Basic Information

Faculty

• Faculty of Science

Email Address

• Email Address

  ohtomo.akihiro.7rkyoto-u.ac.jp

Professional Memberships

• From Apr. 2019, To Present

  The Spectroscopical Society of Japan
• From Apr. 2018, To Present

  The Chemical Society of Japan
• From Jun. 2017, To Present

  Japan Society for Molecular Science
• From Apr. 2013, To Present

  The Biophysical Society of Japan

Academic Degree

• 25 Mar. 2014

  大阪大学修士（理学）
• 25 Sep. 2019

  大阪大学博士（理学）

Academic Resume (Graduate Schools)

• 大阪大学, 大学院理学研究科化学専攻博士後期課程, 修了
• 大阪大学, 大学院理学研究科化学専攻博士前期課程, 修了

Academic Resume (Undergraduate School/Majors)

• 大阪大学, 理学部化学科, 卒業

Research History

• From Oct. 2024, To Present

  Kyoto University, Graduate School of Science Division of Chemistry, 助教
• From May 2020, To Oct. 2024

  Institute for Molecular Science
• From Apr. 2020, To May 2020

  Japan Society for the Promotion of Science, 特別研究員PD
• From Oct. 2019, To Mar. 2020

  Japan Society for the Promotion of Science, 特別研究員PD（資格変更）
• From Apr. 2019, To Sep. 2019

  Japan Society for the Promotion of Science, 特別研究員DC2
• From Apr. 2014, To Sep. 2016

  日清食品ホールディングス株式会社, グローバル食品安全研究所

ID,URL

• ORCID ID

  0000-0001-6709-4206

• J-Global ID

  202001016497988950

• Researcher number

  30886560

researchmap URL

• https://researchmap.jp/otomoa

Research

Research Areas

• Natural sciences, Bio-, chemical, and soft-matter physics

Papers

• Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins

  Takanori Harashima; Akihiro Otomo; Ryota Iino

  Nature Communications, 16 Jan. 2025, Peer-reviewed

  
• ATP synthesis of Enterococcus hirae V-ATPase driven by sodium motive force

  Akihiro Otomo; Lucy Gao Hui Zhu; Yasuko Okuni; Mayuko Yamamoto; Ryota Iino

  27 Dec. 2024, Lead author, Corresponding author

  
• Na+-V-ATPase inhibitor curbs VRE growth and unveils Na+ pathway structure

  Kano Suzuki; Yoshiyuki Goto; Akihiro Otomo; Kouki Shimizu; Shohei Abe; Katsuhiko Moriyama; Satoshi Yasuda; Yusuke Hashimoto; Jun Kurushima; Sho Mikuriya; Fabiana L. Imai; Naruhiko Adachi; Masato Kawasaki; Yumi Sato; Satoshi Ogasawara; So Iwata; Toshiya Senda; Mitsunori Ikeguchi; Haruyoshi Tomita; Ryota Iino; Toshio Moriya; Takeshi Murata

  Nature Structural & Molecular Biology, 21 Nov. 2024, Peer-reviewed

  
• Visualizing Single V-ATPase Rotation Using Janus Nanoparticles

  Akihiro Otomo; Jared Wiemann; Swagata Bhattacharyya; Mayuko Yamamoto; Yan Yu; Ryota Iino

  Nano Letters, 11 Dec. 2024, Peer-reviewed, Lead author

  
• Unusual Vibrational Coupling of the Schiff Base in the Retinal Chromophore of Sodium Ion-Pumping Rhodopsins

  Taiki Nakamura; Yuka Shinozaki; Akihiro Otomo; Taito Urui; Misao Mizuno; Rei Abe-Yoshizumi; Manami Hashimoto; Keiichi Kojima; Yuki Sudo; Hideki Kandori; Yasuhisa Mizutani

  The Journal of Physical Chemistry B, 15 Aug. 2024, Peer-reviewed

  
• Mechanism-based design of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins

  Takanori Harashima; Akihiro Otomo; RYOTA IINO

  bioRxiv, 28 May 2024

  
• Sub-Tip-Radius Near-Field Interactions in Nano-FTIR Vibrational Spectroscopy on Single Proteins

  Jun Nishida; Akihiro Otomo; Takanori Koitaya; Akitoshi Shiotari; Taketoshi Minato; Ryota Iino; Takashi Kumagai

  Nano Letters, 09 Jan. 2024, Peer-reviewed

  
• Protein dynamics of a light-driven Na⁺ pump rhodopsin probed using a tryptophan residue near the retinal chromophore

  Akihiro Otomo; Misao Mizuno; Keiichi Inoue; Hideki Kandori; Yasuhisa Mizutani

  Biophysics and Physicobiology, 25 Feb. 2023, Peer-reviewed, Lead author

  
• Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between Vo and V1 motors.

  Akihiro Otomo; Tatsuya Iida; Yasuko Okuni; Hiroshi Ueno; Takeshi Murata; Ryota Iino

  Proceedings of the National Academy of Sciences of the United States of America, 18 Oct. 2022, Peer-reviewed, Lead author

  
• Tackle “Molecular Engine” by early-career researchers

  Akihiro Otomo; Takahiro Kosugi

  Biophysics and Physicobiology, 2022, Peer-reviewed, Lead author, Corresponding author

  
• Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates.

