水と生体分子が織り成す生命現象の化学に関する研究の総括

• Project/Area Number: 15076101
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities (2007-2008); The University of Tokyo (2003-2006)
• Principal Investigator: 桑島 邦博 National Institutes of Natural Sciences Okazaki Research Facilities, 岡崎統合バイオサイエンスセンター, 教授 (70091444)
• Co-Investigator(Kenkyū-buntansha): 後藤 祐児 大阪大学, 蛋白質研究所, 教授 (40153770) ; 寺嶋 正秀 京都大学, 大学院・理学研究科, 教授 (00188674) ; 片岡 幹雄 奈良先端科学技術大学院大学, 物質創成科学研究科, 教授 (30150254) ; 平田 文男 自然科学研究機構, 分子科学研究所・理論計算分子科学研究領域, 教授 (90218785)
• Project Period (FY): 2003 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥78,000,000 (Direct Cost: ¥78,000,000); Fiscal Year 2008: ¥3,000,000 (Direct Cost: ¥3,000,000); Fiscal Year 2007: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2006: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2005: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2004: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2003: ¥15,000,000 (Direct Cost: ¥15,000,000)
• Keywords: 生物物理 / 化学物理 / 生体分子 / 水 / 自己組織化 / 分子認識 / 分子シミュレーション / アミロイド / 生命現象 / 物理化学 / 水溶液 / 蛋白質 / ダイナミクス / 機能

Research Abstract

特定領域研究「水と生体分子が織り成す生命現象の化学」(領域代表:桑島邦博)は、「分子レベルの生命現象を第一原理より化学と物理学の立場から解き明かす」ことを目的として平成15年度から19年度までの5年間実施された。本研究では、この特定領域研究の成果とりまとめを行うことを目的とした。
以下の研究が実施された。
(1)成果とりまとめのための書籍出版特定領域研究の研究成果を書籍(題名:Water and Biomolecules-The Physical Chemistry of Life Phenomena)にまとめた。本研究の研究代表者(桑島)と研究分担者・連携研究者(後藤、平田、寺嶋、片岡)が編集者となり、特定領域研究の計画班班員と5回開催された特定領域研究公開国際シンポジウムの招待講演者の中から執筆者15名を選び、「水と生体分子」を中心テーマとしたモノグラフ・スタイルの英文書籍をSpringer社から出版した。
(2)公開ワークショップの開催上記の書籍執筆者の中から代表的な6名を選び、平成21年3月16日に愛知県岡崎市・岡崎コンファレンスセンターにて"Chemistry of Biological Processes Created by Water and Biomolecules"と題する公開ワークショップを開催した。新学術領域研究「揺らぎと生体機能」との合同シンポジウムとして行った。
研究体制は、研究代表者の桑島と特定領域研究総括班メンバーであった後藤、平田、寺嶋、片岡の4名が研究分担者または連携研究者として加わった。分子科学研究所の平田は、研究分担者と同等の責務を負うが、研究代表者の桑島と実質上同じ研究機関に属するので、研究費の配分は行わず、連携研究者として研究に参画した。

