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2015 Fiscal Year Annual Research Report

生命分子システムにおける動的秩序形成と高次機能発現の研究に関する総括

Administrative Group

Project AreaDynamical ordering of biomolecular systems for creation of integrated functions
Project/Area Number 25102001
Research InstitutionOkazaki Research Facilities, National Institutes of Natural Sciences

Principal Investigator

加藤 晃一  大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 教授 (20211849)

Co-Investigator(Kenkyū-buntansha) 佐藤 啓文  京都大学, 工学(系)研究科(研究院), 教授 (70290905)
平岡 秀一  東京大学, 総合文化研究科, 教授 (10322538)
上久保 裕生  奈良先端科学技術大学院大学, 物質創成科学研究科, 准教授 (20311128)
寺嶋 正秀  京都大学, 理学(系)研究科(研究院), 教授 (00188674)
芳坂 貴弘  北陸先端科学技術大学院大学, マテリアルサイエンス研究科, 教授 (30263619)
佐藤 宗太  東北大学, 原子分子材料科学高等研究機構, 准教授 (40401129)
岡本 祐幸  名古屋大学, 理学(系)研究科(研究院), 教授 (70185487)
稲垣 直之  奈良先端科学技術大学院大学, バイオサイエンス研究科, 教授 (20223216)
Project Period (FY) 2013-06-28 – 2018-03-31
Keywords生命分子 / 超分子 / 動的秩序 / 高次機能 / 集合離散
Outline of Annual Research Achievements

本領域の目的を達成するため、総括班メンバーは、全研究期間を通して領域の全体的な研究方針の統合的策定と各研究項目の企画調整等を行っている。平成27年度では、総括班会議を開催し、相互情報交換を通して研究の進捗状況の確認や研究項目間の連携の推進、ならびに領域全体の活動方針の策定を行うとともに、主に以下の活動を通じて、異分野融合の推進と研究領域の発展に努めた。
1.全体班会議、公開シンポジウム、学会におけるワークショップの開催:全体班会議(2015年8月4-6日、淡路)や第4回国際シンポジウム(2015年11月22-23日、福岡)を開催した。これらの会を通して関連分野の国内外の進展状況に関する議論を行うとともに、分野融合的な領域内共同研究の推進を図ることができた。また第53回日本生物物理学会年会、日本化学会第96春季年会において本領域の共催ワークショップを開催し、化学、物理、生物学の専門分野の垣根を越えた議論を領域外へと拡張することができた。
2.若手育成とアウトリーチ活動:第2回「動的秩序と機能」若手研究会(2015年10月5-7日、蒲郡)を開催し、研究活動を実際に推進する大学院生や博士研究員らの視野を広げ、若手研究者の育成に努めた。また、一般の方を広く対象としたアウトリーチ活動「自然科学カフェの集い」を開催し、研究領域の認知と啓蒙に努めるとともに、第2回女子中高生のためのサイエンスカフェを開催し、女子中高生の理系進路選択への支援を行うことができた。
3.広報活動::研究成果や各種会議の成果を掲載したニュースレターを毎月発行し、領域活動と研究進捗状況に関する情報発信を行うことができた。

Current Status of Research Progress
Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

本領域の活動と相補した新学術領域「グリアアセンブリによる脳機能発現の制御と病態」および「統合的神経機能の制御を標的とした糖鎖の作動原理解明」と連携したシンポジウムを共催し、領域間相互作用によって分子レベルから細胞・組織・個体レベルに至る超階層的な生命システムの研究の発展に取り組むことができた。

Strategy for Future Research Activity

本領域の目的を達成するために、総括班は、本領域がこれまで異なるフィールドで活躍してきた科学者の学際的な議論と連携を可能とする“知の梁山泊”として機能することを重視し、各班が研究項目の垣根を越えて緊密に連携する環境を構築する。そのために、引き続き以下の活動を行う。
1.総括班会議の開催:計画研究、公募研究を通した全体的な研究の発展と分野融合に気を配り、活動のバランスと発展に対して提言を行い、領域形成の達成に向けて必要な行動を行う。異分野融合や若手研究者を基軸とする班内・班間の共同研究を重視し、必要に応じた特別プロジェクト用の援助を行う。
2.全体会議、若手の会、学会におけるシンポジウムの開催:宿泊形式での全体会議の実施に加え、若手研究者に共同研究活動と成果発表の舞台を与えるための機会を積極的に設ける。その際には、特定の共通課題に焦点をあてて、理論と実験の立場からの見解をぶつけあい、化学、物理、生物学の専門分野の垣根を越えたディスカッションが進展することを重視する。また、いくつかの学会において問題意識を共有するためのシンポジウムの企画を促す。
3.公開ワークショップの開催:広く国内外の研究者に開かれたワークショップを開催し、研究領域の発展に努めるとともに異分野の融合を図る。ワークショップでは、関連分野の世界的な発展の状況を含めて議論する。
4.アウトリーチ活動の実施:サイエンスカフェの開催をはじめとするアウトリーチ活動を実施し、一般の方に対しても広く研究領域の認知と啓蒙に努める。
5.研究成果の発表:研究成果や各種会議の成果を領域ホームページやニュースレターに掲載し、情報提供と研究進捗状況の発信を行う。あるいは学術雑誌記事として広報していく。

  • Research Products

    (106 results)

All 2016 2015 Other

All Int'l Joint Research (1 results) Journal Article (56 results) (of which Peer Reviewed: 55 results,  Open Access: 5 results) Presentation (46 results) (of which Int'l Joint Research: 24 results,  Invited: 40 results) Funded Workshop (3 results)

  • [Int'l Joint Research] 台湾国立交通大学(台湾)

    • Country Name
      その他の国・地域
    • Counterpart Institution
      台湾国立交通大学
  • [Journal Article] Characterization of Thylakoid Membrane in Filamentous Cyanobacteria and Green Alga with Dual-detector Fluorescence Lifetime Imaging Microscopy with a Systematic Change of Incident Laser Power2016

    • Author(s)
      S. Nozue, A. Mukuno, Y. Tsuda, T. Shiina, M. Terazima, S. Kumazaki
    • Journal Title

      Biochim.Biophys.Acta.

