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2013 Fiscal Year Final Research Report

Study on the hydration structural changes in coupling with the internal motions of proteins using time-resolved fluorscence measurement

Research Project

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Project/Area Number 22244054
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionKeio University

Principal Investigator

NAKASAKO Masayoshi  慶應義塾大学, 理工学部, 教授 (30227764)

Project Period (FY) 2010-04-01 – 2014-03-31
Keywordsタンパク質水和 / 水和構造 / 分子動力学シミュレーション / 蛍光分光 / 和周波測定 / 非線形光学 / X線結晶構造解析 / 主成分分析
Research Abstract

Proteins are engaged in the elementary processes of life in cells and fold and function only in aqueous environment. To understand why water is indispensable for proteins it is necessary to visualize the hydration structures of proteins at spatial resolution of atomic level and ps temporal resolution. In this research project, through developing time-resolved fluorescence measurement system dedicated for proteins, we analyzed the dynamics of protein hydration from the experimental point of view using the fluorescence measurement and structure analyses as well as molecular dynamics simulation.

Research Products

(30 results)

All 2014 2013 2012 2011 2010 Other

All Journal Article Presentation Book Remarks

  • [Journal Article] Light-induced conformational changes of LOV (Light Oxygen Voltage-sensing domain) 1 and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin2014

    • Author(s)
      K. Okajima, Y. Aihara, Y. Takayama, M. Nakajima, S. Kashojiya, T. Hikima, T. Oroguchi, A. Kobayashi, Y. Sekiguchi, M. Yamamoto, T. Suzuki, A. Nagatani, M. Nakasako and S. Tokutomi
    • Journal Title

      Journal of Biological Chemistry

      Volume: 289 Pages: 413-422

    • DOI

      10.1074/jbc.M113.515403

    • Peer Reviewed
  • [Journal Article] Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins2013

    • Author(s)
      D. Matsuoka and M. Nakasako
    • Journal Title

      Chemical Physics

      Volume: 419 Pages: 59-64

    • DOI

      10.1016/j.chemphys.2012.12.040

    • Peer Reviewed
  • [Journal Article] Three-dimensional structure determination protocol for non-crystalline biomolecules using x-ray free-electron laser diffraction imaging2013

    • Author(s)
      T. Oroguchi and M. Nakasako
    • Journal Title

      Physical Review E

      Volume: 87 Pages: 022712(15)

    • DOI

      10.1103/PhysRevE.87.021227

    • Peer Reviewed
  • [Journal Article] 先端的X線光源による細胞の空間階層イメージング2013

    • Author(s)
      中迫雅由, 山本雅貴
    • Journal Title

      パリティ

      Volume: 28, No. 7 Pages: 16-19

    • URL

      http://pub.maruzen.co.jp/book_magazine/magazine/parity-back/parity2013/2013_07/1307_cont.html

    • Peer Reviewed
  • [Journal Article] 蛋白質水和構造の実験研究2013

    • Author(s)
      中迫雅由, 苙口友隆, 高山裕貴, 中島真, 松井夕花
    • Journal Title

      アンサンブル

      Volume: 15 Pages: 7-18

    • URL

      http://mol-sim.c.ooco.jp/

    • Peer Reviewed
  • [Journal Article] Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent X-ray diffraction microscopy2012

    • Author(s)
      Y. Takayama and M. Nakasako
    • Journal Title

      Review of Scientific Instruments

      Volume: 83 Pages: 054301(6)

    • DOI

      10.1063/1.4718359

    • Peer Reviewed
  • [Journal Article] A few low-frequency normal modes predominantly contribute to conformationalresponse of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity2011

    • Author(s)
      Takayama and M. Nakasako
    • Journal Title

      Biophysical Chemistry

      Volume: 159 Pages: 237-246

    • DOI

      10.1016/j.bpc.2011.07.001

    • Peer Reviewed
  • [Journal Article] New monoclinic form of bovine pancreatic ribonuclease A from a high-salt solution and intermolecular interactions2011

    • Author(s)
      H.Takusagawa, S. Yamamura, S. Endo, Y. Sugawara, T. Inagaki, and M. Nakasako
    • Journal Title

      Journal of Crystal Growth

      Volume: 319 Pages: 49-56

    • DOI

      10.1016/j.jcrysgro.2011.01.037

    • Peer Reviewed
  • [Journal Article] Light-induced movement of LOV2 domain in Asp720Asn-mutated LOV2-kinase fragment of Arabidopsis phototropin 22011

    • Author(s)
      Y. Takayama, M. Nakasako, K. Okajima, A. Iwata, S. Kashojiya, Y. Matsui and S. Tokutomi
    • Journal Title

      Biochemistry

      Volume: 50 Pages: 1174-1183

    • DOI

      10.1021/bi101689b

    • Peer Reviewed
  • [Journal Article] 生命にはなぜ水が必要なのか-たんぱく質の機能と水和構造の相関2011

    • Author(s)
      中迫雅由、松岳大輔
    • Journal Title

      応用物理

      Volume: 80 Pages: 903-907

    • URL

      http://www.jsap.or.jp/ap/2011/10/ob800903.xml

    • Peer Reviewed
  • [Presentation] Empirical hydration distribution functions around polar atoms for studying hydration structures of proteins2013

    • Author(s)
      D. Matsuoka and M. Nakasako
    • Organizer
      The 13-th Korea Institute of Advanced Study (KIAS) Conference
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2013-09-26
    • Invited
  • [Presentation] 分子動力学計算によるグルタミン酸脱水素酵素ドメイン運動に協奏した水和構造変化の観察2013

