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:2001;567-580.
15. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
16. Lao, D.M., Shimizu, T., 2001. A method for discriminating a signal peptide and a putative 1st transmembrane segment. In: Valafar, F. (Ed.), Proceedings of 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '01). CSREA Press, Las Vegas, pp. 119-125.
17. Lao D.M., Arai M., Ikeda M., Shimizu T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics. 18:2002a;1562-1566.
18. Lao D.M., Okuno T., Shimizu T. Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. In Silico Biol. 2:2002b;485-494.
19. McGuffin L.J., Bryson K., Jones D.T. The PSIPRED protein structure prediction server. Bioinformatics. 16:2000;404-405.
20. Nielsen, H., Krogh, A., 1998. Prediction of signal peptides and signal anchors by a hidden Markov model. In: Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D., Sensen, C. (Eds.), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 122-130.
21. Otaki J.M., Firestein S. Length analyses of mammalian G-protein-coupled receptors. J. Theor. Biol. 211:2001;77-100.
22. Poluliakh, N., Saito, K., Shimizu, T., 2000. Transmembrane topology pattern and detection of transmembrane protein functions. In: Dunker, A.K., Konagaya, A., Miyano, S., Takagi, T. (Eds.), Genome Informatics 2000. Universal Academy Press, Tokyo, pp. 334-335.
23. Remm M., Sonnhammer E. Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Res. 10:2000;1679-1689.
24. Smith D.P. Drosophila odor receptors revealed. Neuron. 22:1999;203-204.
25. Sugiyama Y., Poluliakh N., Shimizu T. Identification of transmembrane protein functions by binary topology patterns. Protein Eng. 16:2003;479-488.
26. Takeda S., Kadowaki S., Haga T., Takaesu H., Mitaku S. Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Lett. 520:2002;97-101.
27. The C. elegans Sequencing Consortium, 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
28. Theologis A., et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 408:2000;816-820.
29. Tusnády G.E., Bakos E., Varadi A., Sarkadi B. Membrane topology distinguishes a subfamily of the ATP-binding cassette (ABC) transporters. FEBS Lett. 402:1997;1-3.
30. Tusnády G.E., Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283:1998;489-506.
31. Tusnády G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:2001;849-850.
32. Vosshall L.B., Amrein H., Morozov P.S., Rzhetsky A., Axel R. A spatial map of olfactory receptor expression in the Drosophila antenna. Cell. 96:1999;725-736.