      Volume: 1857 Pages: 46-59

    • DOI

      10.1016/j.bbabio.2015.10.003

    • Peer Reviewed
  • [Journal Article] Time-Resolved Fluctuation during the Photochemical Reaction of a Photoreceptor Protein: Phototropin1LOV2-Linker2016

    • Author(s)
      K. Kuroi, F. Sato, Y. Nakasone, K. Zikihara, S. Tokutomi, M. Terazima
    • Journal Title

      Phys.Chem.Chem.Phys.

      Volume: 18 Pages: 6228-6238

    • DOI

      10.1039/c5cp07472j

    • Peer Reviewed
  • [Journal Article] Incorporation of a Doubly Functionalized Synthetic Amino Acid into Proteins for Creating Chemical and Light-Induced Conjugates2016

    • Author(s)
      A. Yamaguchi, T. Matsuda, K. Ohtake T. Yanagisawa, S. Yokoyama, Y. Fujiwara, T. Watanabe, T. Hohsaka, K. Sakamoto
    • Journal Title

      Bioconjugate Chem.

      Volume: 27 Pages: 198-206

    • DOI

      10.1021/acs.bioconjchem.5b00602

    • Peer Reviewed
  • [Journal Article] One-pot Synthesis of [n]Cyclo-1,3-pyrenylenes via Ni-mediated Macrocyclization2016

    • Author(s)
      K. Ikemoto, S. Sato, H. Isobe
    • Journal Title

      Chem. Lett.

      Volume: 45 Pages: 217-219

    • DOI

      10.1246/cl.151112

    • Peer Reviewed
  • [Journal Article] Modular Synthesis of Aromatic Hydrocarbon Macrocycles for Simplified, Single-Layer Organic Light-Emitting Devices2016

    • Author(s)
      K. Ikemoto, A. Yoshii, T. Izumi, H. Taka, H. Kita, J. Y. Xue, R. Kobayashi, S. Sato, H. Isobe
    • Journal Title

      J. Org. Chem.

      Volume: 81 Pages: 662-666

    • DOI

      10.1021/acs.joc.5b02620

    • Peer Reviewed
  • [Journal Article] Aromatic Hydrocarbon Macrocycles for Highly Efficient Organic Light-emitting Devices with Single-layer Architectures2016

    • Author(s)
      J. Y. Xue, T. Izumi, A. Yoshii, K. Ikemoto, T. Koretsune, R. Akashi, R. Arita, H. Taka, H. Kita, S. Sato, H. Isobe
    • Journal Title

      Chem. Sci.

      Volume: 7 Pages: 896-904

    • DOI

      10.1039/C5SC03807C

    • Peer Reviewed
  • [Journal Article] Membrane-induced dichotomous conformation of amyloid β with the disordered N-terminal segment followed by the stable C-terminal β structure2016

    • Author(s)
      M. Yagi-Utsumi, K. Kato, K. Nishimura
    • Journal Title

      PLoS ONE

      Volume: 11 Pages: e0146405

    • DOI

      10.1371/journal.pone.0146405

    • Peer Reviewed
  • [Journal Article] Application of site-specific spin labeling for NMR detecting inhibitor-induced conformational change of HIV-1 reverse transcriptase2016

    • Author(s)
      S. Seetaha, M. Yagi-Utsumi, T. Yamaguchi, K. Ishii, S. Hannongbua, K. Choowongkomon, K. Kato
    • Journal Title

      ChemMedChem

      Volume: 11 Pages: 363-366

    • DOI

      10.1002/cmdc.201500554

    • Peer Reviewed
  • [Journal Article] Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control2016

    • Author(s)
      T. Satoh, T. Toshimori, G. Yan, T. Yamaguchi, K. Kato
    • Journal Title

      Sci. Rep.

      Volume: 6 Pages: 20575

    • DOI

      10.1038/srep20575

    • Peer Reviewed / Open Access
  • [Journal Article] Mass spectrometric characterization of HIV-1 reverse transcriptase interactions with non-nucleoside reverse transcriptase inhibitors2016

    • Author(s)
      R. Thammaporn, K. Ishii, M. Yagi-Utsumi, S. Uchiyama, S. Hannongbua, K. Kato
    • Journal Title

      Biol. Pharm. Bull.

      Volume: 39 Pages: 450-454

    • DOI

      10.1248/bpb.b15-00880

    • Peer Reviewed
  • [Journal Article] An Integral Equation Theory for Solvation Effects on the Molecular Structural Fluctuation2015

    • Author(s)
      Y. Matsumura ,H. Sato
    • Journal Title

      J. Chem. Phys.

      Volume: 143 Pages: No. 1, 014104

    • DOI

      10.1063/1.4923038

    • Peer Reviewed
  • [Journal Article] Domain-Swapped Dimer of Pseudomonas Aeruginosa Cytochrome c551: Structural Insights into Domain Wapping of Cytochrome c Family Proteins2015

    • Author(s)
      S. Nagao, M. Ueda, H. Osuka, H. Komori, H. Kamikubo, M. Kataoka Y. Higuchi, S. Hirota
    • Journal Title

      PLoS ONE

      Volume: 10 Pages: e0123653

    • DOI

      10.1371/journal.pone.0123653

    • Peer Reviewed
  • [Journal Article] Reaction dynamics of the UV-B photosensor UVR82015

    • Author(s)
      T. Miyamori, Y. Nakasone, K. Hitomi, J.M. Christie, E. D. Getzoff, M.Terazima
    • Journal Title

      Photochem.Photobiol.Sci

      Volume: 14 Pages: 995-1004

    • DOI

      10.1039/c5pp00012b

    • Peer Reviewed
  • [Journal Article] Photo-induced inter-protein interaction changes in the time domain; a blue light sensor protein PixD2015

    • Author(s)
      M. Terazima
    • Journal Title

      Rapid Comm. Photosci.

