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2010 Fiscal Year Final Research Report

Analysis of hierarchical structure of proteins network

Research Project

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Project/Area Number 21770174
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Biophysics
Research InstitutionNara Institute of Science and Technology

Principal Investigator

KAMIKUBO Hironari  Nara Institute of Science and Technology, 物質創成科学研究科, 准教授 (20311128)

Project Period (FY) 2009 – 2010
KeywordsX線溶液散乱 / クラスリン被覆小胞輸送 / マルチドメイン蛋白質 / ドメイン再配置
Research Abstract

Concerning signal transduction and intracellular vesicular traffic, multi-domain proteins comprised of several functional domains act a central role in the biological functions. In this work, to elucidate the molecular mechanism of the hierarchical regulation involving multi-domain proteins, domain rearrangement of multi-domain proteins initiated by stimulating each domain, and intermolecular and intermolecular regulation associated with the domain rearrangement were examined by using x-ray scattering and dynamic light scattering. In the results, the multi-domain proteins of GGA involved in vesicular traffic and Ppr in a two component regulatory system exhibit intermolecular dissociation and association of their domains during their function expression, and the domain rearrangements are expected to regulate molecular events of protein ensembles involving the multi-domain proteins.

  • Research Products

    (59 results)

All 2011 2010 2009 Other

All Journal Article (8 results) Presentation (47 results) Book (2 results) Remarks (2 results)

  • [Journal Article] Systematic alanine insertion reveals the essential regions that encode structure formation and activity of dihydrofolate reductas.2011

    • Author(s)
      Shiba R., Umeyama M., Tsukasa S., Kamikubo H., Yamazaki Y., Yamaguchi M., Iwakura M., Kataoka M.
    • Journal Title

      BIOPHYSICS 7

      Pages: 1-10

  • [Journal Article] Size-controlled aggregation of cube-shaped EuS nanocrystals with magneto-optic properties in solution.2011

    • Author(s)
      Tanaka A., Kamikubo H., Kataoka M., Hasegawa Y., Kawai T.
    • Journal Title

      Langmuir 27

      Pages: 104-108

  • [Journal Article] フォトアクティブイェロープロテインの中性子結晶構造解析2010

    • Author(s)
      上久保裕生、山口繁生、片岡幹雄
    • Journal Title

      RADIOISOTOPES 59

      Pages: 289-297

  • [Journal Article] Cytochrome c polymerization by successive domain swapping at the C-terminal helix.2010

    • Author(s)
      Hirota S., Hattori Y., Nagao S., Taketa M., Komori H., Kamikubo H., Wang Z., Takahashi I., Negi S., Sugiura Y., Kataoka M., Higuchi Y.
    • Journal Title

      Proc. Natl. Acad. Sci. USA. 107

      Pages: 12854-12859

  • [Journal Article] Self-assembling Formation and Enhanced Magnetic Properties of Three-dimensional Super-lattice Structures Composed of Cube- and Sphere-shaped EuS nanocrsytals.2010

    • Author(s)
      Tanaka A., Kamikubo H., Doi Y., Hinatsu Y., Kataoka M., Kawai T., Hasegawa Y.
    • Journal Title

      Chemistry of Materials 22

      Pages: 1776-1781

  • [Journal Article] Non-local interaction responsible for the tertiary structural formation of Staphylococcal nuclease.2010

    • Author(s)
      Kato S., Kamikubo H., Hirano S., Yamazaki Y., Kataoka M.
    • Journal Title

      Biophys. J. 98

      Pages: 678-786

  • [Journal Article] Effect of conformational states on protein dynamical transition.2009

    • Author(s)
      Nakagawa H., Kamikubo H., Kataoka M.
    • Journal Title

      Biochim Biophys Acta. 1804

      Pages: 27-33

  • [Journal Article] Self-aggregation of magnetic semiconductor EuS nanocrystals.2009

    • Author(s)
      Tanaka A., Hasegawa Y., Kamikubo H., Kataoka M., Kawai T.
    • Journal Title

      THIN SOLID FILMS 518

      Pages: 870-872

  • [Presentation] Fluctuation controls enzymatic activity of Staphylococcal nuclease.2010

