Development of a novel nuclear resonance vibrational spectrometer to elucidate the mechanism in the active center of iron enzymes

• Project/Area Number: 16H04172
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Analytical chemistry
• Research Institution: Japan Synchrotron Radiation Research Institute
• Principal Investigator: Yoda Yoshitaka 公益財団法人高輝度光科学研究センター, 利用研究促進部門, 主幹研究員 (90240366)
• Research Collaborator: Cramer Stephen P.
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2017: ¥11,830,000 (Direct Cost: ¥9,100,000、Indirect Cost: ¥2,730,000); Fiscal Year 2016: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
• Keywords: 量子ビーム / 酵素反応 / 核共鳴振動分光 / 核共鳴非弾性散乱 / 核共鳴散乱 / 生物化学 / 高分解能モノクロメータ / ヒドロゲナーゼ / 酵素 / 鉄酵素 / 放射光 / Ｘ線光学

Outline of Final Research Achievements

Nuclear resonance vibrational spectroscopy is a powerful tool to investigate the active center of the iron metalloenzymes because it selectively probe the vibrational motion of Fe-57. But the observable vibrational modes were limited due to the lower resolution or the lower counting rates of the signals. We have developed a novel nuclear resonance vibrational spectrometer and observed the iron-hydrogen bending mode in hydrogenase which reversibly catalyze the molecular hydrogen. It contributes to the deep understanding of the mechanism of the hydrogenase.

Academic Significance and Societal Importance of the Research Achievements

活性中心に金属をもつ金属酵素のなかで鉄酵素は水素を酸化還元するヒドロゲナーゼをはじめ、エネルギー問題・食糧問題・医療などと密接に関わっているものが多い。すでに結果も出始めているが、開発した核共鳴振動分光装置の利用による鉄酵素の活性機構の解明を通じて、タンパク質の動的機能の理解を深めることができる。一方、得られた知見は大きな投資が行われている水素と酸素を水に変換する燃料電池電極を始めとする人工触媒の開発において重要なヒントを与えると期待されている。