      Volume: 4 Pages: 1-8

    • Peer Reviewed
  • [Journal Article] Self-Assembly Process of Dodecanuclear Pt(II)-Linked Cyclic Hexagon2015

    • Author(s)
      A. Baba, T. Kojiam,S. Hiraoka
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 137 Pages: 7664-7667

    • DOI

      10.1021/jacs.5b04852

    • Peer Reviewed
  • [Journal Article] What Do We Learn from the Molecular Self-Assembly Process?2015

    • Author(s)
      S. Hiraoka
    • Journal Title

      Chem. Rec.

      Volume: 15 Pages: 1144-1147

    • DOI

      10.1002/tcr.201510005

    • Peer Reviewed
  • [Journal Article] Liposome-Based in Vitro Evolution of Aminoacyl-tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation2015

    • Author(s)
      A. Uyeda, T. Watanabe, Y. Kato, H. Watanabe, T. Yomo, T. Hohsaka, T. Matsuura
    • Journal Title

      chemBioChem.

      Volume: 16 Pages: 1797-1802

    • DOI

      10.1002/cbic.201500174

    • Peer Reviewed
  • [Journal Article] Geometrically Restricted Intermediates in the Self-Assembly of an M12L24 Cuboctahedral Complex2015

    • Author(s)
      D. Fujita, H. Yokoyama, Y. Ueda, S. Sato, M. Fujita
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 54 Pages: 155-158

  • [Journal Article] Theoretical Studies on a Carbonaceous Molecular Bearing: Association Thermodynamics and Dual-mode Rolling Dynamics2015

    • Author(s)
      H. Isobe, K. Nakamura, S. Hitosugi, S. Sato, H.,Tokoyama, H. Yamakado, K. Ohno, H. Kono
    • Journal Title

      Chem. Sci.

      Volume: 6 Pages: 2746-2753

    • DOI

      10.1039/C5SC00335K

    • Peer Reviewed
  • [Journal Article] A Self-Assembled Spherical Complex Displaying a Gangliosidic Glycan Cluster Capable of Interacting with Amyloidogenic Proteins2015

    • Author(s)
      S. Sato, Y. Yoshimasa, D. Fujita, M. Yagi-Utsumi, T. Yamaguchi, K. Kato, M. Fujita
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 54 Pages: 8435-8439

    • DOI

      10.1002/anie.201501981

    • Peer Reviewed
  • [Journal Article] Modulation of Energy Conversion Processes in Carbonaceous Molecular Bearings2015

    • Author(s)
      S. Hitosugi, K. Ohkubo, Y. Kawashima, T. Matsuno, S. Kamata, K. Nakamura, H. Kono, S. Sato, S. Fukuzumi, *H. Isobe
    • Journal Title

      Chem. Asian J.

      Volume: 10 Pages: 2404-2410

    • DOI

      10.1002/asia.201500673

    • Peer Reviewed
  • [Journal Article] MNovel Titanium Complexes with a Reversible Structure Change on Solvent Adsorption and Desorption2015

    • Author(s)
      M. Kobayashi, T. Okuhara, H. Kato, S. Sato, M. Kakihana
    • Journal Title

      Chem. Lett

      Volume: 44 Pages: 1050-1052

    • DOI

      10.1246/cl.150393

    • Peer Reviewed
  • [Journal Article] DOSY NMR, X-ray Structural and Ion-Mobility Mass Spectrometric Studies on Electron-Deficient and Electron-Rich M6L4 Coordination Cages2015

    • Author(s)
      P. Bonakdarzadeh, F. Topic, E. Kalenius, S. Bhowmik, S. Sato, M. Groessl, R. Knochenmuss, K. Rissanen
    • Journal Title

      Inorg. Chem.

      Volume: 54 Pages: 6055-6061

    • DOI

      10.1021/acs.inorgchem.5b01082

    • Peer Reviewed
  • [Journal Article] Finely Resolved Threshold for the Sharp M12L24/M24L48 Structural Switch in Multi-Component MnL2n Polyhedral Assemblies: X-ray, MS, NMR, and Ultracentrifugation Analyses2015

    • Author(s)
      H. Yokoyama, Y. Ueda, D. Fujita, S. Sato, M. Fujita
    • Journal Title

      Chem. Asian J.

      Volume: 10 Pages: 2292-2295

    • DOI

      10.1002/asia.201500519

    • Peer Reviewed
  • [Journal Article] Bridging Adhesion of a Protein onto an Inorganic Surface Using Self-Assembled Dual Functionalized Spheres2015

    • Author(s)
      S. Sato, M. Ikemi, T. Kikuchi, S. Matsumura, K. Shiba, M. Fujita
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 137 Pages: 12890-12896

    • DOI

      10.1021/jacs.5b06184

    • Peer Reviewed
  • [Journal Article] Synthesis and Oxidation Catalysis of a Ti-Substituted Phosphotungstate, and Identification of the Active Oxygen Species2015

    • Author(s)
      E. Takahashi, K. Kamata, Y. Kikukawa, S. Sato, K. Suzuki, K. Yamaguchi, N. Mizuno
    • Journal Title

      Catal. Sci. Technol.

