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クラスリン小胞輸送に関与する蛋白質群の蛋白質-蛋白質相互作用の構造学的解析

Research Project

Project/Area Number 18770136
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

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

Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥3,600,000 (Direct Cost: ¥3,600,000)
Fiscal Year 2007: ¥1,500,000 (Direct Cost: ¥1,500,000)
Fiscal Year 2006: ¥2,100,000 (Direct Cost: ¥2,100,000)
Keywordsクラスリン被覆小胞輸送 / X線溶液散乱 / マルチドメイン蛋白質 / ドメイン配置構造 / クラスリン被服小胞 / X線散乱測定 / 構造解析
Research Abstract

本研究では,ゴルジ体において積み荷蛋白質を認識し選別しているマルチドメイン蛋白質(GGA)に注目しその機能解明を目的として、X線溶液散乱測定法を用い、ドメイン配置構造や相互作用蛋白質結合時のドメイン配置構造変化を解析したきた。ドメイン間や、マルチドメイン-相互作用蛋白質間の相互作用は一般に弱く、解離定数は数M〜数100MM程度の値を示す。このような弱い相互作用で関連づけられた複合体の溶液構造を解析するために、新たに滴定X線溶液散乱測定法を考案してきた。その結果、GGA1蛋白質に低分子量G蛋白質が結合することによって、ドメイン配置構造に変化が生じ、各ドメインの露出表面が変化することを明らかにしてきた。この形態変化から、ドメイン配置構造変化によって、標的蛋白質との親和性が、調節されていることが示唆された。実際、このドメイン再配置によって、他のドメインの相互作用蛋白質(積み荷蛋白質受容体)に対する結合親和性に変化が見られることが、滴定X線溶液散乱によって明らかにされた。これは、ドメイン再配置を介した、標的蛋白質結合調節機構を直接推測した最初の研究結果である。
更に、GGAの他のホモログについても同様に、ドメイン配置構造を解析した結果、GGA1が溶液中で単量体として存在しているのに対し、GGA3は、GGA1単量体構造を基本構造単位とした2量体として存在していることが明らかとなった。更に、低分子量G蛋白質存在下での溶液構造を解析したところ、GGA3の2量体は解離し、GGA1・低分子量G蛋白質複合体と同様の形態を示すことが明らかとなった。これまでの報告によると、GGA1とGGA3は、非常に類似したドメインからなるにもかかわらず、輸送に対する役割が異なっていることが示唆されている。特に、GGA1は、単独でクラスリン被覆小胞輸送するのではなく、他のアダプター蛋白質と共役して初めて被覆小胞を輸送できるようになる可能性が示唆されている。現在は、会合体型性能の違いが、単独でのクラスリン被覆小胞形成能に関与しているのではないかと考え、引き続き研究を進めている。

Report

(2 results)
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (40 results)

All 2008 2007 2006 Other

All Journal Article (20 results) (of which Peer Reviewed: 10 results) Presentation (20 results)

  • [Journal Article] Attempt to Simplify the Amino-Acid Sequence of Photoactive Yellow Protein with a Set of Simple Rules2007

    • Author(s)
      K. Shirai, Y. Yamazaki, H. Kamikubo, Y. Imamoto, M. Kataoka
    • Journal Title

      Proteins: Structu. Funct. Bioinformat 67

      Pages: 821-833

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering2007

    • Author(s)
      H. Kamikubo, N. Shimizu, M. Harigai, Y. Yamazaki, Y. Imamoto, M. Kataoka
    • Journal Title

      Biophys. J. 92

      Pages: 3633-3642

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of Rab27b small GTPase shows an unexpected swapped dimmer2007

    • Author(s)
      L. Chavas, S. Torii, H. Kamikubo, M. Kawasaki, K. Ihara, R. Kato, M. Kataoka, T. Izumi, S. Wakatsuki
    • Journal Title

      Acta Cryst. D 63

      Pages: 769-779

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Basis for Autoregulatory Interaction between GAE Domain and Hinge Region of GGA12007

    • Author(s)
      M. Inoue, T. Shiba, K. Ihara, Y. Yamada, S. Hirano, H. Kamikubo, M. Kataoka, M. Kawasaki, R. Kato, K. Nakayama, S. Wakatsuki
    • Journal Title

      Traffic 8

      Pages: 904-913

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization and Crystallization of an IscU-type Scaffold Protein with Bound [2Fe 2S] Cluster from the Hyperthermophile, Aquifex aeolicus2007

    • Author(s)
      Y. Shimomura, H. Kamikubo, Y. Nishi, T. Masaki, M. Kataoka, Y. Kobayashi, K. Fukuyama, Y. Takahashi
    • Journal Title

      J Biochem. 142

      Pages: 577-586

    • NAID

      10020095470

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Basis for Autoregulatory Interaction between GAE Domain and Hinge Region of GGA12007

