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New Development of Protein Structure Analysis by Vacuum-Ultraviolet Circular Dichroism Spectroscopy

Research Project

Project/Area Number 18570107
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionHiroshima University

Principal Investigator

GEKKO Kunihiko  Hiroshima University, Graduate School of Science, Emeritus Professor (10023467)

Co-Investigator(Kenkyū-buntansha) OHMAE Eiji  Hiroshima University, Graduate School of Science, Assistant Professor (30284152)
松尾 光一  広島大学, 放射光科学研究センター, 講師(研究機関研究員) (40403620)
Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥4,020,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥420,000)
Fiscal Year 2007: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2006: ¥2,200,000 (Direct Cost: ¥2,200,000)
Keywordssynchrotron / vacuum-ultraviolet cirvular dichroism / proteins / denatured state / secondary-structure analysis / amino-acid sequence
Research Abstract

We constructed the vacuum-ultraviolet circular dichroism (VUVCD) spectrophotometer at Hiroshima University Synchrotron Radiation Center. This spectrophotometer was applied for the secondary-structure analyses of proteins as follows.
1. Secondary-structure analysis of denatured proteins: The VUVCD spectra down to 172 nm in various solvent conditions revealed the considerable amount of secondary structures remaining in the acid-, cold-, heat-, and guanidine-hydrochloride-denatured states of metmyoglobin, staphylococcal nuclease, and thioredoxin. However, the alcohol-denatured states induced by trifluoroethanol and methanol involved a large amount (70%) of α-helix, different from other denatured states.
2. Sequence-based prediction of secondary structures: The sequence-based prediction of secondary structures was improved up to 75% accuracy by combining the neural network method with the contents and numbers of a-helix and 3-strand obtained from the VUVCD data of 30 proteins down to 160 nm. … More VUVCD data could enhance the predictive accuracy to over 80% when combined with the currently best sequence-predictive algorithms.
3. Secondary-structure analysis of protein interacting with lipid: When bound with phospholipid, α-acid-glycoprotein increased the content of α-helix from 11% (2 segments) to 50% (7 segments) and that of β-strand from 40% (11 segments) to 10% (4 segments). These structure changes occurred mainly at the ligand-binding sites, indicating important role of membrane interaction in protein function.
4. Secondary-structure analysis of protein in amyloid: The VUVCD spectra of β_2-microglobulin and its two peptide segments (#21-31, #21-29) down to 175 nm revealed the formation of characteristic β-sheet structures. The details of the amyloid structure are under theoretical analysis.
These results demonstrate that synchrotron-radiation VUVCD spectroscopy gives new and detailed information on the protein secondary structures, greatly expanding its applicability to protein structural biology. Less

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (40 results)

All 2008 2007 2006 Other

All Journal Article (17 results) (of which Peer Reviewed: 4 results) Presentation (23 results)

  • [Journal Article] Improved Sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network2008

    • Author(s)
      Koichi Matsuo
    • Journal Title

      Proteins (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Improved sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network2008

    • Author(s)
      K., Matsuo, H., Watanabe, K., Gekko
    • Journal Title

      Proteins (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Improved sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network2008

    • Author(s)
      Koichi Matsuo
    • Journal Title

      Proteins (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Koichi Matsuo
    • Journal Title

      Biophys. J. 92

      Pages: 4088-4096

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Secondary-structure analysis of trifluoroethanol-denatured proteins using a vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Koichi Matsuo
    • Journal Title

      HiSOR Activity Report 2006

      Pages: 97-98

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Journal Article] Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectrometry2007

    • Author(s)
      K., Matsuo, Y., Sakurada, R., Yonehara, M., Kataoka, K., Gekko
    • Journal Title

      Biophys. J 92

      Pages: 4088-4096

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Secondary-structure analysis of trifluoroethanol-denatured proteins using a vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      K., Matsuo, Y., Sakurada, H., Namatame, M., Taniguchi, K., Gekko
    • Journal Title

      HiSOR Activity Report 2006

      Pages: 97-98

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Vacuum-ultraviolet circular dichroism analysis of biomaterials2006

    • Author(s)
      Kunihiko Gekko
    • Journal Title

      Chirality 18

      Pages: 329-334

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary 2006 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Vacuum-ultraviolet circular dichroism study of amino acids using synchrotron radiation spectroscopy2006

    • Author(s)
      Koichi Matsuo
    • Journal Title

      HiSOR Activity Report 2005

      Pages: 110-111

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Secondary Structure analysis of denatured proteins by vacuum-ultaviolet circular dichroism spectroscopy2006

    • Author(s)
      Koichi Matsuo
    • Journal Title

      HiSOR Activity Report 2005

      Pages: 112-113

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Vacuum-ultraviolet circular dichroism analysis of biomaterials2006

    • Author(s)
      K., Gekko, K., Matsuo
    • Journal Title

      Chirality 18

      Pages: 329-334

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Vacuum-ultraviolet circular dichroism study of amino acids using synchrotron radiation spectrophotometer2006

    • Author(s)
      K., Matsuo, Y., Matsushima, T., Fukuyama, S., Senba, H., Namatame, M., Taniguchi, K., Gekko
    • Journal Title

      HiSOR Activity Report2005

      Pages: 110-111

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2006

    • Author(s)
      K., Matsuo, Y., Sakurada, R., Yonehara, M., Kataoka, H., Namatame, M., Taniguchi, K., Gekko
    • Journal Title

