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Development of experimental techniques for the investigation of transient molecular protein complexes

Planned Research

Project AreaIntegrative understanding of biological processes mediated by transient macromolecular complexes; New technology for visualizing physiologically metastable states.
Project/Area Number 21121003
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionKyushu University

Principal Investigator

KOHDA Daisuke  九州大学, 生体防御医学研究所, 教授 (80186618)

Co-Investigator(Renkei-kenkyūsha) SHIMADA Atsushi  九州大学, 生体防御医学研究所, 准教授 (70391977)
MAYANAGI Kouta  九州大学, 生体防御医学研究所, 助教 (50418571)
SAITOH Takashi  九州大学, 生体防御医学研究所, 助教 (00432914)
IGURA Mayumi  九州大学, 生体防御医学研究所, 学術研究院 (60529965)
Project Period (FY) 2009-07-23 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥153,010,000 (Direct Cost: ¥117,700,000、Indirect Cost: ¥35,310,000)
Fiscal Year 2013: ¥25,350,000 (Direct Cost: ¥19,500,000、Indirect Cost: ¥5,850,000)
Fiscal Year 2012: ¥25,350,000 (Direct Cost: ¥19,500,000、Indirect Cost: ¥5,850,000)
Fiscal Year 2011: ¥20,280,000 (Direct Cost: ¥15,600,000、Indirect Cost: ¥4,680,000)
Fiscal Year 2010: ¥70,980,000 (Direct Cost: ¥54,600,000、Indirect Cost: ¥16,380,000)
Fiscal Year 2009: ¥11,050,000 (Direct Cost: ¥8,500,000、Indirect Cost: ¥2,550,000)
Keywordsタンパク質 / 分子認識 / プレ配列 / Tom20 / オリゴ糖転移酵素 / X線結晶解析 / NMR解析 / 複合体 / 細胞内輸送 / ミトコンドリア / 結晶コンタクト効果 / 融合タンパク質 / 複合体安定化技術 / ジスルフィド結合
Research Abstract

Equilibrium shifting from the unbound states to the bound states is useful to obtain structural and dynamic information of transient protein complexes at atomic resolutions, in particular, the complexes with large amplitude motions inside. We developed two techniques, molecular tethering (via inter-molecular disulfide bonds) and molecular stiffening (via intra-molecular disulfide bonds), for this purpose. We also proposed intentional creation of space in protein crystal lattice, and place a target region in the space created. The key technique is the rigid connection to fix the relative orientation of the protein of interest and a tag protein. These new techniques were applied to analyze the dynamics of a mitochondrial presequence peptide as bound to the mitochondrial receptor Tom20, and the stabilization of oligosaccharyltransferase-peptide complexes for crystallization.

Report

(6 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (58 results)

All 2014 2013 2012 2011 2010 2009 Other

All Journal Article (21 results) (of which Peer Reviewed: 8 results) Presentation (30 results) (of which Invited: 1 results) Book (1 results) Remarks (6 results)

  • [Journal Article] Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus2014

    • Author(s)
      Fujinami, D., Matsumoto, M., Noguchi, T., Sonomoto, K., Kohda, D.
    • Journal Title

      Carbohydr Res

      Volume: 387C Pages: 30-36

    • Related Report
      2013 Final Research Report
  • [Journal Article] Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus.2014

    • Author(s)
      Fujinami D, Matsumoto M, Noguchi T, Sonomoto K, Kohda D
    • Journal Title

      Carbohydr Res

      Volume: 387C Pages: 30-36

    • DOI

      10.1016/j.carres.2014.01.021

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Energetics of the presequence-binding poses in mitochondrial protein import through Tom202013

    • Author(s)
      Komuro, Y., Miyashita, N., Mori, T., Muneyuki, E., Saitoh, T., Kohda, D., Sugita, Y.
    • Journal Title

      J Phys Chem B

      Volume: 117 Pages: 2864-2871

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance2013

    • Author(s)
      Nyirenda, J., Matsumoto, S., Saitoh, T., Maita, N., Noda, N. N., Inagaki, F., Kohda, D.
    • Journal Title

      Structure

      Volume: 21 Pages: 32-41

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases2013

    • Author(s)
      Matsumoto, S., Shimada, A., Kohda, D.
    • Journal Title

      BMC Struct Biol

      Volume: 13 Pages: 11-11

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation2013

    • Author(s)
      Matsumoto, S., Shimada, A., Nyirenda, J., Igura, M., Kawano, Y., Kohda, D.
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 110 Pages: 17868-17873

