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蛋白質分子認識過程における水和構造のダイナミクス

Research Project

Project/Area Number 15076210
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionKeio University

Principal Investigator

中迫 雅由  Keio University, 理工学部, 教授 (30227764)

Co-Investigator(Kenkyū-buntansha) 岡 俊彦  慶應義塾大学, 理工学部, 助手 (60344389)
Project Period (FY) 2003 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥77,200,000 (Direct Cost: ¥77,200,000)
Fiscal Year 2007: ¥11,500,000 (Direct Cost: ¥11,500,000)
Fiscal Year 2006: ¥11,500,000 (Direct Cost: ¥11,500,000)
Fiscal Year 2005: ¥11,500,000 (Direct Cost: ¥11,500,000)
Fiscal Year 2004: ¥26,600,000 (Direct Cost: ¥26,600,000)
Fiscal Year 2003: ¥16,100,000 (Direct Cost: ¥16,100,000)
Keywords生物物理 / ナノマシン / 表面・界面物性 / 放射線・X線・粒子線 / 生体分子 / 蛋白質構造 / 蛋白質水和 / 低温結晶構造解析 / 光受容蛋白質 / X線散乱・回折 / 蛋白質立体構造 / 蛋白質水和構造 / X線回折・散乱 / 結晶構造 / 時間相関 / 阻害剤
Research Abstract

1.グルタミン酸脱水素酵素のドメイン運動と水和構造変化
高分解能X線結晶構造解析により、グルタミン酸脱水素酵素のドメイン運動のスナップショットの立体構造を水和水も含めて明らかにし、液中GDH六量体の分子動力学(MD)計算を実施した。また、原子間力顕微鏡(AFM)によるGDH結晶の表面構造観察して、ドメイン運動の頻度を見積もった。
2.蛋白質のX線結晶構造解析と水和構造解析
ブラストサイジンSデアミナーゼの結晶構造をその反応機構を追跡可能な、様々な反応中間状態で明らかにした。SPring-8のマイクロビームを用いて青色光受容蛋白質Phototoropin1,2 L0V1 ドメインの結晶構造解析を行った。いずれのドメインも結晶学的非対称単位中で二量体を形成しており、その安定化に水分子が大きく寄与していた。アリールマロン酸脱炭酸酵素(AMDase)の立体構造を実験室での重原子多重同型置換解析によって結晶構造を決定した。結晶学的非対称単位中に4分子が含まれ、それぞれが微妙にドメイン運動によって構造変化するとともに、活性ポケットの入り口にあるループがヘリックス-コイル変化をし、水和水や基質の出入りを妨げる可能性が示唆された。
3.データベースを用いた蛋白質水和の研究
水和構造予測プログラムの開発を行った。PDBに登録されている高分解能X線結晶構造解析による立体構造モデル座標から、親水性アミノ酸残基、極性原子周囲の水和構造を抽出し、各原子団周囲での経験的な分布確率密度を得た。これを利用して、任意の水溶性蛋白質の水和構造を予測するプログラムコードを開発した。また、抗体FVフラグメント高次構造決定因子を統計的に解析するためのプログラムコードを開発し、決定因子が重鎖の相補性決定領域3内の特定の領域にあることを見出すことができた。
4.サブゼロ温度領域X線回折実験用結晶冷却装置の開発前年度からの開発を継続して行い、より冷却効率の高い熱交換器を搭載した。シタロン脱水酵素の置換体結晶を用いて、データ収集のための手技を検討中した。

Report

(5 results)
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (52 results)

All 2008 2007 2006 2005 2004 Other

All Journal Article (35 results) (of which Peer Reviewed: 5 results) Presentation (11 results) Book (2 results) Publications (4 results)

  • [Journal Article] タンパク質の水和構造を探る2008

    • Author(s)
      中迫雅由
    • Journal Title

      Molecular Science Journal 2

      Pages: 22-22

    • NAID

      130002126190

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 非弾性散乱の生物への応用について2008

    • Author(s)
      城地保昌、中迫雅由、難波啓一
    • Journal Title

      日本結晶学会誌 50

      Pages: 78-82

    • NAID

      10021085479

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus2008

    • Author(s)
      Masayoshi Nakasako, Rika Obata, Ryosuke Okubo, Shyuichi Nakayama, Kenji Miyamoto and Hiromichi Ohta
    • Journal Title

      Acta Crystallographica Section F

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of LOVI-dimerization of phototropin 1and 2 from Arabidopsis2008

    • Author(s)
      Masayoshi Nakasako, Kazunori zikihara, Daisuke Matsuoka, Hitomi Katsura and Satoru Tokutomi
    • Journal Title