      Volume: 5 Pages: 4778-4789

    • DOI

      10.1039/C5CY01031D

    • Peer Reviewed
  • [Journal Article] Synthesis and Dynamic Structures of a Hybrid Nanohoop Molecule Composed of Anthanthrenylene and Phenylene Panels2015

    • Author(s)
      P. Sarkar, S. Sato, S. Kamata, T. Matsuno, H. Isobe
    • Journal Title

      Chem. Lett.

      Volume: 44 Pages: 1581-1583

    • DOI

      10.1246/cl.150801

    • Peer Reviewed
  • [Journal Article] Belt-shaped Cyclonaphthylenes2015

    • Author(s)
      Z. Sun, P. Sarkar, T. Suenaga, S. Sato, H. Isobe
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 54 Pages: 12800-12804

    • DOI

      10.1002/anie.201506424

    • Peer Reviewed
  • [Journal Article] NMR-based structural validation of therapeutic antibody produced in Nicotiana benthamiana2015

    • Author(s)
      H. Yagi, N. Fukuzawa, Y. Tasaka, K. Matsuo, Y. Zhang, T. Yamaguchi, S. Kondo, S. Nakazawa, N. Hashii, N. Kawasaki, T. Matsumura and K. Kato
    • Journal Title

      Plant Cell Rep.

      Volume: 34 Pages: 959-968

    • DOI

      10.1007/s00299-015-1757-1

    • Peer Reviewed
  • [Journal Article] Stable isotope labeling of glycoprotein expressed in silkworms using immunoglobulin G as a test molecule2015

    • Author(s)
      H. Yagi, M. Nakamura, J. Yokoyama, Y. Zhang, T. Yamaguchi, S. Kondo, J. Kobayashi, T. Kato, E. Y. Park, S. Nakazawa, N. Hashii, N. Kawasaki and K. Kato
    • Journal Title

      J. Biomol. NMR

      Volume: 62 Pages: 157-167

    • DOI

      10.1007/s10858-015-9930-y

    • Peer Reviewed
  • [Journal Article] Backbone 1H, 13C, and 15N resonance assignments of the Fc fragment of human immunoglobulin G glycoprotein2015

    • Author(s)
      3.H. Yagi, Y. Zhang, M. Yagi-Utsumi, T. Yamaguchi, S. Iida, Y. Yamaguchi and K. Kato
    • Journal Title

      Biomol. NMR Assign.

      Volume: 9 Pages: 257-260

    • DOI

      10.1007/s12104-014-9586-7

    • Peer Reviewed
  • [Journal Article] 離合集散が織りなす生命分子機能の研究フロンティア2015

    • Author(s)
      加藤晃一, 稲垣直之
    • Journal Title

      実験医学

      Volume: 33 Pages: 1316-1320

    • Peer Reviewed
  • [Journal Article] Structural and dynamic views of GM1 ganglioside2015

    • Author(s)
      M. Yagi-Utsumi and K. Kato
    • Journal Title

      Glycoconjugate J.

      Volume: 32 Pages: 105-112

    • DOI

      10.1007/s10719-015-9587-5

    • Peer Reviewed
  • [Journal Article] Structural basis of redox-dependent substrate binding of protein disulfide isomerase2015

    • Author(s)
      M. Yagi-Utsumi, T. Satoh and K. Kato
    • Journal Title

      Sci. Rep.

      Volume: 5 Pages: 13909

    • DOI

      10.1038/srep13909

    • Peer Reviewed / Open Access
  • [Journal Article] Redox-coupled structural changes of the catalytic a’domain of protein disulfide isomerase2015

    • Author(s)
      K. Inagaki, T. Satoh, M. Yagi-Utsumi, A.-C. Le Gulluche, T. Anzai, Y. Uekusa, Y. Kamiya and K. Kato
    • Journal Title

      FEBS Lett.

      Volume: 589 Pages: 2690-2694

    • DOI

      10.1016/j.febslet.2015.07.041

    • Peer Reviewed
  • [Journal Article] Importance of the side chain at position 296 of antibody Fc in interactions with FcγRIIIa and other Fcγ receptors2015

    • Author(s)
      Y. Isoda, H. Yagi, T. Satoh, M. Shibata-Koyama, K. Masuda, M. Satoh, K. Kato and S. Iida
    • Journal Title

      PLoS ONE

      Volume: 10 Pages: e0140120

    • DOI

      10.1371/journal.pone.0140120

    • Peer Reviewed
  • [Journal Article] pH-dependent assembly and segregation of the coiled-coil segments of yeast putative cargo receptors Emp46p and Emp47p2015

    • Author(s)
      K. Ishii, H. Enda, M. Noda, M. Kajino, A. Kim, E. Kurimoto, K. Sato, A. Nakano, Y. Kobayashi, H. Yagi, S. Uchiyama and K. Kato
    • Journal Title

      PLoS ONE

      Volume: 10 Pages: e0140287

    • DOI

      10.1371/journal.pone.0140287

    • Peer Reviewed
  • [Journal Article] NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities2015

    • Author(s)
      R. Thammaporn, M. Yagi-Utsumi, T. Yamaguchi, P. Boonsri, P. Saparpakorn, K. Choowongkomon, S. Techasakul, K. Kato and S. Hannongbua
    • Journal Title

      Sci. Rep.