Research Products

• [Journal Article] A comprehensive model for packing and hydration for amyloid fibrils of β2-microglobulin. (2009)
  • Author(s): Y.-H.Lee
  • Journal Title: J.Biol.Chem. 284(4) Pages: 2169-2175
  • Peer Reviewed
• [Journal Article] Hydration affects both harmonic and anharmonic nature of protein dynamics (2008)
  • Author(s): Hiroshi Nakagawa
  • Journal Title: Biophysical Journal 95 Pages: 2916-2923
  • Peer Reviewed
• [Journal Article] Signal transmission through the HtrII transducer alters the interaction of two α-helices in the HAMP domain (2008)
  • Author(s): K.Inoue
  • Journal Title: J.Mol.Biol. 376 Pages: 963-970
  • Peer Reviewed
• [Journal Article] Equilibrium and Kinetics of the Folding and Unfolding of Canine Milk Lysozyme (2007)
  • Author(s): NAKATANI, Hiroyasu
  • Journal Title: Biochemistry 46 Pages: 5238-5251
  • Peer Reviewed
• [Journal Article] Unfolding Pathways of Goat a-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories (2007)
  • Author(s): OROGUCHI, Tomotaka
  • Journal Title: J.Mol.Biol. 371 Pages: 1354-1364
  • Peer Reviewed
• [Journal Article] Heat-triggered conversion of protofibrils into mature amyloid fibrils of β2-microglobulin (2007)
  • Author(s): SASAHARA, Kenji
  • Journal Title: Biochemistry 46 Pages: 3286-3293
  • Peer Reviewed
• [Journal Article] Statistical-Mechanical Theory of Ultrasonic Absorption in Molecular Liquids (2007)
  • Author(s): A. E. Kobryn and F. Hirata
  • Journal Title: J.Chem.Phys. 126(4) Pages: 44504-44504
  • Peer Reviewed
• [Journal Article] Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering (2007)
  • Author(s): Hironari Kamikubo
  • Journal Title: Biophysical Journal 92 Pages: 3633-3642
  • Peer Reviewed
• [Journal Article] A line-scanning multiphoton fluorescelnce spectromicroscope applied to the study of the thylakoid membrane in cyanobacteria and chloroplasts (2007)
  • Author(s): KUMAZAKI, Shigeichi
  • Journal Title: Photosynthesis research 91 Pages: 211-211
  • Peer Reviewed
• [Journal Article] Surprisingly high correlation between early and late stages in non-two-state protein folding (2006)
  • Author(s): Kamagata, K.
  • Journal Title: J. Mol. Biol. 357 Pages: 1647-1654
• [Journal Article] The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein (2006)
  • Author(s): Enoki, S.
  • Journal Title: J. Mol. Biol. 361 Pages: 969-982
• [Journal Article] Mechanism by which the amyloid-like fibrils of a ・2-microglobulin fragment are induced by fluorine-substituted alchols (2006)
  • Author(s): Yamaguchi, K.
  • Journal Title: J. Mol. Biol. 363 Pages: 279-288
• [Journal Article] Selective ion-binding by protein probed with the 3D-RISM theory (2006)
  • Author(s): Yoshida, N.
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 12042-12043
• [Journal Article] A single CH/・ weak hydrogen bond governs stability and photocycle of photoactive yellow protein (2006)
  • Author(s): Imamoto, Y.
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 10646-10647
• [Journal Article] Time-resolved thermodynamics : Heat capacity change of transient species during photo-reaction of PYP (2006)
  • Author(s): Khan, J. S.
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 1002-1008
• [Journal Article] Characterization of kinetic folding intermediates of recombinant canine milk lysozyme by stopped-flow circular dichroism. (2005)
  • Author(s): Nakao, M.
  • Journal Title: Biochemistry 44 Pages: 6685-6692
• [Journal Article] Atomically detailed description of the unfolding of α-lactalbumin by the combined use of experiments and simulations. (2005)
  • Author(s): Oroguchi, T.
  • Journal Title: J.Mol.Biol. 354 Pages: 164-172
• [Journal Article] Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease. (2005)
  • Author(s): Hirano, S.
  • Journal Title: Proteins : Struct.Funct.Bioinformat. 58 Pages: 271-277
• [Journal Article] Seeding-dependent maturation of β2-microglobulin amyloid fibrils at neutral pH. (2005)
  • Author(s): Kihara, M.
  • Journal Title: J.Mol.Biol. 280 Pages: 12012-12018
• [Journal Article] Conformational dynamics of Phototropin 2 LOV2 domain with the linker upon photoexciation. (2005)
  • Author(s): Eitoku, T.
