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

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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

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

  • Biological physics/Chemical physics/Soft matter physics (X-ray nano imaging)

  • Biological physics/Chemical physics/Soft matter physics (hydration of biomolecules)

  • Biological physics/Chemical physics/Soft matter physics (Protein Crystallography)

  • Biological physics/Chemical physics/Soft matter physics (Biophysics)

  • Biological physics/Chemical physics/Soft matter physics (Synchrotron radiation)

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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

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

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

    Nakasako Masayoshi, Springer Nature, 2018.05

    Scope: all contents

  • 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

  • Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free-electron laser

    A. Kobayashi, Y. Takayama, T. Hirakawa, K. Okajima, M. Oide, T. Oroguchi, Y. Inui, M. Yamamoto, S. Matsunaga and M. Nakasako

    Scientific Reports (Springer-Nature)  in press ( 1 ) in press 2021.02

    Research paper (scientific journal), Joint Work, Accepted

     View Summary

    Visualization of intracellular structures and their spatial organization inside cells without any modification is essential to understand the mechanisms underlying the biological functions of cells. Here, we investigated the intracellular structure of cyanobacteria Prochlorococcus in the interphase by X-ray diffraction imaging using X-ray free-electron laser. A number of diffraction patterns from single cells smaller than 1 µm in size were collected with high signal-to-noise ratio with a resolution of up to 30 nm. From diffraction patterns, a set of electron density maps projected along the direction of the incident X-ray were retrieved with high reliability. The most characteristic structure found to be common among the cells was a C-shaped arrangement of 100-nm sized high-density spots, which surrounded a low-density area of 100 nm. Furthermore, a three-dimensional map reconstructed from the projection maps of individual cells was non-uniform, indicating the presence of common structures among cyanobacteria cells in the interphase. By referring to the fluorescent images for distributions of thylakoid membranes, nucleoids, and carboxysomes, we inferred and represented their spatial arrangements in the three-dimensional map. The arrangement allowed us to discuss the relevance of the intracellular organization to the biological functions of cyanobacteria.

  • Red light‑induced structure changes in phytochrome A from Pisum sativum

    Mao Oide and Masayoshi Nakasako

    Scientific Reports (Springer-Nature)  11 ( 1 ) 2827(1) - 2827(11) 2021.02

    Research paper (scientific journal), Joint Work, Accepted

     View Summary

    Phytochrome A (phyA) is a photoreceptor protein of plants that regulates the red/far-red light photomorphogenic responses of plants essential for growth and development. PhyA, composed of approximately 1100 amino acid residues, folds into photosensory and output signaling modules. The photosensory module covalently binds phytochromobilin as a chromophore for photoreversible interconversion between inactive red light-absorbing (Pr) and active far-red light-absorbing (Pfr) forms to act as a light-driven phosphorylation enzyme. To understand the molecular mechanism in the initial process of photomorphogenic response, we studied the molecular structures of large phyA (LphyA) from Pisum sativum, which lacks the 52 residues in the N-terminal, by small-angle X-ray scattering combined with multivariate analyses applied to molecular models predicted from the scattering profiles. According to our analyses, Pr was in a dimer and had a four-leaf shape, and the subunit was approximated as a bent rod of 175 × 50 Å. The scattering profile of Pfr was calculated from that recorded for a mixture of Pr and Pfr under red-light irradiation by using their population determined from the absorption spectrum. The Pfr dimer exhibited a butterfly shape composed of subunits with a straight rod of 175 × 50 Å. The shape differences between Pr and Pfr indicated conformational changes in the Pr/Pfr interconversion which would be essential to the interaction with protein molecules involved in transcriptional control.

  • Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data of Hyper-thermostable Glutamate Dehydrogenase

    Oroguchi T., Oide M., Wakabayashi T., Nakasako M.

    Journal of Physical Chemistry B (Journal of Physical Chemistry B)  124 ( 39 ) 8479 - 8494 2020.10

    ISSN  15206106

     View Summary

    © 2020 American Chemical Society. Molecular dynamics (MD) simulations in biophysically relevant time scales of microseconds is a powerful tool for studying biomolecular processes, but results often display force field dependency. Therefore, assessment of force field accuracy using experimental data of biomolecules in solution is essential for simulation studies. Here, we propose the use of structural models obtained via cryo-electron microscopy (cryoEM), which provides biomolecular structures in vitreous ice mimicking the environment in solution. The accuracy of the AMBER (ff99SB-ILDN-NMR, ff14SB, ff15ipq, and ff15FB) and CHARMM (CHARMM22 and CHARMM36m) force fields was assessed by comparing their MD trajectories with the cryoEM data of thermostable hexameric glutamate dehydrogenase (GDH), which included a cryoEM map at a resolution of approximately 3 Å and structure models of subunits reflecting metastable conformations in domain motion occurring in GDH. In the assessment, we validated the force fields with respect to the reproducibility and stability of secondary structures and intersubunit interactions in the cryoEM data. Furthermore, we evaluated the force fields regarding the reproducibility of the energy landscape in the domain motion expected from the cryoEM data. As a result, among the six force fields, ff15FB and ff99SB-ILDN-NMR displayed good agreement with the experiment. The present study demonstrated the advantages of the high-resolution cryoEM map and suggested the optimal force field to reproduce experimentally observed protein structures.

  • Domain organization in plant blue-light receptor phototropin2 of arabidopsis thaliana studied by small-angle x-ray scattering

    Nakasako M., Oide M., Takayama Y., Oroguchi T., Okajima K.