    • Author(s)
      M.Inoue, T.Shiba, K.Ihara, Y.Yamada, S.Hirano, H.Kamikubo, M.Kataoka, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki
    • Journal Title

      Traffic (In press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering2007

    • Author(s)
      H.Kamikubo, N.Shimizu, M.Harigai, Y.Yamazaki, Y.Imamoto, M.Kataoka
    • Journal Title

      Biophys. J. (In press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Attempt to Simplify the Amino-Acid Sequence of Photoactive Yellow Protein with a Set of Simple Rules2007

    • Author(s)
      K.Shirai, Y.Yamazaki, H.Kamikubo, Y.Imamoto, M.Kataoka
    • Journal Title

      Proteins : Structu. Funct. Bioinformat. (In press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Preparation of large crystal of photoactive yellow protein for neutron and high resolution crystal structure analysis2007

    • Author(s)
      S.Yamaguchi, H.Kamikubo, N.Shimizu, Y.Yamazaki, Y.Imamoto, M.Kataoka
    • Journal Title

      Photochem. Photobiol 83

      Pages: 336-338

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Array of aromatic amino acid side chains located near the chromophore of photoactive yellow protein2007

    • Author(s)
      T.Morishita, M.Harigai, Y.Yamazaki, H.Kamikubo, M.Kataoka, Y.Imamoto
    • Journal Title

      Photochem. Photobiol. 83

      Pages: 40-49

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Conformational preference of polyglycine in solution to elongated structure2006

    • Author(s)
      S.Ohnishi, H.Kamikubo, M.Onitsuka, M.Kataoka, D.Shortle
    • Journal Title

      J. Am. Chem. Soc. 128

      Pages: 16338-16344

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Dynamical heterogeneity of protein dynamics studied by elastic incoherent neutron scattering and molecular simulations.2006

    • Author(s)
      H.Nakagawa, A.Tokuhisa, H.Kamikubo, Y.Joti, A.Kitao, M.Kataoka
    • Journal Title

      Materials Science and Engineering A442

      Pages: 356-360

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pKa Regulation in Photoactive Yellow Protein.2006

    • Author(s)
      N.Shimizu, H.Kamikubo, Y.Yamazaki, Y.Imamoto, M.Kataoka
    • Journal Title

      Biochemistry 45

      Pages: 3542-3547

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila.2006

    • Author(s)
      H.Tsuihiji, Y.Yamazaki, H.Kamikubo, Y.Imamoto, M.Kataoka
    • Journal Title

      J. Biosci. Bioeng. 101

      Pages: 263-270

    • NAID

      110004704904

    • Related Report
      2006 Annual Research Report
  • [Journal Article] pH-Dependent equilibrium between long-lived near-UV intermediates of photoactive yellow protein.2006

    • Author(s)
      N.Shimizu, Y.Imamoto, M.Harigai, H.Kamikubo, Y.Yamazaki, M.Kataoka
    • Journal Title

      J. Biol. Chem. 281

      Pages: 4318-4325

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants

    • Author(s)
      M. Onitsuka, H. Kamikubo, Y. Yamazaki, M. Kataoka
    • Journal Title

      Proteins: Structu. Funct. Bioinformat (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of the N-Terminal Region in the Function of the Photosynthetic Bacterium Transcription Regulator PpsR

    • Author(s)
      Y. Yamazaki, H. Fukuzumi, H. Kamikubo, M. Kataoka.
    • Journal Title

      Photochem. Photobiol (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Photoreaction of the Photoactive Yellow Protein Domain in the Light Sensor Histidine Kinase Ppr is Influenced by the C-terminal Domain

    • Author(s)
      H. Kamikubo, T. Koyama, M. Hayashi, K. Shirai, Y. Yamazaki, Y. Imamoto, M. Kataoka
    • Journal Title

      Photochem. Photobiol (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Diverse roles of glycine residues conserved in photoactive yellow protein

    • Author(s)
      Y. Imamoto, S. Tatsumi, M. Harigai, Y. Yamazaki, H. Kamikubo, M. Kataoka
    • Journal Title

      Biophys. J (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: Implications for asymmetric cell division in Drosophila

    • Author(s)
      M. S. Yousef, H. Kamikubo, M. Kataoka, R. Kato, S. Wakatsuki
    • Journal Title

      Protein Sci. (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] Elucidation of the folding process of the disulfide-bond introduced mutants of Staphylococcal nuclease2008

    • Author(s)
      Kato S., Kamikubo H., Kataoka M
    • Organizer
      The 5th Open Workshop for "Chemistry of Biological Processes Created by Water and Biomolecules"
    • Place of Presentation
      Nara(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] The effect of alanine insertion for folding process2008

    • Author(s)
      Sawada H., Kamikubo H., Onitsuka M., Yamazaki Y., Kataoka M
    • Organizer
      The 5th Open Workshop for "Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      Nara(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Extraction of the regions encoded foldability and/or functionability from dihydrofolate reductase by a systematic alanine insertion2008

