Basic Information

Affiliated programs (koza)

• Graduate School of Science, 物理学・宇宙物理学（物理学第一分野）専攻 核物性学講座, 助教

Email Address

• Email Address

  shimizu.masahiro.3nkyoto-u.ac.jp

Academic Degree

• 23 Mar. 2015

  京都大学修士（理学）
• 26 Mar. 2018

  京都大学博士（理学）

Academic Resume (Undergraduate School/Majors)

• 慶應義塾大学, 理工学部化学科, 卒業

Research History

• From Dec. 2024, To Feb. 2025

  Stanford University, visiting assistant professor
• From Sep. 2023, To Present

  Kyoto University, Institute for Integrated Radiation and Nuclear Science, 助教
• From Apr. 2023, To Aug. 2023

  Kyoto University, Institute for Integrated Radiation and Nuclear Science, 特任助教
• From Apr. 2020, To Aug. 2023

  Kyoto University, Institute for Integrated Radiation and Nuclear Science, Postdoctoral researcher
• From Apr. 2018, To Mar. 2020

  Kanazawa University, Institute for Frontier Science Initiative, Postdoctoral researcher

ID,URL

• J-Global ID

  201901014010270576

researchmap URL

• https://researchmap.jp/r76ll9

Research

Research Areas

• Life sciences, Biophysics

Papers

• Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux

  Ken Morishima; Rintaro Inoue; Tatsuo Nakagawa; Masahiro Shimizu; Ritsuki Sakamoto; Tatsuro Oda; Koichi Mayumi; Masaaki Sugiyama

  Journal of Applied Crystallography, 11 Feb. 2025

  
• Ensemble Modeling of Biomolecules by Small-angle X-ray Scattering and Coarse-grained Molecular Dynamics Simulation

  Masahiro SHIMIZU; Masaaki SUGIYAMA

  Seibutsu Butsuri, Jul. 2024, Peer-reviewed, Lead author

  
• Asymmetric fluctuation of overlapping dinucleosome studied by cryo-electron microscopy and small-angle X-ray scattering

  Masahiro Shimizu; Hiroki Tanaka; Masahiro Nishimura; Nobuhiro Sato; Kayo Nozawa; Haruhiko Ehara; Shun-ichi Sekine; Ken Morishima; Rintaro Inoue; Yoshimasa Takizawa; Hitoshi Kurumizaka; Masaaki Sugiyama

  PNAS Nexus, 27 Oct. 2024, Peer-reviewed, Lead author

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• Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties

  Masahiro Nishimura; Takeru Fujii; Hiroki Tanaka; Kazumitsu Maehara; Ken Morishima; Masahiro Shimizu; Yuki Kobayashi; Kayo Nozawa; Yoshimasa Takizawa; Masaaki Sugiyama; Yasuyuki Ohkawa; Hitoshi Kurumizaka

  Communications Biology, 08 Jan. 2024

  
• Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy

  Akihito Nishiyama; Masahiro Shimizu; Tomoyuki Narita; Noriyuki Kodera; Yuriko Ozeki; Akira Yokoyama; Kouta Mayanagi; Takehiro Yamaguchi; Mariko Hakamata; Amina Kaboso Shaban; Yoshitaka Tateishi; Kosuke Ito; Sohkichi Matsumoto

  Nucleic Acids Research, 04 Dec. 2023, Peer-reviewed

  
• Efficient Multiple Domain Ligation for Proteins using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance

  Aya Okuda; Masahiro Shimizu; Rintaro Inoue; Reiko Urade; Masaaki Sugiyama

  Angewandte Chemie International Edition, 08 Nov. 2022, Peer-reviewed, Lead author

  
• Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations

  Masahiro Shimizu; Aya Okuda; Ken Morishima; Rintaro Inoue; Nobuhiro Sato; Yasuhiro Yunoki; Reiko Urade; Masaaki Sugiyama

  Scientific Reports, Jun. 2022, Peer-reviewed, Lead author, Corresponding author

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• Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach.