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases.2013

    • Author(s)
      Matsumoto S, Shimada A, Kohda D
    • Journal Title

      BMC Struct Biol

      Volume: 13 Issue: 1

    • DOI

      10.1186/1472-6807-13-11

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation.2013

    • Author(s)
      Matsumoto S, Shimada A, Nyirenda J, Igura M, Kawano Y, Kohda D
    • Journal Title

      Proc Natl Acad Sci USA

      Volume: 110 Issue: 44 Pages: 17868-17873

    • DOI

      10.1073/pnas.1309777110

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance2013

    • Author(s)
      James Nyirenda, et al.
    • Journal Title

      Structure

      Volume: 21 Issue: 1 Pages: 32-41

    • DOI

      10.1016/j.str.2012.10.011

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Energetics of the presequence-binding poses in mitochondrial protein import through Tom20.2013

    • Author(s)
      Komuro Y, Miyashita N, Mori T, Muneyuki E, Saitoh T, Kohda D, Sugita Y.
    • Journal Title

      J Phys Chem B

      Volume: 117 Issue: 10 Pages: 2864-71

    • DOI

      10.1021/jp400113e

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the C-terminal globular domain of oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A resolution2012

    • Author(s)
      Matsumoto, S., Igura, M., Nyirenda, J., Matsumoto, M., Yuzawa, S., Noda, N., Inagaki, F., Kohda, D.
    • Journal Title

      Biochemistry

      Volume: 51 Pages: 4157-4166

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystal structure of the C-terminal globular domain of oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75Å resolution.2012

    • Author(s)
      Matsumoto, S., Igura, M., Nyirenda, J., Matsumoto. M, Yuzawa, S., Noda, N., Inagaki, F., Kohda, D.
    • Journal Title

      Biochemistry

      Volume: 51 Issue: 20 Pages: 4157-4166

    • DOI

      10.1021/bi300076u

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative assessment of the preferences for the amino acid residues flanking archaeal N-linked glycosylation sites2011

    • Author(s)
      Igura, M., Kohda, D.
    • Journal Title

      Glycobiology

      Volume: 21 Pages: 575-583

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
  • [Journal Article] Selective control of oligosaccharide transfer efficiency for the N-glycosylation sequon by a point mutation in oligosaccharyltransferase2011

    • Author(s)
      Igura, M., Kohda, D.
    • Journal Title

      J Biol Chem

      Volume: 286 Pages: 13255-13260

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
  • [Journal Article] Crystallographic snapshots of Tom20-mitochondrial presequence interactions with disulfide-stabilized peptides2011

    • Author(s)
      Saitoh, T., Igura, M., Miyazaki, Y., Ose, T., Maita, N., Kohda, D.
    • Journal Title

      Biochemistry

      Volume: 50 Pages: 5487-5496

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
  • [Journal Article] 共有結合を用いた平衡シフトによる過渡的タンパク質複合体からの構造情報の取得2011

    • Author(s)
      神田大輔,齊藤貴士
    • Journal Title

      生化学

      Volume: 第83巻第10号 Pages: 902-911

    • NAID

      10029850124

    • Related Report
      2013 Final Research Report
  • [Journal Article] Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases2010

    • Author(s)
      Maita, N., Nyirenda, J., Igura, M., Kamishikiryo, J., Kohda, D.
    • Journal Title

      J Biol Chem

      Volume: 285 Pages: 4941-4950

    • Related Report
      2013 Final Research Report
  • [Journal Article] Crystallographic and functional analyses of J-domain of JAC1 essential for chloroplast photorelocation movement in Arabidopsis thaliana2010

    • Author(s)
      Takano, A., Suetsugu, N., Wada, M., Kohda, D.
    • Journal Title

      Plant Cell Physiol

      Volume: 51 Pages: 1372-1376

    • Related Report
      2013 Final Research Report 2010 Annual Research Report
  • [Journal Article] Structure and activity of JAC1 J-domain implicate the involvement of the cochaperone activity with HSC70 in chloroplast photorelocation movement2010

    • Author(s)
      Suetsugu, N., Takano, A., Kohda, D., Wada, M.
    • Journal Title

      Plant Signal Behav

      Volume: 5 Pages: 1602-1606

    • Related Report
      2013 Final Research Report
  • [Journal Article] Stalled replication forks : making ends meet for recognition and stabilization.2010

    • Author(s)
      Masai H, Tanaka T, Kohda D.
    • Journal Title

      Bioessays

      Volume: 32 Pages: 687-697

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative Structural Biology of Eubacterial and Archaeal Oligosaccharyltransferases2010