      Volume: 5 Pages: 15806

    • DOI

      10.1038/srep15806

    • Peer Reviewed / Open Access
  • [Journal Article] Forcible destruction of severely misfolded mammalian glycoproteins by the non-glycoprotein ERAD pathway2015

    • Author(s)
      S. Ninagawa, T. Okada, Y. Sumitomo, S. Horimoto, T. Sugimoto, T. Ishikawa, S. Takeda, T. Yamamoto, T. Suzuki, Y. Kamiya, K. Kato and K. Mori
    • Journal Title

      J. Cell Biol.

      Volume: 211 Pages: 775-784

    • DOI

      10.1083/jcb.201504109

    • Peer Reviewed
  • [Journal Article] A hybrid strategy for the preparation of 13C-labeled high-mannose-type oligosaccharides with terminal glucosylation for NMR study2015

    • Author(s)
      T. Zhu, T. Yamaguchi, T. Satoh and K. Kato
    • Journal Title

      Chem. Lett.

      Volume: 44 Pages: 1744-1746

    • DOI

      10.1246/cl.150898

    • Peer Reviewed
  • [Journal Article] Isotope effect on the circular dichroism spectrum of methyl α-D-glucopyranoside in aqueous solution2015

    • Author(s)
      Y. Kanematsu, Y. Kamiya, K. Matsuo, K. Gekko, K. Kato and M. Tachikawa
    • Journal Title

      Sci. Rep.

      Volume: 5 Pages: 17900

    • DOI

      10.1038/srep17900

    • Peer Reviewed / Open Access
  • [Journal Article] Disassembly of the self-assembled, double-ring structure of proteasome α7 homo-tetradecamer by α62015

    • Author(s)
      K. Ishii, M. Noda, H. Yagi, R. Thammaporn, S. Seetaha, T. Satoh, K. Kato and S. Uchiyama
    • Journal Title

      Sci. Rep.

      Volume: 5 Pages: 18167

    • DOI

      10.1038/srep18167

    • Peer Reviewed / Open Access
  • [Journal Article] 生命現象の解明に挑むサイボーグ超分子―機能を維持したまま生体分子クラスターを人工分子に移植2015

    • Author(s)
      佐藤宗太, 加藤晃一, 藤田 誠
    • Journal Title

      化学

      Volume: 70 Pages: 31-36

    • Peer Reviewed
  • [Journal Article] Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides2015

    • Author(s)
      K. Kato and T. Yamaguchi
    • Journal Title

      Glycoconjugate J.

      Volume: 32 Pages: 505-513

    • DOI

      10.1007/s10719-015-9599-1

    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations to clarify the concentration dependency of protein aggregation2015

    • Author(s)
      N. Nishikawa, Y. Sakae, and Y. Okamoto
    • Journal Title

      JPS Conference Proceedings

      Volume: 5 Pages: 011020(7pages)

    • Peer Reviewed
  • [Journal Article] Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation2015

    • Author(s)
      N. Nishikawa, P.H. Nguyen, P. Derreumaux, and Y. Okamoto
    • Journal Title

      Molecular Simulation

      Volume: 41 Pages: 1041-1044

    • DOI

      10.1080/08927022.2014.938445

    • Peer Reviewed
  • [Journal Article] Conformational search simulations of Trp-cage using genetic crossover2015

    • Author(s)
      Y. Sakae, T. Hiroyasu, M. Miki, K. Ishii, and Y. Okamoto
    • Journal Title

      Molecular Simulation

      Volume: 41 Pages: 1045-1049

    • DOI

      1080/08927022.2015.1016937

    • Peer Reviewed
  • [Journal Article] Equilibrium molecular thermodynamics from Kirkwood sampling2015

    • Author(s)
      S. Somani, Y. Okamoto, A.J. Ballard, D.J. Wales
    • Journal Title

      J. Phys. Chem. B

      Volume: 119 Pages: 6155-6169

    • DOI

      10.1021/acs.jpcb.5b01800

    • Peer Reviewed
  • [Journal Article] New Implementations of Replica-exchange Method for Simulations of Complex Systems: Dsigned-walk and Deterministic Replica-exchange Methods2015

    • Author(s)
      R. Urano, Y. Okamoto
    • Journal Title

      Phys. Procedia.

      Volume: 68 Pages: 100-104

    • DOI

      10.1016/j.phpro.2015.07.116

    • Peer Reviewed
  • [Journal Article] Predictions of Tertiary Structures of a-helical Membrane Proteins by Replica-exchange Method with Consideration of Helix Deformations2015

    • Author(s)
      R. Urano, H. Kokubo, Y. Okamoto
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 84 Pages: 084802(12pages)

    • DOI

      10.7566/JPSJ.84.084802

    • Peer Reviewed
  • [Journal Article] Designed-walk Replica-exchange Method for Simulations of Complex Systems2015

    • Author(s)
      R. Urano, Y. Okamoto
    • Journal Title

      Comput. Phys. Commun.

      Volume: - Pages: 380-383

    • DOI

      10.1016/j.cpc.2015.07.007

    • Peer Reviewed
  • [Journal Article] Deterministic Replica-exchange Method without Pseudo Random Numbers for Simulations of Complex Systems2015

    • Author(s)
      R. Urano, Y. Okamoto
    • Journal Title

      Comput. Phys. Commun.