      Journal of Molecular Biology

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structures of Blasticidin S Deaminase (BSD):Implications for Dynamic Properties of Catalytic Zinc2007

    • Author(s)
      Takashi Kumasaka, Masaki Yamamoto, Makio Furuichi, Masayoshi Nakasako, Aik-Hong The, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki
    • Journal Title

      Journal of Biological Chemistry 228

      Pages: 37103-37111

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovery of MBI-D resistant buster compounds - inquiry of effective compound among derivatives of MBI-D products.2006

    • Author(s)
      Y.Kurahashi, S.Kagabu, N.Yamada, Y.Mitsugi, M.Shimizu, M.Nakasako, I.Yamaguchi
    • Journal Title

      J. Pesticide. Sci 31

      Pages: 85-94

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A fluorescent antibiotic resistance marker for rapid production of transgenic rice plants.2006

    • Author(s)
      T.Ochiai-Fukuda, N.Takahashi-Ando, S.Ohsato, T.Igawa, K.Kadokura, H.Hamamoto, M.Nasako, T.Kudo, T.Shibata, I.Yamaguchi, M.Kimura
    • Journal Title

      J. Biotech 122

      Pages: 521-527

    • Related Report
      2006 Annual Research Report
  • [Journal Article] High-resolution powder diffraction study of purple membrane with a large Guinier-type camera.2006

    • Author(s)
      T.Oka, K.Miura, K.Inoue, T.Ueki, N.Yagi
    • Journal Title

      J. Synch. Rad. 13

      Pages: 281-284

    • Related Report
      2006 Annual Research Report
  • [Journal Article] タンパク質の水和水と機能2006

    • Author(s)
      肥後順一, 中迫雅由
    • Journal Title

      生物物理 46

      Pages: 220-223

    • NAID

      110004751712

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A fluorescent antibiotic resistance marker for rapid production of transgenic rice plants.2006

    • Author(s)
      Ochiai-Fukuda, T. et al.
    • Journal Title

      J.Biotech. in press(印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Hydrogen-bond patterns in the hydration structure of a protein.2005

    • Author(s)
      Yokomizo, T.Nakasako, M., Yamazaki, T., Shindo, H.Higo, J.
    • Journal Title

      Chem.Phys.Lett. 401

      Pages: 332-336

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Light-induced global structural changes of phytochrome A regulating photomorphogenesis in plants.2005

    • Author(s)
      Nakasako, M., Iwata, T., Inoue K., Tokutomi S.
    • Journal Title

      FEBS J. 272

      Pages: 603-612

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base : Microsecond time-resolved X-ray diffraction study of purple membrane.2005

    • Author(s)
      Oka, T., Inoue, K., Kataoka, M., Yagi, N.
    • Journal Title

      Biophys.J. 88

      Pages: 436-442

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein.2005

    • Author(s)
      Nakasako M., Matsuoka, D., Zikihara.K., Tokutomi, S.
    • Journal Title

      FEBS Lett. 579

      Pages: 1067-1071

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Patterns and networks of hydrogen-bonds in the hydration structure of human lysozyme.2005

    • Author(s)
      Yokomizo, T., Higo, J., Nakasako, M.
    • Journal Title

      Chem.Phys.Lett. 410

      Pages: 31-35

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Conformational dynamics of complementarity determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten.2005

    • Author(s)
      Nakasako, M., Oka, T., Masumo, M., Takahashi, H., Shimada, I.et al.
    • Journal Title

      J.Mol.Biol. 351

      Pages: 627-640

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structural analysis of cell membrane complex of a hair fibre by micro-beam X-ray diffraction.2005

    • Author(s)
      Ohta, N., Oka, T.Inoue, K., Yagi, N., Kato, S., Hatta, I.
    • Journal Title

      J.Appl.Cryst. 38

      Pages: 274-279

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Discovery of MBI-D resistant buster compounds-inquiry of effective compound among derivatives of MBI-D products.2005

    • Author(s)
      Kurahashi, Y., Kagabu, S., Yamada, N., Mitsugi, Y., Shimizu, M., Nakasako, M., Yamaguchi, I.
    • Journal Title

      J.Pesticide.Sci. 88

      Pages: 436-442

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Tertiary and quaternary structures of phytochrome A.2005

    • Author(s)
      Nakasako M., Tokutomi, S.
    • Journal Title

      Light Sensing in Plants(Eds. Wada, M., Shimazaki, K., Iino, M.) Springer Verlag 第一版

      Pages: 43-49

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Water-protein interactions studied by cryogenic X-ray crystallography.2005