  • Journal Title: J.Am.Chem.Soc. 127 Pages: 13238-13244
• [Journal Article] Water Molecules in a Protein Cavity Detected by a Statistical-Mechanical Theory. (2005)
  • Author(s): Imai, T.
  • Journal Title: J.Am.Chem.Soc 127 Pages: 15334-15335
• [Journal Article] 水と生体分子の物理化学の新展開([新連載]水と生体分子が織りなす生命現象(1)) (2005)
  • Author(s): 桑島 邦博
  • Journal Title: 現代化学 No.42 Pages: 49-54
• [Journal Article] Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins (2004)
  • Author(s): K.Kamagata
  • Journal Title: J.Mol.Biol. 339 Pages: 951-965
• [Journal Article] Direct observation of Ab amyloid fibril growth and inhibition (2004)
  • Author(s): Tadato Ban
  • Journal Title: J.Mol.Biol. 344 Pages: 757-767
• [Journal Article] Solvation Thermodynamics of Protein Studied by the 3D-RISM Theory (2004)
  • Author(s): T.IAMI
  • Journal Title: Chem.Phys.Lett. 395 Pages: 1-6
• [Journal Article] Protein Dynamical Heterogeneity Derived from Neutron Incoherent Elastic Scattering (2004)
  • Author(s): H.Nakagawa
  • Journal Title: J.Phys.Soc.Jpn. 73 Pages: 491-495
• [Journal Article] The escape process of carbon monoxide from myoglobin to solution at physiological temperature (2004)
  • Author(s): Y.Nishihara
  • Journal Title: J.Am.Chem.Soc. 11877-11888 Pages: 11877-11888
• [Presentation] Structure of the photointermediate of PYP and the propagation mechanism of structural change (2008)
  • Author(s): 片岡 幹雄
  • Organizer: Cordon Research Conference on Photosensory Receptors & Signal Transduction
  • Place of Presentation: ヴェンチュラ(アメリカ合衆国カリフォルニア州)
  • Year and Date: 2008-01-30
• [Presentation] A statistical mechanics theory of molecular recognition, and it's alication to aquqporin (2008)
  • Author(s): F. Hirata
  • Organizer: The 5th Open Work Shop on "Chemistry of Biological Processes Created by Water and Biomolecules, "
  • Place of Presentation: Nara
• [Presentation] 真性体および組換え体aラクトアルブミンの構造の安定性とダイナミクス (2007)
  • Author(s): 桑島 邦博
  • Organizer: 平成19年度日本酪農科学シンポジウム
  • Place of Presentation: 岐阜県岐阜市
  • Year and Date: 2007-08-24
• [Presentation] Molecular Mechanism of Protein Folding (2007)
  • Author(s): KUWAJIMA, Kunihiro
  • Organizer: 1st International Symposium on Nanomedicine-from Basic to Applications
  • Place of Presentation: Okazaki,Aichi,Japan
• [Presentation] Folding o Canine Milk Lysozyme: A Ca^<2+>-Binding Lysozyme (2007)
  • Author(s): KUWAJIMA, Kunihiro
  • Organizer: The 7th KIAS-Soongsil Conference on Protein Structure and Function
  • Place of Presentation: Seoul.Korea
• [Presentation] Direct observation of amyloid fibril growth and propagation (2007)
  • Author(s): GOTO, Yuji
  • Organizer: Conference on Structure and Dynamics in Soft Matter and Biomolecules: From Single Molecuels to Ensembles
  • Place of Presentation: Trieste,Italy
• [Presentation] Dynamics of Protein-Protein Interaction of Photoresponse Proteins in a Wide Time Range Studied by Laser Induced Teansient Grating Spectroscopy (2007)
  • Author(s): TERAZIMA, Masahide
  • Organizer: 12th European Conference on Spectroscopy of Biological Molecules
  • Place of Presentation: Paris,France
• [Book] Water and Biomolecules-Physical Chemistry of Life Phenomena (2009)
  • Author(s): K.Kuwajima
  • Total Pages: 307
  • Publisher: Springer-Verlag, Berlin & Heidelberg
• [Book] 生物物理ハンドブック (2007)
  • Author(s): 桑島 邦博
  • Total Pages: 662
  • Publisher: 朝倉書店
• [Remarks]
  • URL: http://gagliano.ims.ac.jp/tokutei/index.html
• [Publications] M.Arai: "Effects of the difference in the unfolded-state ensemble on the folding of Escherichia coli dihydrofolate reductase."J.Mol.Biol.. 329. 779-791 (2003)
• [Publications] K.Kamagata: "Multiple parallel-pathway folding of proline-free staphylococcal nuclease."J.Mol.Biol.. 332. 1143-1153 (2003)
• [Publications] 後藤 祐児: "タンパク質のフォールデイングとアミロイド線維形成:タンパク質、昼の顔と夜の顔"実験医学. 21. 898-902 (2003)
• [Publications] M.Harigai: "Role of an N-terminal loop in the secondary structural change of photoactive yellow protein"Biochemistry. 42. 13893-13900 (2003)
• [Publications] 寺嶋 正秀: "蛋白質におけるエネルギー散逸過程"レーザー研究. 31. 195-201 (2003)
• [Publications] 平田 文男: "Molecular Theory of Solvation"Kluwer-SpringerAcademic, Dordrecht, Netherlands. 358 (2003)