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業績リスト

2018年度

  • Shimada A, Hatano K, Tadehara H, Yano N, Shinzawa-Itoh K, Yamashita E, Muramoto K*, Tsukihara T* and Yoshikawa S*. (*Corresponding author): X-ray structural analyses of azide-bound cytochrome c oxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem. 293, 14868-14879 (2018) doi: 10.1074/jbc.RA118.003123
  • M. Ganasen, H. Togashi, H. Takeda, H. Asakura, T. Tosha, K. Yamashita, K. Hirata, Y. Nariai, T. Urano, X. Yuan, I. Hamza, A. G. Mauk, Y. Shiro, H. Sugimoto*, H. Sawai* (*Corresponding author): “Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate”Communications Biology120 (2018) doi: 10.1038/s42003-018-0121-8
  • G. S. A. Wright#, A. Saeki#, T. Hikima, Y. Nishizono, T. Hisano, M. Kamaya, K. Nukina, H. Nishitani, H. Nakamura, M. Yamamoto, S. V. Antonyuk, S. S. Hasnain, Y. Shiro*, H. Sawai* (#equal contribution, *Corresponding author):“Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system.”Science Signaling 11, eaaq0825 (2018) doi: 10.1126/scisignal.aaq0825 Summary Abstract Reprint Full text
  • R. Yamagiwa, T. Kurahashi, M. Takeda, M. Adachi, H. Nakamura, H. Arai, Y. Shiro, H. Sawai*, T. Tosha*:“Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses." Biochimica et Biophysica Acta - Bioenergetics 1859, 333-341 (2018) doi: 10.1016/j.bbabio.2018.02.009
  • N. Gonska, D. Young, R. Yuki, T. Okamoto, T. Hisano, S. Antonyuk, S. S. Hasnain, K. Muramoto, Y. Shiro*, T. Tosha*, P. Adelroth*:“Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme.” Scientific Reports 8, 3637 (2018)
  • R. Makino*, Y. Obata, M. Tsubaki, T. Iizuka, Y. Hamajima, Y. Kato-Yamada, K. Mashima, Y. Shiro*:“Mechanistic Insights into the Activation of Soluble Guanylate Cyclase by Carbon Monoxide: A Multistep Mechanism Proposed for the BAY 41-2272 Induced Formation of 5-Coordinate CO-Heme.” Biochemistry 57, 1620-1631 (2018) doi: 10.1021/acs.biochem.7b01240
  • H. Sawai* and Y. Shiro: “CHAPTER 3: Haem-based Sensors of Dioxygen”in Gas Sensing in Cells (Royal Society of Chemistry Metallobiology Series), S. Aono Ed., pp47-83 (2018) doi: 10.1039/9781788012836-00047, ISBN: 978-1-78262-895-8