  Yasuhiro Yunoki; Atsushi Matsumoto; Ken Morishima; Anne Martel; Lionel Porcar; Nobuhiro Sato; Rina Yogo; Taiki Tominaga; Rintaro Inoue; Maho Yagi-Utsumi; Aya Okuda; Masahiro Shimizu; Reiko Urade; Kazuki Terauchi; Hidetoshi Kono; Hirokazu Yagi; Koichi Kato; Masaaki Sugiyama

  Communications biology, 10 Mar. 2022, Peer-reviewed

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• An ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz for high-speed atomic force microscopy

  Masahiro Shimizu; Chihiro Okamoto; Kenichi Umeda; Shinji Watanabe; Toshio Ando; Noriyuki Kodera

  Review of Scientific Instruments, 01 Jan. 2022, Peer-reviewed, Lead author

  
• Elucidation of the mechanism of subunit exchange in αB crystallin oligomers

  Rintaro Inoue; Yusuke Sakamaki; Takumi Takata; Kathleen Wood; Ken Morishima; Nobuhiro Sato; Aya Okuda; Masahiro Shimizu; Reiko Urade; Noriko Fujii; Masaaki Sugiyama

  Scientific Reports, Dec. 2021, Peer-reviewed

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• Architecture of zero-latency ultrafast amplitude detector for high-speed atomic force microscopy

  Kenichi Umeda; Chihiro Okamoto; Masahiro Shimizu; Shinji Watanabe; Toshio Ando; Noriyuki Kodera

  Applied Physics Letters, 01 Nov. 2021, Peer-reviewed

  
• Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation

  Aya Okuda; Masahiro Shimizu; Ken Morishima; Rintaro Inoue; Nobuhiro Sato; Reiko Urade; Masaaki Sugiyama

  Scientific Reports, Mar. 2021, Peer-reviewed, Lead author

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• Deuteration Aiming for Neutron Scattering

  Aya Okuda; Rintaro Inoue; Ken Morishima; Tomohide Saio; Yasuhiro Yunoki; Maho Yagi-Utsumi; Hirokazu Yagi; Masahiro Shimizu; Nobuhiro Sato; Reiko Urade; Koichi Kato; Masaaki Sugiyama

  Biophysics and Physicobiology, 2021, Peer-reviewed

  
• Dynamics of proteins with different molecular structures under solution condition

  Rintaro Inoue; Takashi Oda; Hiroshi Nakagawa; Taiki Tominaga; Tomohide Saio; Yukinobu Kawakita; Masahiro Shimizu; Aya Okuda; Ken Morishima; Nobuhiro Sato; Reiko Urade; Mamoru Sato; Masaaki Sugiyama

  Scientific Reports, Dec. 2020, Peer-reviewed

  
• Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays

  Shuhei Watanabe; Yuichi Mishima; Masahiro Shimizu; Isao Suetake; Shoji Takada

  Biophysical Journal, Apr. 2018, Peer-reviewed

  
• Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes

  Masahiro Shimizu; Shoji Takada

  Journal of Chemical Theory and Computation, Feb. 2018, Peer-reviewed, Lead author

  
• Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights

  Masahiro Shimizu; Yasunori Noguchi; Yukari Sakiyama; Hironori Kawakami; Tsutomu Katayama; Shoji Takada

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Dec. 2016, Peer-reviewed, Lead author

  

Misc.

• Overall structure of the fully assembled KaiABC complex in cyanobacterial circadian system analyzed by an integrated solution scattering-computational approach

  柚木康弘; 松本淳; 守島健; MARTEL Anne; PORCAR Lionel; 佐藤信浩; 與語理那; 與語理那; 與語理那; 富永大輝; 井上倫太郎; 矢木真穂; 矢木真穂; 矢木真穂; 奥田綾; 清水将裕; 裏出令子; 寺内一姫; 河野秀俊; 矢木宏和; 矢木宏和; 加藤晃一; 加藤晃一; 加藤晃一; 杉山正明

  時間生物学, 2022

  
• 低酸素環境と疾患(がん、感染症)の分子論 低酸素休眠抗酸菌の主要タンパク質Mycobacterial DNA-binding protein 1(My cobacterial DNA-binding protein 1, a major protein in hypoxic dormant mycobacteria)

  西山 晃史; 古寺 哲幸; 清水 将裕; Savitskaya Anna; Enany Shymaa; 真柳 浩太; 山口 雄大; 尾関 百合子; 立石 善隆; 松本 壮吉

  日本細菌学雑誌, Feb. 2021

  

Presentations

• Solution scattering towards details in flexibility of intrinsically disordered proteins

  Masahiro Shimizu; Ken Morishima; Aya Okuda; Rintaro Inoue; Akihito Nishiyama; Sohkichi Matsumoto; Masaaki Sugiyama