  Taito Urui; Misao Mizuno; Akihiro Otomo; Hideki Kandori; Yasuhisa Mizutani

  The journal of physical chemistry. B, 08 Jul. 2021, Peer-reviewed

  
• Allosteric Communication with the Retinal Chromophore upon Ion Binding in a Light-Driven Sodium Ion-Pumping Rhodopsin.

  Akihiro Otomo; Misao Mizuno; Keiichi Inoue; Hideki Kandori; Yasuhisa Mizutani

  Biochemistry, 04 Feb. 2020, Peer-reviewed, Lead author

  
• Resonance Raman Investigation of the Chromophore Structure of Heliorhodopsins.

  Akihiro Otomo; Misao Mizuno; Manish Singh; Wataru Shihoya; Keiichi Inoue; Osamu Nureki; Oded Béjà; Hideki Kandori; Yasuhisa Mizutani

  The journal of physical chemistry letters, 15 Nov. 2018, Peer-reviewed, Lead author

  
• A Study of the Dynamics of the Heme Pocket and C-helix in CooA upon CO Dissociation Using Time-Resolved Visible and UV Resonance Raman Spectroscopy.

  Akihiro Otomo; Haruto Ishikawa; Misao Mizuno; Tetsunari Kimura; Minoru Kubo; Yoshitsugu Shiro; Shigetoshi Aono; Yasuhisa Mizutani

  The journal of physical chemistry. B, 18 Aug. 2016, Peer-reviewed, Lead author

  

Misc.

• Sub-tip-radius near-field interactions in nano-FTIR vibrational spectroscopy on single protein particles

  Jun Nishida; Akihiro Otomo; Ryota Iino; Takashi Kumagai

  Enhanced Spectroscopies and Nanoimaging 2023, 03 Oct. 2023

  
• Structural changes in the heme and heme pocket upon CO dissociation of CooA observed by time-resolved resonance Raman spectroscopy

  A. Otomo; H. Ishikawa; M. Mizuno; Y. Mizutani; S. Aono

  JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, Mar. 2014

  

Presentations

• Sodium motive force-driven ATP synthesis by EhV-ATPase

  Akihiro Otomo; Lucy ZHU; Mayuko Yamamoto; Yasuko Okuni; Ryota Iino

  21st International Union for Pure and Applied Biophysics and 62nd Biophysics Society of Japan, 26 Jun. 2024, Invited

  
• Molecular Studies on Rotary V-ATPase

  日本生物物理学会北海道支部講演会, 14 Jun. 2024, Invited

  
• Conversion of ion selectivity of rotary V-ATPase

  大友章裕; Yuan-E Lee; Raymond N Burton-Smith; 山守優; 鈴木花野; 村田武士; 富井健太郎; 村田和義; 飯野亮太

  第24回日本蛋白質科学会年会, 13 Jun. 2024

  
• 腸球菌由来V-ATPaseはナトリウムイオン駆動力でATPを合成する

  大友 章裕; Lucy Gao Hui Zhu; 山本 真由子; 大国 泰子; 飯野 亮太

  2023年度 生物物理学会中部支部討論会, 19 Mar. 2024

  
• 腸球菌由来V-ATPaseはナトリウムイオン駆動力でATPを合成する

  日本生体エネルギー研究会 第49回討論会, 15 Dec. 2023

  
• １分子散乱イメージングによる回転分子モーター V-ATPaseの回転機構の解明

  第9回バイオダイナミクス研究会, 14 Dec. 2023, Invited

  
• Enterococcus hirae V-ATPase synthesizes ATP driven by the sodium motive force

  Akihiro Otomo; Lucy Zhu; Takanori Harashima; Ryota Iino

  第61回日本生物物理学会年会, 15 Nov. 2023

  
• Sodium motive force-driven ATP synthesis of EhV-ATPase

  第12回分子モーター討論会, 27 Sep. 2023

  
• 多重配列アライメントとスクリーニング法による新規モータータンパク質の創生

  大友 章裕; Song Chihong、Raymo; N. Burton-Smith; 富井 健太郎; 村田 和義; 小嶋 誠司; 飯野 亮太

  令和4年度 日本生物物理学会 中部支部講演会, 31 Mar. 2023

  
• １分子散乱イメージングによる回転分子モータータンパク質の構造ダイナミクス研究

  物性研究所機能物性セミナー, 16 Feb. 2023, Invited

  
• 生体内エネルギー変換機構の解明に向けた回転モータータンパク質改変体の創生

  大友 章裕; 原島 崇徳; 飯野 亮太

  日本生体エネルギー研究会 第48回討論会, 15 Dec. 2022

  
• Single-molecule analysis and engineering of Na+-pumping V-ATPase

  Akihiro Otomo, Ryota Iino

  East Asian Single-Molecule Biophysics Symposium, Oct. 2022, Invited

  
• Single-molecule analysis and engineering of rotary V-ATPase

  Akihiro Otomo, Tatsuya Iida, Hiroshi Ueno, Takeshi Murata, Ryota Iino

  第60回日本生物物理学会年会, 30 Sep. 2022

  
• Integrated research on rotary V-ATPase approached by single-molecule observation, biochemical assay, and protein engineering