    • Author(s)
      苙口友隆, 中島 真, 中迫雅由
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      鳥取
    • Year and Date
      2013-06-14
  • [Presentation] Cryogenic X-ray diffraction for illustrating hierarchical structures in cells2013

    • Author(s)
      M. Nakasako
    • Organizer
      International Symposium on Protein Folding and its Biological Significance
    • Place of Presentation
      Okazaki, Japan
    • Year and Date
      2013-03-05
    • Invited
  • [Presentation] 経験的水和分布関数の構築と水和構造予測への応用2013

    • Author(s)
      中迫雅由, 松岳大輔
    • Organizer
      情報計算化学生物学会
    • Place of Presentation
      東京
    • Year and Date
      2013-02-15
    • Invited
  • [Presentation] A protocol for structure analysis of non-crystalline particles with X-ray free electron laser2012

    • Author(s)
      T. Oroguchi, M. Nakasako
    • Organizer
      生物物理学会第50回年会
    • Place of Presentation
      名古屋
    • Year and Date
      2012-09-23
  • [Presentation] タンパク質疎水性表面に関する水和構造予測アルゴリズムの開発2012

    • Author(s)
      中迫雅由, 松岳大輔
    • Organizer
      特定領域高次分子系成果公開シンポジウム
    • Place of Presentation
      横浜
    • Year and Date
      2012-05-26
  • [Presentation] Static and Dynamical Pictures of Protein Hydration - to understadn why water is indispensable for structures and functions of proteins2012

    • Author(s)
      M. Nakasako
    • Organizer
      JST International Symposium on Multi-scale Simulation of Condensed-phase Reacting Systems
    • Place of Presentation
      Nagoya
    • Year and Date
      2012-05-11
    • Invited
  • [Presentation] X線自由電子レーザーによる生体超分子の新規構造解析法の提案及びシミュレーション2012

    • Author(s)
      苙口友隆, 中迫雅由
    • Organizer
      第25回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      鳥栖
    • Year and Date
      2012-01-08
  • [Presentation] 低温コヒーレントX線回折顕微鏡法の為の湿度制御下凍結水和生体試料作製装置の開発2011

    • Author(s)
      高山裕貴, 中迫雅由
    • Organizer
      日本結晶学会年会2011
    • Place of Presentation
      札幌
    • Year and Date
      2011-11-25
  • [Presentation] Preparation method of frozen-hydrated biological samples under controlled humidity for coherent X-ray diffraction microscopy2011

    • Author(s)
      Y. Takayama and M. Nakasako
    • Organizer
      生物物理学会第49回年会
    • Place of Presentation
      姫路
    • Year and Date
      2011-09-17
  • [Presentation] データベース解析による蛋白質水和構造の特徴抽出とその応用2011

    • Author(s)
      松岳大輔, 中迫雅由
    • Organizer
      放射光学会第3回若手研究会
    • Place of Presentation
      姫路
    • Year and Date
      2011-08-18
  • [Presentation] 植物青色光受容体フォトトロピン2 の立体構造研究2011

    • Author(s)
      中迫雅由, 高山裕貴, 岩田彩, 松井夕花, 岡島公司, 嘉祥寺谷幸子, 徳富哲
    • Organizer
      第24回日本放射光学会年会放射光科学合同シンポジウム
    • Place of Presentation
      つくば
    • Year and Date
      2011-01-09
  • [Presentation] RNaseA 新規三斜晶の構造と分子間相互作用の解析2010

    • Author(s)
      田草川英昇, 山村滋典, 猿渡茂, 菅原洋子, 稲垣敏幸, 中迫雅由
    • Organizer
      平成22年度日本結晶学会年会
    • Place of Presentation
      大阪
    • Year and Date
      2010-12-03
  • [Presentation] タンパク質疎水性表面に関する水和構造予測アルゴリズムの開発2010

    • Author(s)
      松岳大輔, 中迫雅由
    • Organizer
      特定領域「高次系分子科学」第四回公開シンポジウム
    • Place of Presentation
      仙台
    • Year and Date
      2010-11-25
  • [Presentation] 経験的水和分布関数を用いた水和水分子位置の評価2010

    • Author(s)
      松岳大輔, 高山裕貴, 中迫雅由
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-22
  • [Presentation] 経験的水和水分布関数を用いた蛋白質水和構造予測2010

    • Author(s)
      松岳大輔, 中迫雅由
    • Organizer
      第10回日本蛋白質科学会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-17
  • [Presentation] 蛋白質結晶湿度制御装置の開発と蛋白質運動性制御への応用2010

    • Author(s)
      高山裕貴, 中迫雅由
    • Organizer
      第10回日本蛋白質科学会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-17
  • [Book] 『タンパク質結晶の最前線』経験的水和分布関数の構築と蛋白質水和構造予測への応用2013

    • Author(s)
      松岳大輔, 中迫雅由
    • Total Pages
      221-229
    • Publisher
      シーエムシー出版
  • [Book] 『標準免疫学第三版』第二部, 構成的メカニズム:認識のメカニズム, F.BCR/抗体による認識2013

    • Author(s)
      中迫雅由
    • Total Pages
      107-114
    • Publisher
      医学書院
  • [Remarks]

    • URL

      http://www.phys.keio.ac.jp/guidance/labs/nakasako/nakasako-lab.html

URL: 

Published: 2015-06-25  

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