Nakasako, Masayoshi

写真a

Affiliation

Faculty of Science and Technology, Department of Physics (Yagami)

Position

Professor

External Links

Career 【 Display / hide

  • 1990.04
    -
    1993.12

    東京大学 薬学部 薬品物理分析研究室 助手

  • 1994.01
    -
    1997.05

    理化学研究所 生物物理研究室 研究員

  • 1996.04
    -
    1997.03

    東京大学 分子細胞生物学研究所 蛋白質解析分野 非常勤講師

  • 1996.10
    -
    1999.09

    科学技術振興事業団さきがけ研究21場と反応領域 兼務研究員

  • 1997.06
    -
    2001.03

    理化学研究所 和光研究所 協力研究員

display all >>

Academic Background 【 Display / hide

  • 1984.03

    Shizuoka University, Faculty of Science, 物理学科

    University, Graduated

  • 1987.03

    Tohoku University, Graduate School, Division of Natural Science, 物理学第二専攻

    Graduate School, Completed, Master's course

  • 1990.03

    Tohoku University, Graduate School, Division of Natural Science, 物理学第二専攻

    Graduate School, Other, Doctoral course

Academic Degrees 【 Display / hide

  • 理学, Tohoku University, 1990.04

Matters concerning Career Achievements 【 Display / hide

  • 2006.04
    -
    Present

    2006年度 理工学部RI取扱従事者教育訓練 講義資料

  • 2010.04

    2010年度 理工学部RI取扱従事者教育訓練 講義資料

 

Research Areas 【 Display / hide

  • Natural Science / Biophysics, chemical physics and soft matter physics (X-ray nano imaging)

Research Keywords 【 Display / hide

  • Analyses of hydration structures of proteins

  • Coherent X-ray diffraction imaging

  • protein crystallography at cryogenic temperature

  • Structure analyses of non-crystalline particles

Research Themes 【 Display / hide

  • hydration of protein molecules, 

    1995
    -
    Present

  • X線自由電子レーザーのバイオサイエンス分野での利用技術開発, 

    2006
    -
    Present

  • Utilization of Synchrotron radiation, 

    1985
    -
    Present

  • Protein structure analyses, 

    1991
    -
    Present

 

Books 【 Display / hide

  • Hydration Structures of Proteins -Atomic Details-

    Masayoshi Nakasako, Springer-Nature, 2021.10,  Page: 309

    , Accepted

  • X-ray diffraction imaging of biological cells (Springer Ser. Optic. Sciences Vol.210)

    Nakasako Masayoshi, Springer Nature, 2018.05

    Scope: all contents , Accepted

  • Coherent X-ray DIFFRACTION IMAGINg of Cyanidioschyzon merolae

    Sekiguchi Y., Kobayashi A., Takayama Y., Oide M., Fukuda A., Yamamoto T., Okajima K., Oroguchi T., Hirakawa T., Inui Y., Matsunaga S., Yamamoto M., Nakasako M., Cyanidioschyzon merolae: A New Model Eukaryote for Cell and Organelle Biology, 2018.03

     View Summary

    Coherent X-ray diffraction imaging (CXDI) is a lensless imaging technique for visualizing the structures of noncrystalline particles at a resolution of several tens of nanometers. The targets are particles with dimensions in the sub-micrometer to micrometer range. We carried out CXDI experiments at 66 K to investigate the internal structures of a whole frozen-hydrated cell and a chloroplast of Cyanidioschyzon merolae and a cyanobacteria cell by using coherent X-ray light sources, such as synchrotron and X-ray free-electron laser facilities. Owing to the short wavelength of the X-rays used (0.225 nm), the absorption and multiple scattering of X-rays inside the specimens were negligible. Diffraction patterns from each specimen particle adsorbed onto a thin membrane were collected at resolutions better than 50 μm -1 in reciprocal space. Therefore, structures of specimen particles can be illustrated at a resolution higher than 200 nm in real space. The most probable electron density map was retrieved from each diffraction pattern. Theinternal structures of the specimens are described here, particularly the structural correlation of the chloroplast of C. merolae and the cyanobacteria cell. Based on the experimental results, we discuss the feasibility of CXDI in the structural analyses of biological cells and cellular organelles.