    • Author(s)
      Shiba R., Kamikubo H., Umeyama M., Yamazaki Y., Iwakura M., Kataoka M
    • Organizer
      The 5th Open Workshop for "Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      Nara(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Direct observation of short hydrogen bond in Photoactive Yellow Protein by neutron crystallographic study2008

    • Author(s)
      Yamaguchi S., Kamikubo H., Kurihara K., Yamazaki Y., Ohnishi Y., Kuroki R., Niimura N., and Kataoka M
    • Organizer
      The 5th Open Workshop for "Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      Nara(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular mechanism of induced folding of C-terminal truncated staphylococcal nuclease2008

    • Author(s)
      Onitsuka M., Kamikubo H., Yamazaki Y., Kataoka M
    • Organizer
      The 5th Open Workshop for "Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      Nara(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Wide Angle X-ray Solution Scattering Reveals The Structure Of Photoin termediate Of Photoactive Yellow Protein2007

    • Author(s)
      Kamikubo H., Sawada H., Kataoka M
    • Organizer
      9th International Conference on Biology and Synchrotron Radiation
    • Place of Presentation
      England
    • Related Report
      2007 Annual Research Report
  • [Presentation] Solution structural analysis of GGA and the complexes with its binding partners using solution X-ray scattering.2007

    • Author(s)
      H. Kamikubo, K. Hirako, H. Sawada, M. Kawasaki, R. Kato, K. Nakayama, S. Wakatsuki, M. Kataoka
    • Organizer
      9th International Conference on Biology and Synchrotron Radiation
    • Place of Presentation
      England
    • Related Report
      2007 Annual Research Report
  • [Presentation] Determination Of Hydrogen Positions Of Photoactive Yellow Protein.2007

    • Author(s)
      Yamaguchi S., Kamikubo H., Kurihara K., Shimizu N., Yamazaki Y., Ohnishi Y., Kuroki R., Niimura N., Kataoka M.
    • Organizer
      th International Conference on Biology and Synchrotron Radiation
    • Place of Presentation
      England
    • Related Report
      2007 Annual Research Report
  • [Presentation] Determination of hydrogen positions of photoactive yellow protein2007

    • Author(s)
      Yamaguchi S., Kamikubo H., Kurihara K., Shimizu N., Yamazaki Y., Ohnishi Y., Kuroki R., Niimura N., Kataoka M.
    • Organizer
      2nd International Symposium on Diffraction Structural Biology
    • Place of Presentation
      Tokyo(Japan)
    • Related Report
      2007 Annual Research Report
  • [Presentation] 研究室系X線溶液散乱装置の立ち上げ2007

    • Author(s)
      上久保裕生, 山崎洋一, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] C末端欠損スタフィロコッカルヌクレアーゼが示す誘導折り畳み反応の分子メカニズム2007

    • Author(s)
      鬼塚正義, 上久保裕生, 山崎洋一, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] アラニン挿入変異が折れ畳み過程に及ぼす影響2007

    • Author(s)
      澤田宏起, 上久保裕生, 鬼塚正義, 山崎洋一, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] ジヒドロ葉酸還元酵素におけるフォールディングエレメントや活性部位の接続部位に含まれる情報の抽出2007

    • Author(s)
      政さやか, 上久保裕生, 梅山美香, 山崎洋一, 巌倉正寛, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] 網羅的アラニン挿入変異法によるジヒドロ葉酸還元酵素の構造形成および機能発現領域の抽出2007

    • Author(s)
      芝るみ, 上久保裕生, 梅山美香, 山崎洋一, 巌倉正寛, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] 紅色光合成細菌Rhosospirillum centenum由来PYP様ドメインの光反応サイクルの特性2007

    • Author(s)
      小山知則, 上久保裕生, 山崎洋一, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] Photoactive Yellow Proteinを用いた中性子結晶構造解析2007

    • Author(s)
      山口繁生, 上久保裕生, 栗原和男, 山崎洋一, 大西裕季, 黒木良太, 新村信雄, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] Rhodobacter capsulatus PYPの分光学的特性の解析2007

    • Author(s)
      山崎洋一, 上久保裕生, 今元泰, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] Rhodobacter capsulatus由来PYPの光反応におけるpH依存性2007

    • Author(s)
      浴口真幸, 山崎洋一, 上久保裕生, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] Ala/ValスキャニングによるPhotoactive Yellow Proteinの構造・機能に対する重要なアミノ酸残基のマッピング2007

    • Author(s)
      永田大介, 山崎洋一, 上久保裕生, 今元泰, 片岡幹雄
    • Organizer
      第45回生物物理学会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] 光合成細菌Rhodobacter capsulatus由来PYPの分光学的特性2007

    • Author(s)
      山崎洋一, 上久保裕生, 今元泰, 片岡幹雄
    • Organizer
      第14回日本光生物学協会年会
    • Place of Presentation
      生駒
    • Related Report
      2007 Annual Research Report

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

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