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量子生命科学研究所

構造生物学研究チーム_2023年度以前の成果

掲載日：2024年4月1日更新
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2022年度の成果

原著論文

  1. *Yamamoto, M., Inoue, R., Kurisaki, I., Matsuo, T., Hishikawa, Y., Zhao, W., Sekiguchi, K. “Protein large-scale motions revealed by quantum beams -a new era in understanding protein dynamics-” Biophys. Physicobiol. 19, e190035 (2022)
  2. *Matsuo, T., *Peters, J. “Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering” Life. 12, 1259 (2022)
  3. Misuraca, L., Matsuo, T., Cissé , A., LoRicco, J., Caliò , A., Zanotti, J-M., Demé, B., *Oger, P., *Peters, J. “High temperature molecular motions within a model protomembrane architecture” Phys. Chem. Chem. Phys. 24, 15083-15090 (2022)
  4. Hiromoto, T., Ikura, T., Honjo, E., Blaber, M., Kuroki, R., *Tamada, T. “Creation of cross-linked crystals with intermolecular disulfide bonds connecting symmetry-related molecules allows retention of tertiary structure in different solvent conditions” Front. Mol. Biosci. 9: 908394 (2022)
  5. Hanazono, Y., Hirano, Y., Takeda, K., Kusaka, K., *Tamada, T., *Miki, K. “Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis” Sci. Adv. 8, eabn2276 (2022)
  6. Matsuo, T., Cissé , A., Plazanet, M., Natali, F., Koza, M. M., Olliver, J., Bicout, D. J., *Peters, J. “The dynamical Matryoshka model: 3. Diffusive nature of the atomic motions contained in a new dynamical model for deciphering local lipid dynamics” Biochim. Biophys. Acta Biomembr. 1864, 183949 (2022)
  7. Cisse, A., Matsuo, T., Plazanet, M., Natali, F., Koza, M. M., Olliver, J., Bicout, D. J., *Peters, J. “The dynamical Matryoshka model: 2. Modeling of local 1 lipid dynamics at the sub-nanosecond timescale in phospholipid membranes” Biochim. Biophys. Acta Biomembr. 1864, 183950 (2022)
  8. Bicout, D. J., Cisse, A., Matsuo, T., *Peters, J. “The dynamical Matryoshka model: 1. Incoherent neutron scattering functions for lipid dynamics in bilayers” Biochim. Biophys. Acta Biomembr. 1864, 183944. (2022)
  9. #Furuike, Y., #Ouyang, D., #Tominaga, T., Matsuo, T., Mukaiyama, A., Kawakita, Y., *Fujiwara, S., *Akiyama, S. “Cross-scale analysis of temperature compensation in the cyanobacterial circadian clock system” Commun. Phys. 5, 75 (2022)
  10. Kono, F., Kurihara, K., *Tamada, T. “Current status of neutron crystallography in structural biology” Biophys. Physicobiol. 19, e190009 (2022)
  11. *Murakawa, T., Kurihara, K., Adachi, M., Kusaka, K., Tanizawa, K., *Okajima, T. “Reevaluation of protein neutron crystallography with and without X-ray/neutron joint refinement” IUCrJ. 9, 342-348 (2022)
  12. *Nakano, T., Akamatsu, K., Tsuda M., Tsujimoto, A., Hirayama, R., Hiromoto, T., Tamada, T., *Ide, H., *Shikazono, N. “Formation of clustered DNA damage in vivo upon irradiation with ionizing radiation: Visualization and analysis with atomic force microscopy” Proc. Natl. Acad. Sci. USA 119, e2119132119 (2022)
  13. *Matsuo, T., Francesco, A. D., *Peters, J. “Molecular dynamics of lysozyme amyloid polymorphs studied by incoherent neutron scattering” Front. Mol. Biosci. 8, 812096 (2022)