Research Products

• [Int'l Joint Research] University California Davis(米国)
• [Int'l Joint Research] University of California, Davis(米国)
• [Journal Article] X-ray beam properties available at the nuclear resonant scattering beamline at SPring-8 (2019)
  • Author(s): Y. Yoda
  • Journal Title: Hyperfine Interactions Volume: 印刷中 Issue: 1
  • DOI: 10.1007/s10751-019-1598-3
  • Peer Reviewed
• [Journal Article] Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment (2018)
  • Author(s): Pham Cindy C.、Mulder David W.、Pelmenschikov Vladimir、King Paul W.、Ratzloff Michael W.、Wang Hongxin、Mishra Nakul、Alp Esen E.、Zhao Jiyong、Hu Michael Y.、Tamasaku Kenji、Yoda Yoshitaka、Cramer Stephen P.
  • Journal Title: Angewandte Chemie International Edition Volume: 57 Issue: 33 Pages: 10605-10609
  • DOI: 10.1002/anie.201805144
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structural Relaxation and Viscoelasticity of a Higher Alcohol with Mesoscopic Structure (2018)
  • Author(s): Tsuyoshi Yamaguchi, Makina Saito, Koji Yoshida, Toshio Yamaguchi, Yoshitaka Yoda, Makoto Seto
  • Journal Title: Journal of Physical Chemistry Letters Volume: 9 Issue: 2 Pages: 298-301
  • DOI: 10.1021/acs.jpclett.7b02907
  • NAID: 120006473543
  • Peer Reviewed
• [Journal Article] Nuclear resonant scattering experiment with fast time response: Photonuclear excitation of 201Hg (2018)
  • Author(s): A. Yoshimi et al.
  • Journal Title: Physical Review C Volume: 97 Issue: 2 Pages: 024607-024607
  • DOI: 10.1103/physrevc.97.024607
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 57Fe Nuclear Resonant Inelastic Scattering of Fe1.1Te (2018)
  • Author(s): M. Kurokuzu S. Kitao, Y. Kobayashi, M. Saito, R. Masuda, T. Mitsui,Y. Yoda, M. Seto
  • Journal Title: Hyperfine Interact. Volume: 239 Issue: 1 Pages: 9-9
  • DOI: 10.1007/s10751-017-1484-9
  • Peer Reviewed
• [Journal Article] Measurement of nuclear resonant scattering on 61Ni with fast scintillation detector using proportional-mode silicon avalanche photodiode (2018)
  • Author(s): Inoue Keisuke、Kobayashi Yasuhiro、Yoda Yoshitaka、Koshimizu Masanori、Nishikido Fumihiko、Haruki Rie、Kishimoto Shunji
  • Journal Title: Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Volume: 880 Pages: 87-91
  • DOI: 10.1016/j.nima.2017.10.029
  • Peer Reviewed
• [Journal Article] Ice crystal growth under the presence of krypton and methane at low temperature (2018)
  • Author(s): Kawauchi Taizo、Yoda Yoshitaka、Fukutani Katsuyuki
  • Journal Title: Journal of Crystal Growth Volume: 483 Pages: 52-56
  • DOI: 10.1016/j.jcrysgro.2017.11.018
  • Peer Reviewed
• [Journal Article] Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF (2017)
  • Author(s): Park Kiyoung、Li Ning、Kwak Yeonju、Srnec Martin、Bell Caleb B.、Liu Lei V.、Wong Shaun D.、Yoda Yoshitaka、Kitao Shinji、Seto Makoto、Hu Michael、Zhao Jiyong、Krebs Carsten、Bollinger J. Martin、Solomon Edward I.
  • Journal Title: Journal of the American Chemical Society Volume: 139 Issue: 20 Pages: 7062-7070
  • DOI: 10.1021/jacs.7b02997
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory (2017)
  • Author(s): Pelmenschikov Vladimir、Birrell James A.、Pham Cindy C.、Mishra Nakul、Wang Hongxin、Sommer Constanze、Reijerse Edward、Richers Casseday P.、Tamasaku Kenji、Yoda Yoshitaka、Rauchfuss Thomas B.、Lubitz Wolfgang、Cramer Stephen P.
  • Journal Title: Journal of the American Chemical Society Volume: 139 Issue: 46 Pages: 16894-16902
  • DOI: 10.1021/jacs.7b09751
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Synchrotron radiation-based quasi-elastic scattering using time-domain interferometry with multi-line gamma rays (2017)
  • Author(s): Saito Makina、Masuda Ryo、Yoda Yoshitaka、Seto Makoto
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 12558-12558
  • DOI: 10.1038/s41598-017-12216-7
  • NAID: 120006349312
  • Peer Reviewed / Open Access