  • 'Coherent X-ray diffraction imaging of Cyanidioschyzon merolae' in Cyanidioschyzon merolae: A New Model Eukaryote for Cell and Organelle Biology

    Yuki Sekiguchi, Amane Kobayashi, Yuki Takayama, Mao Oide, Asahi Fukuda, Takahiro Yamamoto, Koji Okajima, Tomotaka Oroguchi, Takeshi Hirakawa, Yayoi Inui, Sachihiro Matsunaga Masaki Yamamoto and Masayoshi Nakasako, Springer Nature, 2018.02

    Scope: Chapter 10

  • タンパク質結晶の最前線

    松岳大輔、中迫雅由, 2013.12

    Scope: 221-229

display all >>

Papers 【 Display / hide

  • Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging

    Syouyo Yoshida Kosei Harada So Uezu, Yuki Takayama and Masayoshi Nakasako

    Journal of Synchrotron Radiation (Wiley & Sons)  31   113 - 128 2023.11

    Research paper (scientific journal), Joint Work, Corresponding author, Accepted

  • Similarity score for screening phase-retrieved maps in X-ray diffraction imaging – characterization in reciprocal space

    Yuki Takayama and Masayoshi Nakasako

    Journal of Synchrotron Radiation (Wiley & Sons)  31   95 - 112 2023.11

    Research paper (scientific journal), Joint Work, Corresponding author, Accepted

  • Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy

    Taiki Wakabayashi, Mao Oide, Takayuki Kato and Masayoshi Nakasako

    The FEBS Journal (Wiley & Sons)  290   5514 - 5535 2023.09

    Research paper (scientific journal), Corresponding author, Accepted

  • Ultrastructure and fractal property of chromosomes in close‑to‑native yeast nuclei visualized using X‑ray laser diffraction

    So Uezu, TakahiroYamamoto, Mao Oide, YukiTakayama, Koji Okajima, Amane Kobayashi, Masaki Yamamoto, Masayoshi Nakasako

    Scientifc Reports (Springer-Nature)  13   10802(1) - 10802(14) 2023.07

    Research paper (scientific journal), Joint Work, Corresponding author, Accepted

  • Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data

    Kochi Sato, Mao Oide, Masayoshi Nakasako

    Scientifc Reports | (Springer-Nature)  13   2183 (1-15) 2023.02

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

display all >>

Papers, etc., Registered in KOARA 【 Display / hide

Reviews, Commentaries, etc. 【 Display / hide

  • KOTOBUKI-1 apparatus for cryogenic X-ray diffraction imaging

    M. Nakasako, M. Yamamoto

    SPring-8 Research Frontiers 2014    128-129 2015.08

    Rapid communication, short report, research note, etc. (bulletin of university, research institution), Joint Work

  • Blue light-induced conformational chanes in Chlamydomonas phototropin

    K. Okajima M. Nakasako

    SPring-8 Research Frontiers 2014    32-33 2015.08

    Rapid communication, short report, research note, etc. (bulletin of university, research institution), Joint Work

  • Crystal Structure of LOV1 Domains in Arabidopsis Phototropin 1 and 2

    M. Nakasako & S. Tokutomi

    SPring-8 Research Frontiers 2008    32-33 2009.07

    Rapid communication, short report, research note, etc. (bulletin of university, research institution), Joint Work

Presentations 【 Display / hide

  • 低温X線回折イメージング・トモグラフィーを用いた非結晶粒子の三次元構造解析の現状と将来展望

    原田康生、吉田翔庸、高山裕貴、中迫雅由

    第37回 日本放射光学会年会, 

    2024.01

    Poster presentation

  • X線回折イメージングの像回復効率化プロトコルの開発

    吉田翔庸、原田康生、上江洲奏、高山裕貴、中迫雅由

    第37回 日本放射光学会年会, 

    2024.01

    Poster presentation

  • Prediction of hydration structures over membrane proteins using deep learning in combination with the empirical hydration distribution

    Kochi Sato, Mao Oide and Masayoshi Nakasako

    第61回 日本生物物理学会年会 (名古屋) , 

    2023.11

    Oral presentation (general)

  • Conformational and ligand-association dynamics of glutamate dehydrogenase in the mixture with ligands visualized by cryo-EM

    Taiki Wakabayashi, Mao Oide and Masayoshi Nakasako

    第61回 日本生物物理学会年会 (名古屋) , 

    2023.11

    Oral presentation (general)

  • コヒーレントX線回折イメージングCDIの概要

    中迫雅由

    令和5年度 日本結晶学会年会 シンポジウム コヒーレントX線回折イメージングによる構造解析の現状と展望, 

    2023.10

    Oral presentation (invited, special)

display all >>

Research Projects of Competitive Funds, etc. 【 Display / hide

  • クライオ電顕画像から蛋白質の動的構造を描写するための新規計算科学手法の確立と応用

    2021.04
    -
    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Principal investigator