和文誌​

  1. 花園 祐矢、平野　優、玉田 太郎、三木 邦夫「高分解能中性子構造から明らかになったタンパク質中のペプチド結合における新しい描像」日本結晶学会誌、64, 207-208 (2022)
  2. 中川　洋、松尾 龍人「中性子散乱」実験医学別冊、222-227 (2022)
  3. 福田 庸太、平野　優、日下 勝弘、井上　豪、玉田 太郎「中性子結晶構造解析による銅含有亜硝酸還元酵素の反応機構解明」放射光、35, 69-77 (2022)
  4. 末武　勲、松尾 龍人、武藤 梨沙、宗　正智、三島 優一、北條 裕信「エピジェネティクスの分子機構の動的理解と今後の発展－電子スピン共鳴と有機合成とタンパク質研究と－ 」波紋、32, 33-37 (2022)
  5. 平野　優、栗原 和男、玉田 太郎「BIX-3, BIX-4を利用した生命研究」波紋、32, 21-24 (2022)

​2021年度の成果

原著論文​

  1. ​Nakagawa, H., Tamada, T. “Hydration and its hydrogen bonding state on a protein surface in the crystalline state as revealed by molecular dynamics simulation” Front. Chem. 9, 738077. (2021)
  2. Matsuo, T., Nakatani, K., Setoguchi, T., Matsuo, K., *Tamada, T., *Suenaga, Y. “Secondary structure of human De Novo evolved gene product NCYM analyzed by vacuum-ultraviolet circular dichroism” Front. Oncol. 11, 688852. (2021)
  3. Matsuo, T. “Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility” Biology 10, 454. (2021)
  4. Matsuo, T. “A theoretical study on the effects of interdomain flexibility on drug encounter rate for coronavirus nucleocapsid-type proteins ” Biophys. Chem. 272, 106574. (2021)
  5. Kono, F., *Tamada, T. “Neutron crystallography for the elucidation of enzyme catalysis” Curr. Opin. Struct. Biol. 71, 36-42. (2021)
  6. Shobu, T., Shiro, A., Kono, F.,  Muramatsu, T., Yamada, T., Naganuma, M., Ozawa, T. “Internal Strain Distribution of Laser Lap Joints in Steel under Loading Studied by High-Energy Synchrotron Radiation X-rays” Quantum Beam Sci. 5, 17. (2021)
  7. #Inoue, Y., #Hanazono, Y., #Noi, K., #Kawamoto, A., Kimatsuka, M., Harada, R., Takeda, K., Kita, R., Iwamasa, N., Shibara, K., Noguchi, K., Shigeta, Y., Namba, K., Ogura, T., Miki, K., Shinohara, K., Yohda, M. “Split conformation of Chaetomium thermophilum Hsp104 disaggregase”, Structure 29, 721-730. (2021)
  8. Hiromoto, T., Nishikawa, K., *Tamada, T., *Higuchi, Y. “The challenge of visualizing the bridging hydride at the active site and proton network of [NiFe]‑hydrogenase by neutron crystallography” Top. Catal. 64, 622-630. (2021)

和文誌

  1. 河野 史明、栗原 和男、玉田 太郎「中性子結晶解析の進展が明らかにする酵素反応機構」生物物理、61, 216-222 (2021)
  2. 中川　洋、松尾 龍人「X線散乱・中性子散乱」実験医学、39, 211-217 (2021)
  3. 栗原 和男、玉田 太郎「生体高分子用単結晶回折装置BIX-3, BIX-4の現状と今後の展望」波紋、31, 33-35 (2021)