    • Author(s)
      Nakasako, M.
    • Journal Title

      Hydrogen and Hydration in Proteins and Nucleic Acids(Eds.Niimura, N., Mizuno, H., Helliwell, J., Westhof, E.)(KubaPro) 第一版

      Pages: 135-139

    • Related Report
      2005 Annual Research Report
  • [Journal Article] LOV photoreceptors in Plants ; Molecular structure, photoreaction and signal transduction.2005

    • Author(s)
      Matsuoka, D., Nakasako, M., Zikihara, K., Tokutomi, S.
    • Journal Title

      Proceedings of the 15th International Symposium on Flavins and Flavoproteins in press

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 結晶を冷却する2005

    • Author(s)
      中迫雅由
    • Journal Title

      タンパク質の結晶化(京都大学出版会) 第一版

      Pages: 267-281

    • Related Report
      2005 Annual Research Report
  • [Journal Article] タンパク質の水和構造2005

    • Author(s)
      中迫雅由, 肥後順一
    • Journal Title

      現代化学 No.413

      Pages: 48-54

    • Related Report
      2005 Annual Research Report
  • [Journal Article] X線結晶解析2005

    • Author(s)
      中迫雅由
    • Journal Title

      タンパク質科学 -構造・物性・機能(後藤, 桑島, 谷澤編)(化学同人) 第一版

      Pages: 33-43

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Hydrogen-bond patterns in the hydration structure of a protein.2005

    • Author(s)
      Yokomizo, T., Nakasako, M., Yamazaki, T., Shindo, H., Higo, J.
    • Journal Title

      Chemical Physics Letters 401

      Pages: 332-336

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base : Microsecond time-resolved X-ray diffraction study of purple membrane.2005

    • Author(s)
      Oka, T., Inoue, K., Kataoka, M., Yagi, N.
    • Journal Title

      Biophysical Journal 88

      Pages: 436-442

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Light-induced global structural changes of phytochrome A regulating photomorphogenesis in plants.2005

    • Author(s)
      Nakasako, M., Iwata, T., Inoue, K., Tokutomi, S.
    • Journal Title

      The FEBS Journal 272

      Pages: 603-612

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Quaternary structure of LOV-domain containing polypeptides of Arabidopsis FKF1 protein.2005

    • Author(s)
      Nakasako, M., Matsuoka, D., Zikihara, K., Tokutomi, S.
    • Journal Title

      FEBS Letters 579

      Pages: 1067-1071

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Enzymatic characterization of scytalone dehydratase Val75Met variant found in melanin biosynthesis inhibitor (MBI) resistant strains of the rice blast fungus.2004

    • Author(s)
      Yamada, N., Motoyama, T., Nakasako, M., Kagabu, S., Kudo, S., Yamaguchi, I.
    • Journal Title

      Bioscience Biotechnology and Biochemistry 68

      Pages: 615-621

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Water-protein interactions from high-resolution protein crystallography.2004

    • Author(s)
      Nakasako, M.
    • Journal Title

      Philosophical Transaction B Royal Society London 359

      Pages: 1191-1206

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Light-induced structural changes of LOV-domain containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering.2004

    • Author(s)
      Nakasako, M., Iwata, T., Matsuoka, D., Tokutomi, S.
    • Journal Title

      Biochemistry 43

      Pages: 14881-14890

    • Related Report
      2004 Annual Research Report
  • [Journal Article] X-ray imaging microscopy using Fresnel zone plate objective and quasi-monochromatic undulator radiation.2004

    • Author(s)
      Suzuki, Y., Takeuchi, A., Takano, H., Uesugi, K., Oka, T., Inoue, K.
    • Journal Title

      Review of Scientific Instruments 75

      Pages: 1155-1157

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Picometer-scale dynamical observations of individual membrane proteins : the case of bacteriorhodopsin.2004

    • Author(s)
      Okumura, Y., Oka, T., Kataoka, M., Taniguchi, Y., Sasaki, Y.C.
    • Journal Title

      Physical Review E 70

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Microsecond Time-resolved Diffraction and Scattering Measurements System Using Semi-monochromatic X-ray Pulse at SPring-8 BL40XU.2004

    • Author(s)
      Oka, T., Inoue, K., Yagi, N.
    • Journal Title

      Proceedings of the 8-th International Conference on Synchrotron Radiation Instrumentation

      Pages: 1197-1200

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 30年後の放射光生命科学実験に期待すること-生きた細胞を原子分解能でリアルタイムに観察する2004