    • Author(s)
      H.Kamikubo(他2名)
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] Classification of the functional element of dihydrofolate reductase by the systematic alanine insertion.2010

    • Author(s)
      R.Shiba, H.Kamikubo, M.Umeyama, S.Tsukasa, M.Yamaguchi, Y.Yamazaki, M.Iwakura, M.Kataoka.
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] FRET analysis of structural changes in staphylococcal nuclease2010

    • Author(s)
      Y.Kishi, T.Muto, M.Yamaguchi, I.Iijima, Y.Yamazaki, H.Kamikubo, T.Hohsaka, M.Kataoka.
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] Cytochrome c polymerization by successive domain swapping at the C-terminal helix.2010

    • Author(s)
      Z.Wang, Y.Hattori, S.Nagao, M.Takeda, H.Komori, H.Kamikubo, I.Takahashi, S.Negi, Y.Sugiura, M.Kataoka, Y.Higuchi, S.Hirota.
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] Measurements of loop formation in the denatured state of staphylococcal nuclease.2010

    • Author(s)
      M.Yamaguchi, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] The investigation of the relationship between non-local interaction and the effect of single alanine insertion in staphylococcal nuclease.2010

    • Author(s)
      H.Sawada, H.Kamikubo, Y.Yamazaki, M.Kataoka.
    • Organizer
      The 4th International Symposium "Molecuar Science of Fluctuations toward Biological Functions"
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      20101130-20101201
  • [Presentation] Cytochrome c polymerization by successive domain swapping at the C-terminal helix.2010

    • Author(s)
      S.Hirota, Y.Hattori, S.Nagao, M.Takeda, H.i Komori, H.Kamikubo(他6名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Intrinsically less-ordered bacterial effectors : A case of EspB from enterohaemorrhagic Escherichia coli.2010

    • Author(s)
      D.Hamada, H.Kamikubo(他2名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Property of a structural element of SNase-like domain in human p100.2010

    • Author(s)
      Y.Ogawa, H.Kamikubo.(他4名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] The investigation of the relationship between non-local interaction and the effect of single alanine insertion in staphylococcal nuclease.2010

    • Author(s)
      H.Sawada, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] FRET analysis of structural changes in Staphylococcal nuclease.2010

    • Author(s)
      Y.Kishi, M.Yamaguchi, I.Iijima, Y.Yamazaki, H.Kamikubo(他2名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] The role of each residue in the flexible rambda loop of Staphylococcal nuclease on the catalytic activity.2010

    • Author(s)
      C.Ahn, H.Kamikubo, H.i Yoshioka, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Solution structure of the light sensor histidine kinase of Ppr comprised of the PYP and Bph domains.2010

    • Author(s)
      J.Miura, H.Kamikuno, Y.Yamzaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Solution structural analysis of Drosophila GGA.2010

    • Author(s)
      M.Naruse, H. Kamikubo(他6名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Analysis of solution state of the interaction protein of Rc-PYP.2010

    • Author(s)
      M.Hayashi, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Classification of the functional element of dihydrofolate reductase (DHFR) by the systemic alanine insertion.2010

    • Author(s)
      R.Shiba, H.Kamikubo(他6名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Synthesis of an artificial enzyme by implanting the functional elements of SNase.2010

    • Author(s)
      H.Kamikubo, A.Kogasaka, C.Komeda, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Urea denaturation of staphylococcal nuclease monitored by tryptophan-cysteined distance.2010

    • Author(s)
      M.Yamaguchi, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Substitution effects of basic residues in the photoactive yellow protein of Rhodobacter caplsolatus.2010

    • Author(s)
      Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      20100920-20100922
  • [Presentation] Photoactive Yellow Proteinにおける発色団の機能変調2010

    • Author(s)
      山崎洋一, 上久保裕生, 片岡幹雄
    • Organizer
      日本光生物学協会年会
    • Place of Presentation
      大阪
    • Year and Date
      20100810-20100811
  • [Presentation] The effect of alanine insertion mutation for folding process2010

    • Author(s)
      H.Sawada, H.Kamikubo, Y.Yamazaki, M.Kataoka.
    • Organizer
      The 4th Shangai International Conference on Biophysics and Molecolar Biology
    • Place of Presentation
      Shanghai-Jiashan, China
    • Year and Date
      20100808-20100811
  • [Presentation] Extraction of the regions encoded foldability and/or functionability from dihydrofolate reductase by the systematic alanine insertion2010

