Details of a Researcher - Nakasako, Masayoshi

Nakasako, Masayoshi

写真a

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

Position: Professor

External Links

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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

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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

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Academic Degrees 【 Display / hide 】

理学, Tohoku University, 1990.04

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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

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Research Areas 【 Display / hide 】

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

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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

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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

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Present

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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

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Papers 【 Display / hide 】

CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

Taiki Wakabayashi, Mao Oide and Masayoshi Nakasako

Scientific Reports （Springer-Nature) 14 11165(1) - 11165(16) 2024.05

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted
- Access to Document (DOI)
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
- Access to Document (DOI)
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
- Access to Document (DOI)
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
- Access to Document (DOI)
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
- Access to Document (DOI)

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

Structural study of red/far-red-light receptor protein phytochrome B by using cryo-electron microscopy

Nakasako, Masayoshi

学事振興資金研究成果実績報告書（慶應義塾大学) 2019
Visualization on the distribution of nucreic acids in yeast nucleus by using coherent X-ray diffraction

Nakasako, Masayoshi

科学研究費補助金研究成果報告書 2018
Structure analysis of non-crystalline particles with sub-micrometer dimensions using X-ray free electron laser

Nakasako, Masayoshi

科学研究費補助金研究成果報告書 2013
Study on the hydration structural changes in coupling with the internal motions of proteins using time-resolved fluorscence measurement

Nakasako, Masayoshi

科学研究費補助金研究成果報告書 2013
Studies on the correlation between the internal dynamics and hydration of proteins by X-ray crystallography for humidity-controlled protein crystals

NAKASAKO, MASAYOSHI

科学研究費補助金研究成果報告書 2008

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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

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Presentations 【 Display / hide 】

CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

Taiki Wakabayashi, Mao Oide and Masayoshi Nakasako

21st IUPAB (2024) and 62nd BSJ joint congress 2024,

2024.06
,
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

21st IUPAB (2024) and 62nd BSJ joint congress 2024,

2024.06
,
Poster presentation
X-ray diffraction imaging tomography at cryogenic temperature is powerful to reveal 3D structures of biological specimens

Kosei Harada, Yuki Takayama and Masayoshi Nakasako

21st IUPAB (2024) and 62nd BSJ joint congress 2024,

2024.06
,
Poster presentation
cryogenic X-ray ptychographic imaging of cultured cells toward visualization of hierarchical structures of chromatin

Yuta Kinami, Kurumi Nishigami, Kosei Harada, Masayoshi Nakasako, Yukako Oma, Masahiko Harata and Yuki Takayama

21st IUPAB (2024) and 62nd BSJ joint congress 2024,

2024.06
,
Poster presentation
Role of Trp89 in the domain motion and enzymatic activity of glutamate dehydroganase

Taiki Wakabayashi, Mao Oide, Yuka Matsui and Masayoshi Nakasako

第24回　日本蛋白質科学会年会,

2024.06
,
Poster presentation

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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

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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

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Works 【 Display / hide 】

シアノバクテリアの普遍的内部構造を可視化

中迫雅由

2021.04
,
Other, Joint
Red light-induced structure changes in phytochrome A from Pisum sativum

大出真央、中迫雅由

2021.02
,
Other, Joint
シアノバクテリアの普遍的内部構造を可視化－X線自由電子レーザー・イメージングの新しい解析方法を開拓－

中迫雅由

2021.02
,
Other, Joint
低温X線回折イメージング・トモグラフィー技術の確立－細胞丸ごと、内部構造を非侵襲的に可視化－（プレス・リリース）

中迫雅由、大出真央、山本隆寛、岡島公司、苙口友隆、他

2018.10

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Present
,
Other, Joint
科学の峰々　No.96 生命になぜ水が必要なのか？　生体タンパク質分子の構造解析で生命の根源活動に迫る（下）　中迫雅由　慶應義塾大学理工学部物理学科教授

中迫雅由

科学機器 No. 843 2018年9月号,

2018.10

-

Present
,
Other, Single

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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