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Institute for Quantum Life Science

Structural Biology Team

Update：2024年4月1日更新
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構造生物タイトル

構造生物学図Biomolecules, such as proteins, containing many atoms (several million atoms in huge protein complexes) express the specific function while dynamically changing structures. Our research team aims to elucidate the specific function of biomolecules based on “precise” structure information including all atoms with their “dynamic” information by using recent quantum technology, such as complementary use of synchrotron X-ray/neutron diffraction and scattering techniques with quantum chemical calculation and simulations. The ultimate goal of our research group is generation of the “quantum” (above “atomic”) structural biology research field.

 

玉田リーダー

 

 

 

 

 

Team Leader, Taro Tamada

 

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Publications

2023​

  1. Fukuda, Y., *Lintuluoto, M., Kurihara, K., Hasegawa, K., *Inoue, T., *Tamada, T. “Overlooked hydrogen bond in a blue copper protein uncovered by neutron and sub-ångström resolution X-ray crystallography” Biochemistry 63, 339-347. (2024)
  2. Yamamoto, S., Kono, F., Nakatani, K., Hirose, M., Hirai, K., Hippo, Y., Tamada, T., *Suenaga, Y., *Matsuo, T. “Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering” Front. Oncol. 13, 1213678. (2023)　
  3. *Hanazono, Y., Hirano, Y., Tamada, T., Miki, K. “Description of peptide bond planarly from high-resolution neutron crystallography” Biophysics and Physicobiology 20, e200035. (2023)
  4. Ura, T., Sakakibara, N., Hirano, Y., Tamada, T., Takakusagi Y., Shiraki, K., *Mikawa, T. “Activation of oxidoreductases by the formation of enzyme assembly” Sci. Rep. 13, 14381. (2023)
  5. Hiromoto, T., Nishikawa, K., Inoue, S., Ogata, H., Hori, Y., Kusaka, K., Hirano, Y., Kurihara, K., Shigeta, Y., *Tamada, T., *Higuchi, Y. “New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase” Chem. Sci.. 14, 9306-9315. (2023)
  6. *Murakawa, T., Kurihara, K., Shoji, M., Yano, N., Kusaka, K., Kawano, Y., Suzuki, M., Shigeta, Y., Yano, T., Adachi, M., Tanizawa, K., *Okajima, T. “Neutron crystallography of a semiquinone radical intermediate of copper amine oxidase reveals a substrate-assisted conformational change of the peptidyl quinone cofactor” ACS Catal. 13, 12403-23413 (2023)
  7. #Kuroki, C., #Hirano, Y., Nakazawa, M., Sakamoto, T., *Tamada, T., *Ueda, M. “A single mutation Asp43Arg was increased 2.5-fold the catalytic activity and maintained the stability of cold-adapted endo-1,4-beta glucanase (Ef-EG2) from Eisenia fetida” Curr. Res. Biotechnol. 5, 100126. (2023)

2022

  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. *Fujiwara, S. “Dynamical behavior of disordered regions in disease-related proteins revealed by quasielastic neutron scattering”, Medicina 58, 58060795. (2023)
  3. *Chatake, T., Tanaka, I., Kusaka, K., Fujiwara, S. “Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography”, Acta Crystallogr. D78, 770-778. (2023)
  4. *Matsuo, T., *Peters, J. “Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering” Life. 12, 1259 (2022)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. #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)
  12. Kono, F., Kurihara, K., *Tamada, T. “Current status of neutron crystallography in structural biology” Biophys. Physicobiol. 19, e190009 (2022)
  13. *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)
  14. *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)
  15. *Matsuo, T., Francesco, A. D., *Peters, J. “Molecular dynamics of lysozyme amyloid polymorphs studied by incoherent neutron scattering” Front. Mol. Biosci. 8, 812096 (2022)

2021

  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)

2020

  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)

2019

  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”
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