• [Journal Article] Thickness Dependence of Morin Transition Temperature in Iridium-Doped Hematite Layers Studied through Nuclear Resonant Scattering (2017)
  • Author(s): K. Mibu, K. Mikami, M. A. Tanaka, R. Masuda, Y. Yoda, and M. Seto
  • Journal Title: Hyperfine Interactions Volume: 238 Issue: 1 Pages: 921-8
  • DOI: 10.1007/s10751-017-1470-2
  • Peer Reviewed
• [Journal Article] Sm valence states and magnetic properties in SmBe13 and SmTi2Al20 investigated by Sm synchrotron-radiation-based M?ssbauer spectroscopy (2017)
  • Author(s): Tsutsui Satoshi、Kobayashi Yoshio、Nakamura Jin、Kubo Michael K.、Amagasa Shota、Yamada Yasuhiro、Yoda Yoshitaka、Shimizu Yusei、Hidaka Hiroyuki、Yanagisawa Tatsuya、Amitsuka Hiroshi、Yamada Akira、Higashinaka Ryuji、Matsuda Tatsuma D.、Aoki Yuji
  • Journal Title: Hyperfine Interactions Volume: 238 Issue: 1 Pages: 1001-8
  • DOI: 10.1007/s10751-017-1473-z
  • Peer Reviewed
• [Journal Article] Impurity position and lattice distortion in a Mn-doped Bi2Te3 topological insulator investigated by x-ray fluorescence holography and x-ray absorption fine structure (2017)
  • Author(s): S. Hosokawa, J. R. Stellhorn, T. Matsushita, N. Happo, K. Kimura, K. Hayashi, Y. Ebisu, T. Ozaki, H. Ikemoto, H. Setoyama, T. Okajima, Y. Yoda, H. Ishii, Y.-F. Liao, M. Kitaura, and M. Sasaki
  • Journal Title: Physical Review B Volume: 96 Issue: 21 Pages: 214207-214207
  • DOI: 10.1103/physrevb.96.214207
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Effect of silica nanoparticle filler on microscopic polymer α-relaxation dynamics (2017)
  • Author(s): Saito Makina、Mashita Ryo、Kishimoto Hiroyuki、Masuda Ryo、Yoda Yoshitaka、Seto Makoto
  • Journal Title: Hyperfine Interactions Volume: 238 Issue: 1 Pages: 99-99
  • DOI: 10.1007/s10751-017-1466-y
  • Peer Reviewed
• [Journal Article] Evolution of synchrotron-radiation-based Mossbauer absorption spectroscopy for various isotopes (2017)
  • Author(s): Makoto Seto, Ryo Masuda, Yasuhiro Kobayashi, Shinji Kitao, Masayuki Kurokuzu, Makina Saito, Shuuich Hosokawa, Hiroki Ishibashi, Takaya Mitsui, Yoshitaka Yoda, Ko Mibu
  • Journal Title: Hyperfine Interactions Volume: 238 Issue: 1 Pages: 78-78
  • DOI: 10.1007/s10751-017-1446-2
  • Peer Reviewed
• [Journal Article] Fast x-ray detector system with simultaneous measurement of timing and energy for a single photon (2017)
  • Author(s): Masuda T.、Okubo S.、Hara H.、Hiraki T.、Kitao S.、Miyamoto Y.、Okai K.、Ozaki R.、Sasao N.、Seto M.、Uetake S.、Yamaguchi A.、Yoda Y.、Yoshimi A.、Yoshimura K.
  • Journal Title: Review of Scientific Instruments Volume: 88 Issue: 6 Pages: 063105-063105
  • DOI: 10.1063/1.4989405
  • Peer Reviewed
• [Journal Article] High-resolution monochromator for iron nuclear resonance vibrational spectroscopy of biological samples (2016)
  • Author(s): Y. Yoda, K. Okada, H. Wang, S. P. Cramer, and M. Seto
  • Journal Title: Jpn. J. Appl. Phys. Volume: 55 Issue: 12 Pages: 122401-122401
  • DOI: 10.7567/jjap.55.122401
  • NAID: 210000147290
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] 核共鳴振動分光の生物学分野への応用 ― 酵素活性中心のプローブとして― (2016)
  • Author(s): 依田芳卓
  • Journal Title: 放射光 Volume: 29 Pages: 150-157
  • NAID: 40020894987
• [Presentation] Latest research using nuclear resonant scattering at SPring-8 (2019)
  • Author(s): Yoshitaka Yoda
  • Organizer: International Conference on Hyperfine Interactions and their Applications
  • Int'l Joint Research / Invited
• [Presentation] 核共鳴振動分光装置の開発による鉄含有酵素の原子レベルでの考察 (2018)
  • Author(s): 依田 芳卓
  • Organizer: 第42回日本鉄バイオサイエンス学会学術集会
• [Presentation] Nuclear Resonant Scattering Beamline at SPring-8 (2017)
  • Author(s): Yoshitaka Yoda
  • Organizer: 1st nuclear resonant scattering workshop in China
  • Place of Presentation: Institute of High-energy Physics in China
  • Year and Date: 2017-01-20
  • Int'l Joint Research / Invited