  The 61st Annual Meeting of the Biophysical Society of Japan, 16 Nov. 2023, Invited

  
• Analysis of multi-domain protein ER-60 studied by molecular dynamics simulations

  Masahiro Shimizu; Aya Okuda; Rintaro Inoue; Reiko Urade; Masaaki Sugiyama

  日本中性子科学会第23回年会, 13 Sep. 2023

  
• Computational prediction of protein ligation reaction efficiency

  Masahiro Shimizu; Aya Okuda; Rintaro Inoue; Reiko Urade; Masaaki Sugiyama

  The 23rd Annual Meeting of the Protein Science Society of Japan, 05 Jul. 2023

  
• Structural study on four domain protein ER-60 with small angle X-ray scattering profile and coarse-grained molecular dynamics simulations

  Masahiro Shimizu; Aya Okuda; Ken Morishima; Yasuhiro Yunoki; Rintaro Inoue; Nobuhiro Sato; Reiko Urade; Masaaki Sugiyama

  The 22nd Annual Meeting of the Protein Science Society of Japan, 08 Jun. 2022

  
• Modeling structural dynamics of biomolecules using small angle X-ray scattering data and coarse-grained molecular dynamics simulations

  Masahiro Shimizu; Aya Okuda; Ken Morishima; Yasuhiro Yunoki; Nobuhiro Sato; Rintaro Inoue; Reiko Urade; Masaaki Sugiyama

  The 59th Annual Meeting of the Biophysical Society of Japan, 26 Nov. 2021, Invited

  
• 細胞表面動態の高精度計測を目指した高速原子間力顕微鏡装置の開発

  清水将裕; 岡本千優; 今井大達; 渡辺信嗣; 安藤敏夫; 古寺哲幸

  第57回日本生物物理学会年会, 24 Sep. 2019, Invited

  
• Visualization of biomolecules by applying solution scattering data to molecular dynamics simulations

  Masahiro Shimizu

  Mariage of computational and experimental techniques for solution small-angle scattering, 13 Sep. 2019, Invited

  
• Structural dynamics of the intrinsically disordered protein CAMP revealed by high-speed AFM

  Tomoyuki Narita; Masanori Ikeda; Masahiro Shimizu; Kozo Tanaka; Noriyuki Kodera

  The 56th Annual Meeting of the Biophysical Society of Japan, 15 Sep. 2018

  
• Development of a method for analyzing high-speed AFM observations by coarse-grained molecular dynamics simulation

  Masahiro Shimizu; Tomoyuki Narita; Ikumi Muro; Hiroki Konno; Noriyuki Kodera

  The 56th Annual Meeting of The Biophysical Society of Japan, 15 Sep. 2018

  
• タンパク質DNA複合体のマルチスケールモデリング; 粗視化モデルから原子モデル構造の構築

  清水将裕; 高田彰二

  第10回分子科学討論会, 14 Sep. 2016

  
• バクテリアのDNA複製開始複合体の構造モデリングとその機能解析

  清水将裕; 野口泰徳; 崎山友香里; 川上広宜; 片山勉; 高田彰二

  第17回日本蛋白質科学会年会, 21 Jun. 2016, Invited

  
• 構成論的アプローチによる生体内銅イオン輸送の制御機構解明

  清水将裕; 古川良明

  日本化学会第93春季年会, 23 Mar. 2013

  

Industrial Property Rights

• 特許7273408, 特開2021-004859, 特願2019-120245, 走査型プローブ顕微鏡およびＺ駆動装置

  古寺哲幸; 清水将裕; 安藤敏夫

  

Awards

• 27 Nov. 2016

  学生発表賞（日本生物物理学会）
• 21 Jun. 2017

  若手奨励賞（日本蛋白質科学会）

Education

Teaching subject(s)

• From 2024, To 2024

  Research Ethics and Integrity(Science and Technology)

  Spring, 大学院共通, 0.5
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Macromolecular Structure C

  2065, Spring, Graduate School of Science, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Macromolecular Structure B

  2064, Fall, Graduate School of Science, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Macromolecular Structure A

  2063, Spring, Graduate School of Science, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Macromolecular Structure D

  2066, Fall, Graduate School of Science, 2

Administration

Faculty management (title, position)

• From 01 Jun. 2022

  量子ビーム生体高分子統合研究センター センター員