      Volume: 197 Pages: 128-135

    • DOI

      10.1016/j.cpc.2015.08.020

    • Peer Reviewed
  • [Journal Article] Observation of Helix Associations for Insertion of a Retinal Molecule and Distortions of Helix Structures in Bacteriorhodopsin2015

    • Author(s)
      R. Urano, Y. Okamoto
    • Journal Title

      J. Chem. Phys.

      Volume: 143 Pages: 235101(10pages)

    • DOI

      10.1063/1.4935964

    • Peer Reviewed
  • [Journal Article] Actin migration driven by directional assembly and disassembly of membrane anchored actin filaments2015

    • Author(s)
      H. Katsuno, M. Toriyama, Y. Hosokawa, K. Mizuno, K. Ikeda, Y. Sakumura, N. Inagaki
    • Journal Title

      Cell Reports

      Volume: 12 Pages: 648-660

    • DOI

      10.1016/j.celrep.2015.06.048

    • Peer Reviewed
  • [Journal Article] Shootin1-cortactin interaction mediates signal-force transduction for axon outgrowth2015

    • Author(s)
      Y. Kubo, K. Baba, M. Toriyama, Y. Minegishi, T. Sugiura, S. Kozawa, K. Ikeda, N. Inagaki
    • Journal Title

      J. Cell Biol.

      Volume: 210 Pages: 663-676

    • DOI

      10.1083/jcb.20150501

    • Peer Reviewed
  • [Journal Article] Efficient Solid-Phase Gene Delivery Mediated by Cerasome: Effect of Reverse Procedure on Transfection Performances in Comparison with Solution-Based Method2015

    • Author(s)
      K. Tahara, M. Tsukui,T. Maeno, N. Inagaki, J. Kikuchi
    • Journal Title

      Chem. Lett.

      Volume: 44 Pages: 1643-1645

    • DOI

      10.1246/cl.150777

    • Peer Reviewed
  • [Presentation] Generalized-ensemble simulations of complex systems2016

    • Author(s)
      Yuko Okamoto
    • Organizer
      2016 NCTS March Workshop on Critical Phenomena and Complex Systems
    • Place of Presentation
      Hsinchu, Taiwan
    • Year and Date
      2016-03-28 – 2016-03-29
    • Int'l Joint Research / Invited
  • [Presentation] 超分子錯体の自己組織化機構2016

    • Author(s)
      平岡秀一
    • Organizer
      日本化学会第96春季年会特別企画
    • Place of Presentation
      同志社大学(京都府京都市)
    • Year and Date
      2016-03-24
    • Invited
  • [Presentation] Protein dynamics studied by generalized-ensemble simulations2016

    • Author(s)
      Yuko Okamoto
    • Organizer
      The 251st American Chemical Society National Meeting
    • Place of Presentation
      San Diego, U.S.A
    • Year and Date
      2016-03-13 – 2016-03-17
    • Int'l Joint Research / Invited
  • [Presentation] 非天然アミノ酸導入技術のバイオ医薬への応用展開2016

    • Author(s)
      芳坂貴弘
    • Organizer
      第 22 回ペプチドフォーラム
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2016-03-05
    • Invited
  • [Presentation] Structural views of functional glycans of pharmaceutical interest2016

    • Author(s)
      Koichi Kato
    • Organizer
      6th International Symposium on Current Trends in Drug Discovery & Research
    • Place of Presentation
      Lucknow,India
    • Year and Date
      2016-02-27
    • Int'l Joint Research / Invited
  • [Presentation] Self-assembly Process of Coordination Capsules and Cages2016

    • Author(s)
      Shuichi Hiraoka
    • Organizer
      The 9 th Japan-China Joint Symposium on Functional Supramolecular Architectures
    • Place of Presentation
      愛知県岡崎市
    • Year and Date
      2016-02-24
    • Int'l Joint Research / Invited
  • [Presentation] Biological Functions Implanted in Artificial Supramolecules2016

    • Author(s)
      Sota Sato
    • Organizer
      分子研研究会 日韓生体分子科学セミナー
    • Place of Presentation
      岡崎統合バイオサイエンスセンター(愛知県岡崎市)
    • Year and Date
      2016-02-15 – 2016-02-17
    • Invited
  • [Presentation] Structural insights into N-glycan-mediated fate-determination of glycoproteins in cells2016

    • Author(s)
      Tadashi Satoh, Tong Zhu, Takayasu Toshimori, Kousuke Suzuki, Gengwei Yan, Takumi Yamaguchi, Koichi Kato
    • Organizer
      Pure and Applied Chemistry International Conference (PACCON) 2016
    • Place of Presentation
      Bangkok,Thailand
    • Year and Date
      2016-02-11
    • Int'l Joint Research / Invited
  • [Presentation] 糖鎖の構造生物学2016

    • Author(s)
      加藤晃一
    • Organizer
      第57回構造生物応用研究会
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2016-02-04
    • Invited
  • [Presentation] How to detect photoreactions of proteins: Blue light sensors2016

    • Author(s)
      Masahide Terazima
    • Organizer
      International Workshop on Radiation and Photochemistry
    • Place of Presentation
      Pune, Inida
    • Year and Date
      2016-01-10 – 2016-01-12
    • Int'l Joint Research
  • [Presentation] Spectrally Silent Dynamics of Photo-induced Protein-Protein Interaction Change2016

    • Author(s)
      Masahide Terazima
    • Organizer
      Trombay Symposium on Radiation & Photochemistry & 6th Asia Pacific Symposium on Radiation Chemistry
    • Place of Presentation
      Mumbai, INDIA
    • Year and Date
      2016-01-05 – 2016-01-09
    • Int'l Joint Research
  • [Presentation] NMR characterization of dynamic conformational ensembles and interactions of carbohydrate chains2015

    • Author(s)
      Koichi Kato
    • Organizer
      PACIFICHEM 2015
    • Place of Presentation
      Honolulu,USA
    • Year and Date
      2015-12-17
    • Int'l Joint Research / Invited
  • [Presentation] Multi-scale couplings for chemical processes at molecular level: quantum chemistry and statistical mechanics2015