  • 蛋白質機能を駆動する水和構造の時空間階層イメージング

    2017.04
    -
    2019.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas, Principal investigator

  • コヒーレントX線回折による酵母核内の核酸分布イメージング

    2016.04
    -
    2017.03

    Grant-in-Aid for Scientific Research, Research grant, No Setting

  • 時間分解蛍光測定を軸とする蛋白質水和と機能発現の相関解析

    2016.04
    -
    2017.03

    Grant-in-Aid for Scientific Research, Research grant, Principal investigator

  • SACLAにおける低温X線回折イメージング実験の展開と標準化

    2016.04
    -
    2017.03

    JSTキーテクノロジー, Commissioned research, Principal investigator

display all >>

Works 【 Display / hide

display all >>

Intellectual Property Rights, etc. 【 Display / hide

  • 冷却装置及びX線装置

    Date applied: 特開2002-357381  2002.12 

    Date announced: 特開2002-357381  2002.12 

    Patent, Joint

  • 光代謝制御

    Date applied: 特許第3491669号  2001.03 

    Date issued: 特許第3491669号  2004.11

    Patent, Joint

  • X線分析用試料マウント具

    Date applied: 特許第3439571号   

    Date announced: 特別公開№338818   

    Date issued: 特許第3439571号  2003.06

    Patent, Joint

 

Courses Taught 【 Display / hide

  • INDEPENDENT STUDY ON FUNDAMENTAL SCIENCE AND TECHNOLOGY

    2023

  • GRADUATE RESEARCH ON FUNDAMENTAL SCIENCE AND TECHNOLOGY 2

    2023

  • GRADUATE RESEARCH ON FUNDAMENTAL SCIENCE AND TECHNOLOGY 1

    2023

  • ELECTRICITY AND MAGNETISM 2

    2023

  • BIOPHYSICS

    2023

display all >>

Courses Previously Taught 【 Display / hide

  • 自然科学実験

    理工学部

    2018.04
    -
    2019.03

  • 物理学実験第一(ブラウン運動)

    理工学部

    2018.04
    -
    2019.03

  • 生物物理学特論

    理工学研究科

    2018.04
    -
    2019.03

  • 生物物理学

    理工学部

    2018.04
    -
    2019.03

  • 電磁気学第二

    理工学部

    2018.04
    -
    2019.03

display all >>

 

Social Activities 【 Display / hide

  • 理化学研究所 播磨研究所 放射光科学総合研究センター 研究グループ最終評価委員会

    2013.02
    -
    2013.03
  • 理化学研究所 独立主幹最終評価委員会

    2013.02
    -
    2013.03
  • 新学術領域研究専門委員会(3102_天然変性蛋白質)

    2011.12
    -
    2012.03
  • 理化学研究所 独立主幹中間評価委員会

    2011.10
    -
    2011.12
  • 特定放射光施設検討委員会

    2011.09
    -
    Present

display all >>

Memberships in Academic Societies 【 Display / hide

  • 4-th Japan-France Joint Seminar, 

    2012.04
    -
    2013.03
  • 放射光学サイエンス将来計画特別委員会, 

    2010.07
    -
    2011.03
  • 日本生物物理学会, 

    2009.10
    -
    2011.09
  • 財団法人 新世代研究所 水和ナノ構造研究会, 

    2009.04
    -
    2012.03
  • 第4回日本放射光学会若手ワークショップ ―次世代放射光源を用いた生命科学未踏領域への挑戦―組織委員会, 

    2007.05
    -
    2007.08

display all >>

Committee Experiences 【 Display / hide

  • 2013.02
    -
    2013.03

    委員, 理化学研究所 播磨研究所 放射光科学総合研究センター 研究グループ最終評価委員会

  • 2013.02
    -
    2013.03

    委員, 理化学研究所 独立主幹最終評価委員会

  • 2013.02
    -
    2013.03

    Committee Member, 理化学研究所 播磨研究所 放射光科学総合研究センター 研究グループ最終評価委員会

  • 2013.02
    -
    2013.03

    Committee Member, 理化学研究所 独立主幹最終評価委員会

  • 2012.04
    -
    2013.03

    organizer, 4-th Japan-France Joint Seminar

display all >>