    • Author(s)
      中迫雅由
    • Journal Title

      日本放射光学会誌"放射光" 17

      Pages: 268-268

    • NAID

      10013364215

    • Related Report
      2004 Annual Research Report
  • [Presentation] Surface structure of glutamate dehydrogenase crystal observed by atomic forcemicroscopy2008

    • Author(s)
      Sato Tsunero and Nakasako Masayoshi
    • Organizer
      The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules"
    • Place of Presentation
      奈良
    • Year and Date
      2008-01-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Search for determinants regulating the quaternary structures of Fvfiragments of antibodies through a database analysis2008

    • Author(s)
      Masashi Miyawaza and Masayoshi Nakasako
    • Organizer
      The 5-th open workshop "Chemistry of BiologicalProcesses Created by Water and Biomolecules"
    • Place of Presentation
      奈良
    • Year and Date
      2008-01-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal structure of arylmalonate decarboxylase2008

    • Author(s)
      Masayoshi Nakasako, Rika Obata, Kenji Miyamoto and Hiromichi Ohta
    • Organizer
      The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules"
    • Place of Presentation
      奈良
    • Year and Date
      2008-01-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal structures of LOV1 domains of phototropin 1 and 2from Arabidopsis thaliana2008

    • Author(s)
      Masayoshi Nakasako, Daisuke, Matsuoka, Kazunori Zikiharaand Satoru Tokutomi
    • Organizer
      The 5th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules"
    • Place of Presentation
      奈良
    • Year and Date
      2008-01-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Simulation on the X-ray speckle patterns of a hydrated protein moleculewith conformational variations2007

    • Author(s)
      Sakamoto Keita, Hceguchi Mitsunori, Nakasako Masayoshi
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Search for determinants regulating the quaternary structures of Fv fragmentsof antibodies through a database analysis2007

    • Author(s)
      Miyazawa Masashi and Nakasako Masayoshi
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Prediction of Hydration Structures around polar protein atoms througha data-base analysis2007

    • Author(s)
      Matsuoka Daisuke and Nakasako Masavoshi
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal structures of LOV1 domains in Arabidopsis phototropin 1 and 22007

    • Author(s)
      Masayoshi Nakasako, Daisuke, Matsuoka, Kazimori Zikihara, Hitomi Katsura and Satoru Tokutomi
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Observation of the surface of glutamate dehydrogenase crystals by atomicforce microscopy2007

    • Author(s)
      Sato Tsunero and Nakasako Masayoshi
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] X線溶液散乱で何が分かるのか?なぜ放射光なのか?2007

    • Author(s)
      中迫 雅由
    • Organizer
      第2回X線溶液散乱研究会-SPring-8における放射光X線溶液散乱-
    • Place of Presentation
      理化学研究所 播磨研究所
    • Year and Date
      2007-10-11
    • Related Report
      2007 Annual Research Report
  • [Presentation] 蛋白質表面に吸着した水分子と蛋白質運動の相関について2007

    • Author(s)
      中迫 雅由
    • Organizer
      日本物理学会第62回年次大会
    • Place of Presentation
      北海道大学
    • Year and Date
      2007-09-23
    • Related Report
      2007 Annual Research Report
  • [Book] タンパク質の結晶化(坂部ら編)第9章 結晶を冷却する2005

    • Author(s)
      中迫雅由
    • Publisher
      京都大学出版会(印刷中)
    • Related Report
      2004 Annual Research Report
  • [Book] "Light Sensing in Plants" Tertiary and Quaternary Structures of Phytochrome A.2005

    • Author(s)
      Nakasako, M., Tokutomi, S.
    • Publisher
      Springer Verlag(印刷中)
    • Related Report
      2004 Annual Research Report
  • [Publications] Yamada, N., Motoyama, T., Nakasako, M., Kagabu, S., Kudo, T., Yamaguchi, I: "Enzymatic characterization of scytalone dehydratase Val75Met variant found in melanin biosynthesis inhibitor (MBI-D) resistant strains of the rice blast fungus."Biosci.Biotech.Biochem. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nakasako, M: "Water-protein interactions from high-resolution protein crystallography."Phil.Mag.Trans.B. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Oka, T., Inoue, K., Yagi, N.: "Microsecond Time-resolved Diffraction and Scattering Measurements System Using Semi-monochromatic X-ray Pulse at SPring-8 BL40XU."Proceedings of the Eighth International Conference on Synchrotron Radiation Instrumentation. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Suzuki, Y., Takeuchi, A., Takano, H., Uesugi, K., Oka, T., Inoue, K: "X-ray imaging microscopy using Fresnel zone plate objective and quasi-monochromatic undulator radiation."Rev.Sci.Instrum.. (in press). (2004)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2018-03-28  

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