      HiSOR Activity Report2005

      Pages: 112-113

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Selective metal binding by Vanabin2 from the vanadium-rich Ascidian, Ascidia sydneiensis samea2006

    • Author(s)
      Norifumi Kawakami
    • Journal Title

      Biochim, Biophys. Acta 1760

      Pages: 1096-1101

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Evolutional design of a hyper-active cyteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.2006

    • Author(s)
      Masahiro Iwakura
    • Journal Title

      J. Biol. Chem. 281

      Pages: 13234-13246

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Mass spectrometry on hydrogen/deuterium exchange in 70S ribosomal proteins from E. coli2006

    • Author(s)
      Tatsuya Yamamoto
    • Journal Title

      FEBS Lett. 580

      Pages: 3638-3642

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Secondary-Structure Analysis of Denetured Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy

    • Author(s)
      Koichi Matsuo
    • Journal Title

      Biophys. J. in press

    • Related Report
      2006 Annual Research Report
  • [Presentation] Overview of VUV circular dichrosim spectroscopy at HiSOR2008

    • Author(s)
      Kunihiko Gekko
    • Organizer
      The 12th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of alcohol-denatured proteins by VUV circular dichroism spectroscopy2008

    • Author(s)
      Koichi Matsuo
    • Organizer
      The 12th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of disulfide-deleted lysozyme by VUV circular dichroism spectroscopy2008

    • Author(s)
      Hidenori Watanabe
    • Organizer
      The 12th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法を用いたアルコール変性タンパク質の二次構造解析2008

    • Author(s)
      松尾光一
    • Organizer
      第21回日本放射光学会年会
    • Place of Presentation
      滋賀
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] 真空紫外CD分光法とニューラルネットワークの併用によるアミノ酸配列レベルでの蛋白質二次構造解析2008

    • Author(s)
      月向邦彦
    • Organizer
      2008年度日本農芸化学会年会
    • Place of Presentation
      名古屋
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法によるジスルフィド結合除去リゾチームの二次構造解析2008

    • Author(s)
      松尾光一
    • Organizer
      日本化学会第88回春季年会
    • Place of Presentation
      東京
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Overview of VUV circular dichroism spectroscopy at HiSOR2008

    • Author(s)
      K., Gekko, K., Matsuo
    • Organizer
      The 12th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Koichi Matsuo
    • Organizer
      The 11th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Prediction of protein secondary-structure on amino-acid sequence level by vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Hidenori Watanabe
    • Organizer
      The 11th Hiroshima International Symposium on Synchrotron Radiation
    • Place of Presentation
      Hiroshima
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of native proteins by vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Kunihiko Gekko
    • Organizer
      The 11th International Conference on Circular Dichroism
    • Place of Presentation
      Groningen, Netherlands
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of native non-native proteins using vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      Koichi Matsuo
    • Organizer
      The 15th International Conference on Vacuum Ultraviolet Radiation Physics
    • Place of Presentation
      Berlin, Germany
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法による変性タンパク質の二次構造解析2007

    • Author(s)
      松尾光一
    • Organizer
      第20回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      広島
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法によるアミノ酸配列レベルでのタンパク質の二次構造解析2007

    • Author(s)
      渡部秀典
    • Organizer
      第20回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      広島
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法によるα_1-acid glycoproteinの二次構造解析2007

    • Author(s)
      松尾光一
    • Organizer
      日本化学会第87回春季年会
    • Place of Presentation
      大阪
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 真空紫外CD分光法による変性タンパク質の二次構造解析2007

    • Author(s)
      月向邦彦
    • Organizer
      2007年度日本農芸化学会年会
    • Place of Presentation
      東京
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 真空紫外CD分光法によるアルコール変性タンパク質の二次構造解析2007

    • Author(s)
      松尾光一
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      横浜
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] 真空紫外円二色性分光法によるジスルフィド結合除去リゾチームの二次構造解析2007

    • Author(s)
      渡部秀典
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      横浜
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of native and non-native proteins using vacuum-ultraviolet circular dichroism spectroscopy2007

    • Author(s)
      K., Matsuo, K., Gekko
    • Organizer
      The 15th International Conference on Vacuum Ultraviolet Radiation Physics
    • Place of Presentation
      Berlin, Germany
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2006

    • Author(s)
      Koichi Matsuo
    • Organizer
      The 20th Symposium of The Protein Society and 20th Anniversary Celebration
    • Place of Presentation
      San Diego, USA
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Secondary structure analysis of glycoprotein using vucuum-ultraviolet circular dichroism spectroscopy2006

    • Author(s)
      Koichi Matsuo
    • Organizer
      第44回日本生物物理学会年会
    • Place of Presentation
      沖縄
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Secondary structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2006

    • Author(s)
      Yoshie Sakurada
    • Organizer
      第44回日本生物物理学会年会
    • Place of Presentation
      沖縄
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Secondary structure prediction of proteins by vacuum-ultraviolet circular dichroism spectroscopy2006

    • Author(s)
      Hidenori Watanabe
    • Organizer
      第44回日本生物物理学会年会
    • Place of Presentation
      沖縄
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 放射光真空紫外円二色性による糖タンパク質の二次構造解析2006

    • Author(s)
      松尾光一
    • Organizer
      日本化学会西日本大会
    • Place of Presentation
      沖縄
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary

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Published: 2006-04-01   Modified: 2016-04-21  

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