    • Author(s)
      R.Shiba, H. Kamikubo(他6名)
    • Organizer
      The 4th Shangai International Conference on Biophysics and Molecolar Biology
    • Place of Presentation
      Shanghai-Jiashan, China
    • Year and Date
      20100808-20100811
  • [Presentation] 分子内プロトン移動: Photoactive Yellow Proteinの水素結合構造から何がわかるのか2010

    • Author(s)
      上久保裕生
    • Organizer
      分子研研究会「拡がるロドプシンの仲間から"何がわかるか""何をもたらすか"」
    • Place of Presentation
      岡崎
    • Year and Date
      20100323-20100324
  • [Presentation] 精子由来蛋白質IZUMO,その構造と受精膜融合での役割2010

    • Author(s)
      萩原義久, 井上直和, 浜田大三, 上久保裕生, 平田邦生, 片岡幹雄, 山本雅貴, 伊川正人, 岡部勝
    • Organizer
      日本蛋白質科学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-18
  • [Presentation] 網羅的アラニン挿入変異解析法を用いたジヒドロ葉酸還元酵素の機能発現及び構造形成領域の抽出2010

    • Author(s)
      芝るみ, 上久保裕生, 梅山美香, 政さやか, 山口真理子, 山崎洋一, 巌倉正寛, 片岡幹雄
    • Organizer
      日本蛋白質科学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-18
  • [Presentation] 中性子結晶構造解析による蛋白質分子内プロトン移動機構の解明2010

    • Author(s)
      上久保裕生
    • Organizer
      生命物質構造解析研究会
    • Place of Presentation
      東海村
    • Year and Date
      2010-03-25
  • [Presentation] Extraction of the regions encoded foldability and/or functionability from dihydrofolate reductase by the systematic alanine insertion.2009

    • Author(s)
      R.Shiba, H.Kamikubo, M.Umeyama, S.Tsukasa, Y.Yamazaki, M.Yamaguchi, M.Iwakura, M.Kataoka.
    • Organizer
      The 3rd International Symposium on "Molecuar Science of Fluctuations toward Biological Functions
    • Place of Presentation
      名古屋大学,名古屋
    • Year and Date
      20091220-20091221
  • [Presentation] Local structure characterization of staphylococcal nuclease by lifetime measurement of tryptophan triplet state.2009

    • Author(s)
      M.Yamaguchi, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      The 3rd International Symposium on "Molecuar Science of Fluctuations toward Biological Functions
    • Place of Presentation
      名古屋大学,名古屋
    • Year and Date
      20091220-20091221
  • [Presentation] The properties required for the binding before folding mechanism of the intrinsically disordered mutants of staphylococcal nuclease.2009

    • Author(s)
      M.Onitsuka, H.Kamikubo, Y.Yamazaki, M.Kataoka.
    • Organizer
      The 3rd International Symposium on "Molecuar Science of Fluctuations toward Biological Functions
    • Place of Presentation
      名古屋大学,名古屋
    • Year and Date
      20091220-20091221
  • [Presentation] Structural characterization of the intrinsically disordered mutants of staphylococcal nuclease by electron paramagnetic resonance spectroscopy2009

    • Author(s)
      H.Sawada, S.M.Budamagunta, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, C.J.Voss, M.Kataoka.
    • Organizer
      The 3rd International Symposium on "Molecuar Science of Fluctuations toward Biological Functions
    • Place of Presentation
      名古屋大学,名古屋
    • Year and Date
      20091220-20091221
  • [Presentation] Extraction of the structural element of SNase-like domain in human p100 by alanine insertion analysis2009

    • Author(s)
      Y.Ogawa, H.Kamikubo(他4名)
    • Organizer
      The 3rd International Symposium on "Molecuar Science of Fluctuations toward Biological Functions
    • Place of Presentation
      名古屋大学,名古屋
    • Year and Date
      20091220-20091221
  • [Presentation] 中性子結晶構造解析による蛋白質中の低障壁水素結合の発見2009