    • Author(s)
      N.Maita, J.Nyirenda, M.Igura, J.Kamishikiryo, D.Kohda
    • Journal Title

      Journal of Biological Chemistry 285

      Pages: 4941-4950

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] Intentional creation of crystal-contact free space for analyzing large amplitude motions in protein crystals2014

    • Organizer
      International Symposium between Kyushu U. Post Global COE and School of Biomedical Sciences, Monash U
    • Place of Presentation
      Melbourne, Australia
    • Year and Date
      2014-02-07
    • Related Report
      2013 Final Research Report
  • [Presentation] Intentional creation of crystal-contact free space for monitoring large amplitude motions of ligands in protein crystals(workshop, "transient macromolecular complexes involved in multilevel biological phenomena")2013

    • Organizer
      第51回日本生物物理学会
    • Place of Presentation
      京都
    • Year and Date
      2013-10-29
    • Related Report
      2013 Final Research Report
  • [Presentation] Intentional crystal-contact free space to observe the large mobility of ligands in X-ray crystallography2013

    • Author(s)
      Rei Matsuoka
    • Organizer
      Post-GCOE Symposium Retreat in Singapore with NUS and TLL
    • Place of Presentation
      シンガポール
    • Year and Date
      2013-03-05
    • Related Report
      2012 Annual Research Report
  • [Presentation] 蛋白質結晶中に創り出した隙間を利用して分子の動きを観るための新しいX線結晶解析2012

    • Author(s)
      松岡礼
    • Organizer
      第85回日本生化学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-15
    • Related Report
      2012 Annual Research Report
  • [Presentation] Intentional creation of crystal-contact free space for monitoring large amplitude motions of proteins and ligands in protein crystals2012

    • Organizer
      第85回日本生化学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-14
    • Related Report
      2013 Final Research Report
  • [Presentation] Intentional creation of crystal-contact free space for monitoring large amplitude motions of proteins and ligands in protein crystals2012

    • Author(s)
      Daisuke Kohda
    • Organizer
      第85回日本生化学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-14
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 蛋白質結晶中に創り出した隙間を利用して分子の動きを観るための新しいX線結晶解析2012

    • Author(s)
      松岡 礼
    • Organizer
      平成24年度日本結晶学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2012-10-25
    • Related Report
      2012 Annual Research Report
  • [Presentation] Tom20に結合したプレ配列ペプチドのクリスタルコンタクトフリーな結晶構造解析2012

    • Author(s)
      松岡礼
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      2012-06-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] 蛋白質結晶中に創り出した隙間を利用して分子の動きを観るための新しいX線結晶解析2012

    • Organizer
      大阪大学蛋白質研究所セミナー
    • Place of Presentation
      大阪
    • Related Report
      2013 Final Research Report 2012 Annual Research Report
  • [Presentation] Crystallographic and NMR evidence for flexibility in the C-terminal globular domain of oligosaccharyltransferases and its catalytic significance2011

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 10th Global COE International Symposium on Biochemistry and Cell Biology
    • Place of Presentation
      シンガポール,singapore
    • Year and Date
      2011-12-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] NMRと結晶構造解析を駆使して明らかにするタンパク質の新しい分子認識機構2011

    • Organizer
      蛋白質立体構造解析 NEDO特別講座
    • Place of Presentation
      東京
    • Year and Date
      2011-10-20
    • Related Report
      2013 Final Research Report
  • [Presentation] 共有結合を用いた平衡シフトによる過渡的タンパク質複合体の安定化とその応用2011

    • Organizer
      大阪大学蛋白質研究所セミナー「先端的 NMR拠点から生まれる新たな潮流:最新成果,役割,利用」
    • Place of Presentation
      大阪
    • Year and Date
      2011-07-28
    • Related Report
      2013 Final Research Report
  • [Presentation] 共有結合を用いた平衡シフトによる過渡的タンパク質複合体の安定化とその応用2011

    • Author(s)
      神田大輔
    • Organizer
      大阪大学蛋白質研究所セミナー
    • Place of Presentation
      大阪(招待講演)
    • Year and Date
      2011-07-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] Stabilization and Structure Analysis of Mitochondrial Tom20-Presequence Complexes2011

    • Author(s)
      T Saitoh, K Izumi, Y Miyazaki, D Kohda
    • Organizer
      The 7th Global COE International Symposium, the 6th Young Investigators Forum
    • Place of Presentation
      Bintan Island, Indonesia
    • Year and Date
      2011-02-11
    • Related Report
      2010 Annual Research Report
  • [Presentation] A combined NMR and crystallography approach for analyzing the promiscuous recognition of peptidic ligands by proteins2011