  Akihiro Otomo, Ryota Iino

  第60回日本生物物理学会年会, 29 Sep. 2022, Invited

  
• V-ATPaseのイオン結合部位を改造した新規モータータンパク質作製の取り組み

  令和3年度 日本生物物理学会 中部支部講演会, 17 Mar. 2022

  
• Enterococcus hirae由来 V-ATPaseは ”硬 い ”カップリング で 対称性 の 不 一致を気にせず 回転する

  日本生体エネルギー研究会第47回討論会, 16 Dec. 2021

  
• Direct Observation of Stepping Rotation of V-ATPase Reveals Rigid and Non-integer Coupling between Vo and V1 Motors

  第59回日本生物物理学会年会, 25 Nov. 2021

  
• １分子計測法で明らかにする回転型V-ATPaseのイオン輸送と共役した回転機構

  名古屋工業大学 招聘セミナー, 28 May 2021, Invited

  
• Na+輸送性 V-ATPase のイオン輸送と共役した回転ステップの１分子観察

  令和2年度 日本生物物理学会 中部支部講演会, 31 Mar. 2021

  
• Enterococcus hirae由来V-ATPaseのナトリウムイオン濃度に依存した回転運動の1分子解析

  第10回分子モーター討論会, 02 Nov. 2020

  
• Single-molecule analysis of rotation of Enterococcus hirae V-ATPase depending on sodium ion concentration

  日本生物物理学会第58回年会 2020年9月

  
• 時間分解紫外共鳴ラマン分光法によるKR2の構造ダイナミクスの観測

  第13回分子科学討論会, 17 Sep. 2019

  
• Time-resolved UV resonance Raman observation of protein dynamics of a light-driven sodium ion-pumping rhodopsin

  19th International Conference on Time-Resolved Vibrational Spectroscopy, Sep. 2019

  
• KR2のナトリウムイオン輸送時におけるF ヘリックスの構造変化

  ISSPワークショップ「レチナールタンパク質の光機能発現の物理と化学」, Sep. 2019

  
• 新型光受容タンパク質Heliorhodopsinの発色団構造

  日本化学会第99春季年会, Mar. 2019

  
• 異なる環境下における光駆動ナトリウムイオンポンプの安定性

  第12回分子科学討論会, 11 Sep. 2018

  
• Effects of Solubilized Conditions on the Oligomerization of KR2

  18th International Conference on Retinal Proteins, Sep. 2018

  
• A comparison of the structures in two functional conditions of Krokinobacter rhodopsin 2

  26th International Conference on Raman Spectroscopy, Aug. 2018

  
• 光駆動型ナトリウムイオン輸送タンパク質KR2のイオンに依存した立体構造の違い

  第11回分子科学討論会, Sep. 2017

  
• Protein dynamics of CooA upon CO dissociation studied by time-resolved resonance Raman spectroscopy

  日本生物物理学会第51回年会, Oct. 2013

  
• Structural changes in the heme and heme pocket upon CO dissociation of CooA observed by time-resolved resonance Raman spectroscopy

  16th International Conference on Bioinorganic Chemistry, Jul. 2013

  
• ガスセンサータンパク質CooAの一酸化炭素脱離に伴う構造ダイナミクスの観測

  第6回分子科学討論会, Sep. 2012

  

Awards

• 31 Mar. 2021

  令和二年度中部支部講演会最優秀発表賞（日本生物物理学会中部支部会）
• 01 Dec. 2018

  第12回分子科学討論会分子科学会優秀ポスター賞（日本分子科学会）
• 01 Nov. 2019

  第13回分子科学討論会分子科学会優秀講演賞（日本分子科学会）

External funds: Kakenhi

• V-ATPaseのナトリウム駆動力による回転１分子観察とイオン/ATP共役比の改変

  Grant-in-Aid for Early-Career Scientists

  Basic Section 13040:Biophysics, chemical physics and soft matter physics-related

  Institute for Molecular Science

  大友 章裕

  From 01 Apr. 2024, To 31 Mar. 2027, Granted

  １分子計測;分子モーター

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-24K17026/
• Functional and Structural Relationship of V-ATPase Revealed by Single-Molecule Observation

  Grant-in-Aid for Early-Career Scientists

  Basic Section 43040:Biophysics-related

  Institute for Molecular Science

  大友 章裕

  From 01 Apr. 2021, To 31 Mar. 2024, Granted

  １分子計測;V-ATPase;エネルギー変換;ナトリウムポンプ;ナトリウムイオンポンプ

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K15060/
• Elucidation of the rotation mechanism of V-ATPase by electrochemical potential

  Grant-in-Aid for JSPS Fellows

  Basic Section 43040:Biophysics-related

  Institute for Molecular Science

  大友 章裕

  From 24 Apr. 2020, To 31 Mar. 2023, Project Closed

  V-ATPase;１分子計測;分子モーター

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20J01316/