Spectroscopic Study on Protein Functionally-Relevant Modes Excited by Dynamics of Hydration Water

• Project/Area Number: 18K03559
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 13040:Biophysics, chemical physics and soft matter physics-related
• Research Institution: Jichi Medical University
• Principal Investigator: Yamamoto Naoki 自治医科大学, 医学部, 助教 (90580671)
• Co-Investigator(Kenkyū-buntansha): 富永 圭介 神戸大学, 分子フォトサイエンス研究センター, 教授 (30202203) ; 中西 真大 福岡工業大学, 工学部, 助教 (00707763)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: タンパク質水和 / 広帯域誘電分光 / 中性子散乱 / ダイナミクスと機能の相関 / タンパク質ダイナミクス / 水和水 / タンパク質機能活性化 / 水和水回転緩和 / テラヘルツ分光 / タンパク質の水和水 / ベクトルネットワークアナライザ / テラヘルツ時間領域分光 / 回転緩和 / 低振動運動 / タンパク質と水和水のダイナミクス / テラヘルツ時間領域分光計 / サブTHz領域

Outline of Final Research Achievements

We attempted to quantify the complex dielectric spectra of hydrated protein in the sub-THz region (1 THz = 1012 Hz) in temperature and hydration-dependent manner. We were able to obtain the spectra at the region of 0.02-0.3 THz using a vector network analyzer (up to 50 GHz) and a THz time-domain spectrometer (0.5-0.3 THz), which we did not complete in the previous studies. By analyzing broadband dielectric spectra ranging from GHz to THz, it was suggested that there are spectral components possessing both rotational and vibrational properties in the sub-THz region, which we assume protein and hydration dynamics required for the protein functional expression. We also performed neutron scattering experiment on hydrated proteins, resulting in obtaining evidence of apparent contribution of unfreezable hydration water on the protein surface to protein dynamics.

Academic Significance and Societal Importance of the Research Achievements

本研究は、タンパク質まわりに存在する水、水和水がタンパク質ダイナミクスに果たす役割を理解するためのものであり、今回の結果より水和水とタンパク質の動きが互いに影響を及ぼしあうことでタンパク質の機能発現に必要な動きを活性化することが示唆された。また同時にその活性化が複雑な分子論的メカニズムによってもたらされることもわかり、計算機を用いた分子動力学シミュレーション等により理論的な理解を進める必要性があることもわかった。

Research Products

• [Journal Article] Freezable and Unfreezable Hydration Water: Distinct Contributions to Protein Dynamics Revealed by Neutron Scattering (2021)
  • Author(s): Yamamoto Naoki、Kofu Maiko、Nakajima Kenji、Nakagawa Hiroshi、Shibayama Naoya
  • Journal Title: The Journal of Physical Chemistry Letters Volume: 12 Issue: 8 Pages: 2172-2176
  • DOI: 10.1021/acs.jpclett.0c03786
  • Peer Reviewed
• [Presentation] Protein hydration dynamics probed by broadband dielectric spectroscopy and neutron scattering (2020)
  • Author(s): Naoki Yamamoto
  • Organizer: Dynamics of Chemical and Biological Systems, IIT Kampur
  • Invited
• [Presentation] 広帯域誘電分光によるタンパク質水和水ダイナミクスの評価 (2020)
  • Author(s): 山本直樹
  • Organizer: 分子フォト研究会 「誘電応答から見るソフトマターの水和ダイナミクス」
  • Invited
• [Presentation] 広帯域誘電分光を用いたタンパク質水和水のダイナミクス観測 (2019)
  • Author(s): 山本直樹
  • Organizer: テラヘルツ分光で水を研究する会
  • Invited
• [Presentation] Protein hydration water dynamics probed by broadband dielectric spectroscopy (2019)
  • Author(s): Naoki Yamamoto
  • Organizer: International Conference on Chemical and Environmental Sciences 2019, Kolkata
  • Invited
• [Presentation] 広帯域誘電分光による水和タンパク質ダイナミクスの評価 (2019)
  • Author(s): 山本直樹
  • Organizer: 東京大学 物性研究所 極限コヒーレント光科学セミナー
  • Invited
• [Presentation] temperature and hydration dependence of protein dynamics studied by broadband dielectric spectroscopy and neutron scattering (2019)
  • Author(s): Naoki Yamamoto
  • Organizer: Indo-Japan workshop, 2019, Kobe, Japan
  • Invited
• [Presentation] Broadband dielectric spectroscopy on hydrated proteins (2018)
  • Author(s): Naoki Yamamoto, Shota Ito, Kaoru Ohta, Masahiro Nakanishi, Atsuo Tamura, Eri Chatani, Hideki Kandori, Keisuke Tominaga
  • Organizer: Symposium on Advanced Spectroscopic Techniques, University of the Philippines Los Banos
  • Int'l Joint Research / Invited
• [Presentation] Broadband dielectric spectroscopy on proteins from sub-GHz to THz regions (2018)
  • Author(s): Naoki Yamamoto
  • Organizer: Indo-Japan mini-workshop -Frontiers in Molecular Spectroscopy: From Fundamentals to Applications in Chemistry and Biology-、Kobe University
  • Int'l Joint Research / Invited
• [Remarks] 凍る水と凍らない水;タンパク質の機能に関わる動きを制御する水分子の同定に成功
  • URL: https://www.jichi.ac.jp/news/research/20210309/