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2003 Fiscal Year Final Research Report Summary

Genome-wide classification and identification of transmembrane protein structure and function

Research Project

Project/Area Number 14580665
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionHirosaki University

Principal Investigator

SHIMIZU Toshio  Hirosaki University, Facalty of Science and Technology, Professor, 理工学部, 教授 (00110750)

Project Period (FY) 2002 – 2003
Keywordstransmembrane protein / transmembrane topology / consensus prediction / proteome-wide / binary topology pattern / transmembrane topology evolution / internal gene duplication / GPCR
Research Abstract

We first collected experimentally-characterized transmembrane topology models from literatures and constructed them into a database(TMBDB). By using this, we evaluated the performances of several published transmembrane topology prediction methods, and we developed a consensus prediction method(ConPred) which is a combination of some of the proposed methods. By applying ConPred to TM proteomes from 99 completed genomes(88 prokaryotic and 12 eukaryotic), we obtained 52,686 TM protein sequences with reliable TM topologies and analysed the TM topologies of them in detail with respect to their relation to the function. From this analysis, it was revealed that the function of TM protein is closely related to its TM topology, and each functional group pfTM proteins has its own specific TM topology pattern expressed as a binary topology patter. The genome-scale functional classification and identification of GPCRs were also earned out, by applying the binary topology pattern method, and many novel GPCR genes were found by our study. We also investigated die TM topology evolution by internal gene duplication, through the internal sequence similarity comparison within a single sequences.

  • Research Products

    (22 results)

All Other

All Publications (22 results)

  • [Publications] Ikeda, M., Arai, M., Lao, D.M., Shimizu, T.: "Transmembrane topology prediction methods : a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies"Silico Biology. 2. 19-33 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Lao, D.M., Okuno, T., Shimizu, T.: "Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction"Silico Biology. 2. 485-494 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Lao, D.M., Arai, M., Ikeda, M., Shimizu, T.: "The presence of signal peptide significantly affects transmembrane topology prediction"Bioinformatics. 18(12). 1562-1566 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ikeda, M., Arai, M., Okuno, T., Shimizu, T.: "TMPDB : a database of experimentally-characterized transmembrane topologies"Nucleic Acids Research. 31. 406-409 (2003)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Arai, M., Ikeda, M., Shimizu, T.: "Comprehensive analysis of transmembrane topologies in prokaryotic genomes"Gene. 304. 77-86 (2003)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Sugiyama, Y., Polulyakh, N., Shimizu, T.: "Identification of transmembrane protein functions by binary topology patterns"Protein Engineering. 16. 479-488 (2003)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Azumi, K., De Santis, R., De Tomaso, A., Rigoutsos, I., Yoshizaki, F., Pinto, M.R., Marino, R., Shida, K., Ikeda, M., Ikeda, M., Arai, M., Inoue, Y., Shimizu, T., Satoh, N., Rokhsar, D.S., Du Pasquier, L., Kasahara, M., Satake, M., Nonaka, M.: "Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system : "waiting for Godot""Immunogenetics. 55(8). 570-581 (2003)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Inoue, Y., Ikeda, M., Shimizu, T.: "Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern"Computational Biology and Chemistry. 28(1). 39-49 (2004)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Xia, J.-X., Ikeda, M., Shimizu, T.: "ConPred_elite : a highly reliable approach to transmembrane topology prediction"Computational Biology and Chemistry. 28. 51-60 (2004)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Shimizu, T., Mitsuke, H., Noto, K., Arai, M.: "Internal gene duplication in the evolution of prokaryotic transmembrane proteins"Journal of Molecular Biology. 339(1). 1-15 (2004)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Arai, M., Okumura, K., Satake, M., Shimizu, T.: "Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison"Protein Science. (in press). (2004)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ikeda, M., Arai, M., Lao, D.M., Shimizu, T.: "Transmembrane topology prediction methods a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies."In Silico Biol.. 2(1). 19-33 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] 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(4). 485-494 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Lao, D.M., Arai, M., Ikeda, M.Shimizu, T.: "The presence of signal peptide significantly affects transmembrane topology prediction."Bioinformatics. 18(12). 1562-1566 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ikeda, M., Arai, M., Okuno, T., Shimizu, T.: "TMPDB : a database of expenmentally-characterized transmembrane topologies."Nucleic Acids Res.. 31(1). 406-409 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Arai, M., Ikeda, M., Shimizu, T.: "Comprehensive analysis of transmembrane topologies in prokaryotic genomes."Gene. 304. 77-86 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Sugiyama, Y., Polulyakh, N., Shimizu, T.: "Identification of transmembrane protein functions by binary topology patterns."Protein Eng.. 16(7). 479-488 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Azumi, K., De Santis, R., De Tomaso, A., Rigoutsos, I., Yoshizaki, F., Pinto, M.R., Marino, R., Shida, K., Ikeda, M., Ikeda, M., Aiai, M., Inoue, Y., Shimizu, T., Satoh, N., Rokhsar, D.S., Du Pasquier, L., Kasahara, M., Satake, M., Nonaka, M.: "Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system : "waiting for Godot"."Immunogenetics. 55(8). 570-581 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Inoue, Y., Ikeda, M., Shimizu, T.: "Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern."Comput.Biol.Chem.. 28(1). 39-49 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Xia, J.-X., Ikeda, M., Shimizu, T.: "ConPied_elite : a highly reliable approach to transmembrane topology prediction."Comput.Biol.Chem.. 28(1). 51-60 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Shimizu, T., Mitsuke, H., Noto, K., Arai, M.: "Internal gene duplication in the evolution of prokaryotic transmembrane proteins."J.Mol.Biol.. 339(1). 1-15 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Arai, M., Okumura, K., Satake, M., Shimizu, T.: "Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrame topology similarity comparison."Protein Sci.. (in press). (2004)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2005-04-19  

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