    International Journal of Molecular Sciences (International Journal of Molecular Sciences)  21 ( 18 ) 6638(1) - 6638(21) 2020.09

    ISSN  16616596

     View Summary

    © 2020 by the authors. Licensee MDPI, Basel, Switzerland. Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.

  • Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy

    Oide M., Kato T., Oroguchi T., Nakasako M.

    FEBS Journal (FEBS Journal)  287 ( 16 ) 3472 - 3493 2020.08

    ISSN  1742464X

     View Summary

    © 2020 Federation of European Biochemical Societies Analysis of the conformational changes of protein is important to elucidate the mechanisms of protein motions correlating with their function. Here, we studied the spontaneous domain motion of unliganded glutamate dehydrogenase from Thermococcus profundus using cryo-electron microscopy and proposed a novel method to construct free-energy landscape of protein conformations. Each subunit of the homo-hexameric enzyme comprises nucleotide-binding domain (NAD domain) and hexamer-forming core domain. A large active-site cleft is situated between the two domains and varies from open to close according to the motion of a NAD domain. A three-dimensional map reconstructed from all cryo-electron microscopy images displayed disordered volumes of NAD domains, suggesting that NAD domains in the collected images adopted various conformations in domain motion. Focused classifications on NAD domain of subunits provided several maps of possible conformations in domain motion. To deduce what kinds of conformations appeared in EM images, we developed a novel analysis method that describe the EM maps as a linear combination of representative conformations appearing in a 200-ns molecular dynamics simulation as reference. The analysis enabled us to estimate the appearance frequencies of the representative conformations, which illustrated a free-energy landscape in domain motion. In the open/close domain motion, two free-energy basins hindered the direct transformation from open to closed state. Structure models constructed for representative EM maps in classifications demonstrated the correlation between the energy landscape and conformations in domain motion. Based on the results, the domain motion in glutamate dehydrogenase and the analysis method to visualize conformational changes and free-energy landscape were discussed. Database: The EM maps of the four conformations were deposited to Electron Microscopy Data Bank (EMDB) as accession codes EMD-9845 (open), EMD-9846 (half-open1), EMD-9847 (half-open2), and EMD-9848 (closed), respectively. In addition, the structural models built for the four conformations were deposited to the Protein Data Bank (PDB) as accession codes 6JN9 (open), 6JNA (half-open1), 6JNC (half-open2), and 6JND (closed), respectively.

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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

    Prompt report, short report, and 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

    Prompt report, short report, and 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

    Prompt report, short report, and research note, etc. (bulletin of university, research institution), Joint Work

Presentations 【 Display / hide

  • X-ray diffraction imaging study on the distribution and fractal dimensions of chromosomes in yeast nuclei in G1 phase

    So Uezu, Mao Oide, Takahiro Yamamoto, Masayoshi Nakasako

    第59回日本生物物理学会年会, 2021.11, Oral Presentation(general)

  • Red-light induced structural changes in plant photoreceptor protein phytochrome A

    Mao Oide, Masayoshi Nakasako

    第59回日本生物物理学会年会, 2021.11, Oral Presentation(general)

  • Search for binding pathway of co-enzyme around the active-site cleft of glutamate dehydrogenase

    Taiki Wakabayashi, Mao Oide, Takayuki Kato, Masayoshi Nakasako

    第59回日本生物物理学会年会, 2021.11, Oral Presentation(general)

  • Prediction of hydration structures of proteins by using machine learning

    Kochi Sato, Mao Oide, Masayoshi Nakasako

    第59回日本生物物理学会年会, 2021.11, Oral Presentation(general)

  • Red-light induced structural changes in plant photoreceptor protein phytochrome A

    Mao Oide, Masayoshi Nakasako

    第20回日本蛋白質科学会年会, 2021.06, Poster (general)

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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
    -
    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, 中迫 雅由, 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, 中迫 雅由, 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

  • 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

  • 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
    -
    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

  • SACLAにより銅キューブ粒子の内部構造を可視化

    中迫雅由

    FUJI SANKEI BUSINESS i. Science View, 

    2018.09
    -
    Present

    Other

  • 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(上) 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. 842 2018年8月号, 

    2018.08
    -
    Present

    Other, Single

  • 内部構造に大きな偏り-金属ナノ粒子

    中迫雅由、苙口友隆、吉留崇、山本隆寛

    化学工業日報 朝刊 4面, 

    2018.08
    -
    Present

    Other, Joint

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Intellectual Property Rights, etc. 【 Display / hide

  • 冷却装置及びX線装置

    Application No.: 特開2002-357381  2002.12 

    Announcement No.: 特開2002-357381  2002.12 

    Patent, Joint, National application

  • 光代謝制御

    Application No.: 特許第3491669号  2001.03 

    Registration No.: 特許第3491669号  2004.11

    Patent, Joint, National application

  • X線分析用試料マウント具

    Application No.: 特許第3439571号   

    Announcement No.: 特別公開№338818   

    Registration No.: 特許第3439571号  2003.06

    Patent, Joint, National application

 

Courses Taught 【 Display / hide

  • PHYSICS SEMINAR 1

    2021

  • PHYSICS LABORATORIES 2

    2021

  • PHYSICS LABORATORIES 1

    2021

  • LITERATURE OF PHYSICS

    2021

  • LABORATORY IN SCIENCE

    2021

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Courses Previously Taught 【 Display / hide

  • 自然科学実験

    理工学部, 2018

  • 物理学実験第一(ブラウン運動)

    理工学部, 2018

  • 生物物理学特論

    理工学研究科, 2018

  • 生物物理学

    理工学部, 2018

  • 電磁気学第二

    理工学部, 2018

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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

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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

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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

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