    • Author(s)
      Hirofumi Sato
    • Organizer
      PACIFICHEM 2015
    • Place of Presentation
      Honolulu,USA
    • Year and Date
      2015-12-16
    • Int'l Joint Research / Invited
  • [Presentation] Conformation changes and water-protein interaction change for function of proteins2015

    • Author(s)
      Masahide Terazima
    • Organizer
      PACIFICHEM 2015
    • Place of Presentation
      Honolulu,USA
    • Year and Date
      2015-12-15 – 2015-12-20
    • Int'l Joint Research
  • [Presentation] Enhanced sampling methods for exascale computational chemistry2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      PACIFICHEM 2015
    • Place of Presentation
      Honolulu, U.S.A.
    • Year and Date
      2015-12-15 – 2015-12-20
    • Invited
  • [Presentation] Time-resolved detection of inter-protein interaction during protein reaction2015

    • Author(s)
      Masahide Terazima
    • Organizer
      PACIFICHEM 2015
    • Place of Presentation
      Honolulu,USA
    • Year and Date
      2015-12-15 – 2015-12-20
    • Int'l Joint Research
  • [Presentation] Structural insights into protein-fate determination in cells2015

    • Author(s)
      Koichi Kato, Maho Yagi-Utsumi, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, and Tadashi Satoh
    • Organizer
      Okazaki Institute for Integrative Bioscience Retreat 2015
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-12-10
    • Int'l Joint Research / Invited
  • [Presentation] Incorporation of nonnatural amino acids through expansion of the genetic code and its application to fluorescence analysis of proteins2015

    • Author(s)
      Takahiro Hohsaka
    • Organizer
      BMB2015(第38回分子生物学会年会・第88回生化学会大会合同大会)
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-02
    • Int'l Joint Research / Invited
  • [Presentation] Generalized-ensemble algorithms for enhanced configurational sampling Algorithms in Structural Bioinformatics: Sampling in Biomacromolecular Systems2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      AlgoSB Winter School - 2015
    • Place of Presentation
      Corsica, France
    • Year and Date
      2015-11-29 – 2015-12-04
    • Int'l Joint Research / Invited
  • [Presentation] 神経変性疾患関連するアミロイド形成タンパク質の多様な分子間相互作用2015

    • Author(s)
      加藤晃一
    • Organizer
      第6回神経科学と構造生物学の融合研究会
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-11-26
    • Invited
  • [Presentation] 巨大分子の精密合成 ~きちんと分子構造を押さえる~2015

    • Author(s)
      佐藤宗太
    • Organizer
      ブルカー・ダルトニクス MSサミット
    • Place of Presentation
      TKPガーデンシティ横浜(神奈川県横浜市)
    • Year and Date
      2015-11-26
    • Invited
  • [Presentation] NMR views of physiological and pathological roles of glycans2015

    • Author(s)
      Koichi Kato
    • Organizer
      The 47th Annual Meeting of Korean Magnetic Resonance Society
    • Place of Presentation
      Buyeo,Korea
    • Year and Date
      2015-11-05
    • Invited
  • [Presentation] Self-Assembly Process of Coordination Cages and Capsules2015

    • Author(s)
      Shuichi Hiraoka
    • Organizer
      3rd Workshop of Center for Instrumental Analysis, Frontier of Instrumental Analysis using Magnetic Resonance Spectroscopy
    • Place of Presentation
      新潟大学(新潟県新潟市)
    • Year and Date
      2015-10-30
    • Int'l Joint Research / Invited
  • [Presentation] 糖鎖の構造生命科学2015

    • Author(s)
      加藤晃一
    • Organizer
      名古屋大学IGERセミナー
    • Place of Presentation
      名古屋大学(愛知県名古屋市)
    • Year and Date
      2015-10-26
    • Invited
  • [Presentation] 拡張アンサンブル法による量子化学シミュレーション2015

    • Author(s)
      岡本祐幸
    • Organizer
      分子研研究会「理論計算分子科学ワークショップ」
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-10-22
    • Invited
  • [Presentation] 生命分子システムの動的秩序の探査・創生・展開2015

    • Author(s)
      加藤晃一
    • Organizer
      第13回 糖鎖科学コンソーシアムシンポジウム
    • Place of Presentation
      ウィンクあいち(愛知県名古屋市)
    • Year and Date
      2015-10-19
    • Invited
  • [Presentation] メカニズム指向の自己組織化に挑戦!~自己集合性金属錯体の形成機構の解明~2015

    • Author(s)
      平岡秀一
    • Organizer
      第5回CSJ化学フェスタ2015
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2015-10-13
    • Invited
  • [Presentation] Generalized-ensemble simulations of classical and quantum molecular systems2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      The 6th Japan-Czech-Slovak International Symposium for Theoretical Chemistry
    • Place of Presentation
      Smolenice, Slovakia
    • Year and Date
      2015-10-11 – 2015-10-15
    • Int'l Joint Research / Invited
  • [Presentation] Hierarchically Self-Assembled Metal-Organic Complexes as Fusion Materials2015

    • Author(s)
      佐藤宗太
    • Organizer
      Fusion Materials Symposium 2015
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2015-09-19
    • Invited
  • [Presentation] 水-蛋白質界面の電荷状態と蛋白質内部で生じる化学反応2015

    • Author(s)
      上久保裕生
    • Organizer
      第64回高分子討論会
    • Place of Presentation
      東北大学川内キャンパス(宮城県仙台市)
    • Year and Date
      2015-09-16
    • Invited
  • [Presentation] 凝縮系の理論化学2015