2020年度の成果

原著論文​

  1. Kanao, T., Hase, N., Nakayama, H., Yoshida, K., Nishiura, K., Kosaka, M., Kamimura, K., Hirano, Y., *Tamada, T. “Reaction mechanism of tetrathionate hydrolysis on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans” Protein Sci. 30, 328-338. (2020)
  2. Kono, F., Kawai, S., Shimamoto, Y., Ishiwata, S. “Nanoscopic changes in the lattice structure of striated muscle sacromeres involved in the mechanism of spontaneous oscillatory contraction (SPOC)” Sci. Rep. 10, 16372. (2020)  
  3. Hiromoto, T., Nishikawa, K., Inoue, S., Matsuura, H., Hirano, Y., Kurihara, K., Kusaka, K., Cuneo, M., Coates, L., *Tamada, T., *Higuchi, Y. “Toward cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase” Acta Crystallogr. D76, 946-953. (2020)  
  4. Hirano, Y., Tsukamoto, K., Ariki, S., Naka, Y., Ueda, M., *Tamada, T. “X-ray crystallographic structural studies of α-amylase I from Eisenia fetida” Acta Crystallogr. D76, 834-844. (2020)  
  5. #Sunami, T., #Hirano, Y., Tamada, T., Kono, H. “Structural basis for designing an array of engrailed homeodomains” Acta Crystallogr. D76, 824-833. (2020)
  6. Murakawa, T., Kurihara, K., Shoji, M., Shibazaki, C., Sunami, T., Tamada, T., Yano, N., Yamada, T., Kusaka, K., Suzuki, M., Shigeta, Y., Kuroki, R., Hayashi, H., Yano, T., Tanizawa, K, Adachi, M., Okajima, T. “Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing” Proc. Natl. Acad. Sci. USA 117, 10818-10824. (2020)
  7. Matsuo, T. “Usefulness of medium-angle X-ray scattering for structural characterization of flexible proteins studied by computer simulations” ” Biocham.Bipphys. Res. Commun. 525, 830-835. (2020)
  8. Shimada, A., Etoh, Y., Kitoh-Fujisawa, R., Sasaki, A., Shinzawa-Itoh, K., Hiromoto, T., Yamashita, E., Muramoto, K., Tsukihara, T., Yoshikawa, S. “X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms” J. Biol. Chem. 295, 5818-5833. (2020)
  9. Fukuda, Y., Hirano, Y., Kusaka, K., *Inoue, T., *Tamada, T. “High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase” Proc. Natl. Acad. Sci. USA 117, 4071-4077. (2020)

和文誌

  1. 玉田 太郎、平野　優「量子構造生物学の創成と挑戦」OPTRONICS、39, 92-97 (2020)
  2. 三木 邦夫、平野　優「 X線結晶解析による光合成初期過程の構造生物学」膜蛋白質工学ハンドブック、431-444 (2020)

2019年度の成果

原著論文​

  1. Fujiwara, S., Matsuo, T., Sugimoto, Y., Shibata, K. “Segmental Motions of Proteins under Non-Native States Evaluated Using Quasielastic Neutron Scattering” J. Phys. Chem. Lett. 10, 7505-7509. (2019)
  2. Yoshinaka, T., Kosako, H., Yoshizumi, T., Furukawa, R., Hirano, Y., Kuge, O., Tamada, T., Koshiba, T. “Structural basis of mitochondrial scaffolds by prohibitin complexes: insight into a role of the coiled-coil region” iScience 19, 1065-1078. (2019)
  3. Fujiwara, S., Kono, F., Matsuo, T., Sugimoto, Y., Matsumoto, T., Narita, A., Shibata, K. “Dynamic Properties of Human alpha-Synuclein Related to Propensity to Amyloid Fibril Formation” J. Mol. Biol. 431, 3229-3245. (2019)
  4. Adachi, M., Shimizu, R., Shibazaki, C., Satoh, K., Fujiwara, S., Arai, S., Narumi, I., Kuroki, R. “Extended Structure of Pleiotropic DNA Repair-Promoting Protein PprA from the Extreme Radiation Resistance of Deinococcus radiodurans” FASEB J. 33, 3647-3658. (2019)
  5. Matsuo, T., Kono, F., Fujiwara, S. “Effects of the cardiomyopathy-causing E244D mutation of troponin T on the structures of cardiac thin filaments studied by small-angle X-ray scattering” J. Struct. Biol. 205, 196-205. (2019)
  6. Nakamura, T., Hirata, K., Fujimiya, K., Chirifu, M., Arimori, T., Tamada, T., Ikemizu, S., Yamagata, Y. “X-ray Structure Analysis of Human Oxidized Nucleotide Hydrolase MTH1 using Crystals Obtained under Microgravity” Int. J. Microgravity Sci. Appl. 36, 36103. (2019)

和文誌

  1. 藤巻 秀,  五十嵐 龍治,  高草木 洋一,  安達 基泰,  横谷 明徳,  玉田 太郎,  河野 秀俊,  鹿園 直哉,  今岡 達彦,  赤松 憲,  小西 輝昭,  山田 真希子,  八幡 憲明　「最先端の研究開発 量子科学技術研究開発機構 第 4 回 「量子生命科学」の発進」 日本原子力学会誌”アトモス”, 61(6), 43 - 47, 2019-06 
量子生命科学研究所