    • Author(s)
      上久保裕生
    • Organizer
      日本中性子科学会年会
    • Place of Presentation
      東海村
    • Year and Date
      20091209-20091210
  • [Presentation] Low barrier hydrogen bond in photoactive yellow protein and its role in photoreaction2009

    • Author(s)
      S.Yamaguchi, H.Kamikubo, M.Kataoka.
    • Organizer
      The 1st NCTU-NAIST Workshop on "Molecolar/Nano Science"
    • Place of Presentation
      Taiwan
    • Year and Date
      20091111-20091113
  • [Presentation] Structural characterization of the intrinsically disordered mutants of staphylococcal nuclease by electron paramagnetic resonance spectroscopy.2009

    • Author(s)
      H Sawada, M.S.Budamagunta, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, J.C.Voss, M.Kataoka.
    • Organizer
      The 1st NCTU-NAIST Workshop on "Molecolar/Nano Science"
    • Place of Presentation
      Taiwan
    • Year and Date
      20091111-20091113
  • [Presentation] Crystallographic study of the alanine insertion mutants of Staphylococcal nuclease2009

    • Author(s)
      H.Yoshioka, S.Yamaguchi, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Attempt to create an artificial functional protein by exchange of functional elements2009

    • Author(s)
      A.Kogasaka, H.Kamikubo, M.Onitsuka, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Direct structural modolation of the structure element of SNase by using the azobenzene linkage2009

    • Author(s)
      K.Saito, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] ・-value analysis of induced folding : The role of the ligand binding in induced folding of disordered staphylococcal nuclease mutant2009

    • Author(s)
      M.Onitsuka, H.Kamikubo, Y.Yamazaki, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Structural characterization of the intrinsically disordered mutants of staphylococcal nuclease by electron paramagnetic resonance spectroscopy2009

    • Author(s)
      H.Sawada, S.M.Budamagunta, H.Kamikubo, Y.Yamazaki, M.Yamaguchi, C.J.Voss, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Extraction of the regions encoded foldability and/or functionability from dihydrofolate reductase by the systematic alanine insertion2009

    • Author(s)
      R.Shiba, H.Kamikubo, M.Umeyama, S.Tsukasa, Y.Yamazaki, M.Yamaguchi, M.Iwakura, M.Kataoka,
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Extraction of the structural element of SNase-like domain in human p100 by alanine insertion analysis2009

    • Author(s)
      Y.Ogawa, H.Kamikubo(他4名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Interaction mechanism of the photoactive yellow protein of Rhodobacter caplsolatus2009

    • Author(s)
      Y.Yamazaki, N.Ota, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] The low-temperature spectroscopy of Rc-PYP2009

    • Author(s)
      Y.Hamaguchi, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Analysis of the different properties in two PYPs by use of chimera proteins2009

    • Author(s)
      K.Matsumoto, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Low-barrier hydrogen bond in photoactive yellow protein2009

    • Author(s)
      S.Yamaguchi, H.Kamikubo(他4名)
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] Light dependent enzyme activity control by use of interaction of the Rc-PYP2009

    • Author(s)
      H.Kubo, Y.Yamazaki, H.Kamikubo, M.Kataoka.
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091030-20091101
  • [Presentation] イェロープロテインの低障壁水素結合の形成とその役割2009

    • Author(s)
      片岡幹雄、上久保裕生、山口繁生
    • Organizer
      生体分子科学討論会
    • Place of Presentation
      北海道大学,札幌
    • Year and Date
      20090619-20090620
  • [Book] 入門構造生物学(編集:加藤龍一)(2章3節分担)2010

    • Author(s)
      上久保裕生
    • Total Pages
      34-45
    • Publisher
      共立出版
  • [Book] Springer Structure of the photointermediate of photoactive yellow protein and the propagataion mechanism of structural change.(eds. by K.Kuwajima, Y.Goto, F.Hirata, M.Kataoka, M.Terazima)2009

    • Author(s)
      M.Kataoka, H.Kamikubo.
    • Total Pages
      137-147
    • Publisher
      Water and Biomolecules
  • [Remarks] ホームページ等

    • URL

      http://mswebs.naist.jp/LABs/kataoka/index.html

  • [Remarks]

    • URL

      https://sites.google.com/site/kmkbhp/home

URL: 

Published: 2012-02-13   Modified: 2016-04-21  

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