    • Author(s)
      佐藤啓文
    • Organizer
      化学反応経路探索のニューフロンティア2015
    • Place of Presentation
      総合区民会館きゅりあん(東京都品川区)
    • Year and Date
      2015-09-15
    • Invited
  • [Presentation] Generalized-ensemble simulations2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      Hands-on Workshop on Computational Biophysics at Okazaki
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-09-09 – 2015-09-11
    • Invited
  • [Presentation] 古典系および量子系の拡張アンサンブルシミュレーション2015

    • Author(s)
      岡本祐幸
    • Organizer
      スーパーコンピュータワークショップ
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-09-07 – 2015-09-08
    • Invited
  • [Presentation] Structural Views of Glycan Functions in Physiological and Pathological Contexts2015

    • Author(s)
      Koichi Kato, Maho Yagi-Utsumi, Takumi Yamaguchi, Hirokazu Yagi, and Tadashi Satoh
    • Organizer
      9th International Conference on Proteoglycans and 10th Pan-Pacific Connective Tissue (ICP&PPCTSS 2015)
    • Place of Presentation
      Seoul,Korea
    • Year and Date
      2015-08-24
    • Int'l Joint Research / Invited
  • [Presentation] NMR Views of Fate Determination and Functional Regulation of Proteins Mediated by Sugar Chains2015

    • Author(s)
      Koichi Kato
    • Organizer
      The 19th International Society of Magnetic Resonance (ISMAR 2015)
    • Place of Presentation
      Shanghai,China
    • Year and Date
      2015-08-20
    • Int'l Joint Research / Invited
  • [Presentation] Generalized-ensemble simulations of complex systems2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      2015 NCTS International Workshop on Critical Phenomena and Complex Systems
    • Place of Presentation
      Hsinchu, Taiwan
    • Year and Date
      2015-08-15 – 2015-08-17
    • Int'l Joint Research / Invited
  • [Presentation] 生命分子システムにおける動的秩序形成と高次機能発現2015

    • Author(s)
      加藤晃一,山口拓実,矢木真穂,栗原顕輔,佐藤匡史
    • Organizer
      新学術領域「動的秩序と機能」平成27年度全体班会議
    • Place of Presentation
      兵庫県立淡路国際夢舞台会議場(兵庫県淡路市)
    • Year and Date
      2015-08-05
    • Invited
  • [Presentation] Generalized-ensemble algorithms for calculations of ligand binding affinity2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      BIRS Workshop: Free-Energy Calculations. A Mathematical Perspective
    • Place of Presentation
      Oaxaca, Mexico
    • Year and Date
      2015-07-19 – 2015-07-24
    • Int'l Joint Research / Invited
  • [Presentation] 生命分子システムの動的秩序形成の探査・創生・展開2015

    • Author(s)
      加藤晃一
    • Organizer
      第1回秩序化分子システム仙台ワークショップ
    • Place of Presentation
      ホテルニュー水戸屋(宮城県仙台市)
    • Year and Date
      2015-07-11
    • Int'l Joint Research / Invited
  • [Presentation] Generalized-ensemble algorithms for enhanced sampling and free energy calculations2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      Summer Snowmass Biophysics Workshop Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
    • Place of Presentation
      Colorado U.S.A
    • Year and Date
      2015-07-05 – 2015-07-09
    • Invited
  • [Presentation] Efficient sampling methods for identifying transition states2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
    • Place of Presentation
      Colorado U.S.A
    • Year and Date
      2015-06-23 – 2015-06-26
    • Int'l Joint Research / Invited
  • [Presentation] 糖鎖の3次元構造ダイナミクスと分子間相互作用2015

    • Author(s)
      加藤晃一
    • Organizer
      第2回蛋白質工学研究会ワークショップ
    • Place of Presentation
      あわぎんホール(徳島県徳島市)
    • Year and Date
      2015-06-23
    • Invited
  • [Presentation] Compressibility and reactivity of a protein reaction2015

    • Author(s)
      Masahide Terazima
    • Organizer
      19th Symposium on Thermophysical Properties
    • Place of Presentation
      Colorado U.S.A
    • Year and Date
      2015-06-21 – 2015-06-26
    • Int'l Joint Research
  • [Presentation] Efficient sampling methods for complex systems2015

    • Author(s)
      Yuko Okamoto
    • Organizer
      The 19th International Annual Symposium on Computational Science and Engineering (ANSCSE19)
    • Place of Presentation
      Ubon Ratchathani, Thailand
    • Year and Date
      2015-06-17 – 2015-06-19
  • [Presentation] Designing an Artificial Protein by Using a Kind of Building Blocks Responsible for Structure and Function2015

    • Author(s)
      Hironari Kamikubo
    • Organizer
      IMS Asian International Symposium
    • Place of Presentation
      岡崎統合バイオサイエンスセンター(愛知県岡崎市)
    • Year and Date
      2015-06-12
    • Int'l Joint Research / Invited
  • [Presentation] 糖鎖を見る2015

    • Author(s)
      加藤晃一
    • Organizer
      第4回バイオイメージング研究会
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2015-05-08
    • Invited
  • [Funded Workshop] The 4th International Symposium on "Dynamical ordering of biomolecular systems for creation of integrated functions"2015

    • Place of Presentation
      九州大学西新プラザ(福岡県福岡市)
    • Year and Date
      2015-11-22 – 2015-11-23
  • [Funded Workshop] Hands-on Workshop on Computational Biophysics at Okazaki2015

    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2015-09-09 – 2015-09-11
  • [Funded Workshop] アジア連携分子研研究会“Supramolecular Dynamics at the Interface of Chemistry and Biology”2015

    • Place of Presentation
      岡崎統合バイオサイエンスセンター(愛知県岡崎市)
    • Year and Date
      2015-06-12 – 2015-06-13

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Published: 2017-01-06   Modified: 2022-03-01  

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