    • Organizer
      The 4th APNMR Symposium
    • Place of Presentation
      Beijing, China
    • Related Report
      2013 Final Research Report
  • [Presentation] Comparative structural biology of archaeal and eubacterial oligosaccharyl transferases2011

    • Author(s)
      Daisuke Kohda
    • Organizer
      IX European Symposium of The Protein Society
    • Place of Presentation
      ストックホルム,Sweden(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] A combined NMR and crystallography approach for analyzing the promiscuous recognition of peptidic ligands by proteins2011

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 4th APNMR Symposium
    • Place of Presentation
      北京,China(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Comparative Structural Biology of Oligosaccharyltransferases2011

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 71st Okazaki Conference
    • Place of Presentation
      岡崎(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Comparative Structural Biology of Oligosaccharyltransferases2011

    • Author(s)
      Daisuke Kohda
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] 準安定な分子複合体から構造情報を得るための戦略とその応用2010

    • Organizer
      蛋白研セミナー:「蛋白質の機能-構造相関解明のための精密構造解析とその方法~水素原子から細胞まで~」
    • Place of Presentation
      大阪
    • Year and Date
      2010-10-07
    • Related Report
      2013 Final Research Report
  • [Presentation] 準安定な分子複合体から構造情報を得るための新戦略2010

    • Author(s)
      神田大輔
    • Organizer
      第10回日本蛋白質科学会年会ワークショップ
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states - Complex stabilization with molecular tethering and stiffening2010

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 5th Global COE International Symposium Cell Cycle and Differentiation
    • Place of Presentation
      Singapore
    • Year and Date
      2010-02-24
    • Related Report
      2009 Annual Research Report
  • [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states - Complex stabilization with molecular tethering and stiffening2009

    • Author(s)
      Daisuke Kohda
    • Organizer
      the 3rd Asia-Pacific NMR Symposium
    • Place of Presentation
      Jeju Island, Korea
    • Year and Date
      2009-10-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states - Complex stabilization with molecular tethering and stiffening -2009

    • Organizer
      The 3rd Asia-Pacific NMR Symposium
    • Place of Presentation
      Jeju Island, Korea
    • Related Report
      2013 Final Research Report
  • [Presentation] 蛋白質結晶中に創り出した隙間を利用して分子の動きを観るための新しいX線結晶解析

    • Author(s)
      松岡礼,神田大輔
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      鳥取
    • Related Report
      2013 Annual Research Report
  • [Presentation] Intentional creation of crystal-contact free space for monitoring large amplitude motions of ligands in protein crystals

    • Author(s)
      Daisuke Kohda
    • Organizer
      第51回日本生物物理学会
    • Place of Presentation
      第51回日本生物物理学会
    • Related Report
      2013 Annual Research Report
  • [Presentation] Intentional crystal-contact-free space to observe the large amplitude motions of ligands by X-ray crystallography

    • Author(s)
      Rei Matsuoka, Daisuke Kohda
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      兵庫
    • Related Report
      2013 Annual Research Report
  • [Presentation] 蛋白質結晶中に創り出した隙間を利用して分子の動きを観るための新しいX線結晶解析

    • Author(s)
      松岡礼,神田大輔
    • Organizer
      SPring-8萌芽的研究課題ワークショップ
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
  • [Presentation] Intentional creation of crystal-contact free space for analyzing large amplitude motions in protein crystals

    • Author(s)
      Daisuke Kohda
    • Organizer
      International Symposium between Kyushu U. Post Global COE and School of Biomedical Sciences, Monash U.
    • Place of Presentation
      Melbourne, Australia
    • Related Report
      2013 Annual Research Report
  • [Presentation] Intentional crystal-contact-free space to observe the large amplitude motions of ligands by X-ray crystallography

    • Author(s)
      Rei Matsuoka, Daisuke Kohda
    • Organizer
      International Symposium between Kyushu U. Post Global COE and School of Biomedical Sciences, Monash U.
    • Place of Presentation
      Melbourne, Australia
    • Related Report
      2013 Annual Research Report
  • [Book] いきなりはじめる構造生物学2011

    • Author(s)
      神田大輔
    • Total Pages
      260
    • Publisher
      秀潤社
    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.bioreg.kyushu-u.ac.jp/vsb/index.html

    • Related Report
      2013 Final Research Report
  • [Remarks] MIB VSB Top page

    • URL

      http://www.bioreg.kyushu-u.ac.jp/vsb/index.html

    • Related Report
      2013 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所構造生物学分野HP

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/index.html

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/index.html

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/index.html

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/index.html

    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2018-03-28  

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