2017年度

  • K. Oohora, H. Meichin, Y. Kihira, H. Sugimoto, Y. Shiro, T. Hayashi*:“Manganese(V) Porphycene Complex Responsible for Inert C-H Bond Hydroxylation in a Myoglobin Matrix.”Journal of the American Chemical Society 139, 18460-18463 (2017) doi: 10.1021/jacs.7b11288
  • S. Hanai, H. Tsujino, T. Yamashita*, R. Torii, H. Sawai, Y. Shiro, K. Oohora, T. Hayashi, T. Uno:“Roles of N- and C-terminal domains in the ligand-binding properties of cytoglobin.”Journal of Inorganic Biochemistry 179, 1-9 (2017) doi: 10.1016/j.jinorgbio.2017.11.003
  • T. Tosha, T. Nomura, T. Nishida, N. Saeki, K. Okubayashi, R. Yamagiwa, M. Sugahara M, T. Nakane, K. Yamashita, K. Hirata, G. Ueno, T. Kimura, T. Hisano, K. Muramoto, H. Sawai, H. Takeda, E. Mizohata, A. Yamashita, Y. Kanematsu, Y. Takano, E. Nango, R. Tanaka, O. Nureki, O. Shoji, Y. Ikemoto, H. Murakami, S. Owada, K. Tono, M. Yabashi, M. Yamamoto, H. Ago, S. Iwata, H. Sugimoto*, Y. Shiro*, M. Kubo*: “Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.”Nature Communications 8,1585 (2017) doi: 10.1038/s41467-017-01702-1
  • H. Uehara, Y. Shisaka, T. Nishimura, H. Sugimoto, Y. Shiro, Y. Miyake, H. Shinokubo, Y. Watanabe, O. Shoji*: “Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group.” Angewamndte Chemie International Edition 56, 15279-15283 (2017) doi: 10.1002/anie.201707212
  • Y. Naoe, N. Nakamura, N. M. Rahman, T. Tosha, S. Nagatoishi, K. Tsumoto, Y. Shiro*, H. Sugimoto*: “Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.”Proteins 85, 2217-2230 (2017) doi: 10.1002/prot.25386
  • E. Terasaka, K. Yamada, P. H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimoto, Y. Sugita, Y. Shiro*, T. Tosha*: “Dynamics of nitric oxide controlled by protein complex in bacterial system.” Proceedings of the National Academy of Sciences of the United States of America 114, 9888-9893 (2017) doi: 10.1073/pnas.1621301114
  • K. Yasuda, H. Sugimoto, K. Hayashi, T. Takita, K. Yasukawa, M. Ohta, M. Kamakura, S. Ikushiro, Y. Shiro, T. Sakaki*: “Protein engineering of CYP105s for their industrial uses.” Biochimica et Biophysica Acta ? Proteins and Proteomics 1866, 23-31 (2018) doi: 10.1016/j.bbapap.2017.05.014
  • O. Shoji*, S. Yanagisawa, J. K. Stanfield, K. Suzuki, Z. Cong, H. Sugimoto, Y. Shiro, Y. Watanabe*: “Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives.” Angewamndte Chemie International Edition 56, 10324-10329 (2017) doi: 10.1002/anie.201703461
  • K. Yasuda, Y. Yogo, H. Sugimoto, H. Mano, T. Takita, M. Ohta, M. Kamakura, S. Ikushiro, K. Yasukawa, Y. Shiro, T. Sakaki*: “Production of an active form of vitamin D2 by genetically engineered CYP105A1.”Biochemical and Biophysical Research Communications 486, 336-341 (2017) doi: 10.1016/j.bbrc.2017.03.040

2016年度 研究報告書

  • Shoji, T. Fujishiro, K. Nishio, Y. Kano, H. Kimoto, S.-C. Chien, H. Onoda, A. Muramatsu, S. Tanaka, A. Hori, H. Sugimoto, Y. Shiro, Y. Watanabe: “A Substrate-Binding-Sate Mimic H2O2- Dependent Cytochrome P450 Produced by One-point Mutagenesis and Peroxygenation of Non- native Substrate” Catalysis Science & Technology 6, 5806-5811 (2016)
  • T. Tosha and Y. Shiro “Structure and Function of Nitric Oxide Reductases” in Metalloenzymes in Denitrification: Applications and Environmental Impacts (Royal Society of Chemistry Metallobiology Series), I. Moura, J. J. G. Moura and S. R. Pauleta Ed., 2016, p114-140
  • Otomo, A., Ishikawa, H., Mizuno, M., Kimura, T., Kubo, M., Shiro, Y., Aono, S., Mizutani, Y.: “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.” J. Phys. Chem. B 120, 7836-7843 (2016)
  • T. Yamawaki, H. Ishikawa, M. Mizuno, H. Nakamura, Y. Shiro, Y. Mizutani: “Regulatory Implications of Structural Changes in Tyr201 of the Oxygen Sensor Protein FixL” Biochemistry 55, 4027–4035 (2016)
  • Yano N#, Muramoto K#, Shimada A#, Takemura S, Baba J, Fujisawa H, Mochizuki M, Shinzawa- Itoh K, Yamashita E, Tsukihara T, Yoshikawa S. (#equal contribution) “The Mg2+-containing water cluster of mammalian cytochrome c oxidase collects four pumping proton equivalents in each catalytic cycle.” J. Biol. Chem. 291, 23882-23894 (2016).

2015年度 研究報告書

  • R. Makino, E. Obayashi, H. Hori, T. Iizuka, K. Mashima, Y. Shiro, Y. Ishimura: "The Initial O2 Inserting Step of Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study" Biochemistry 54, 3604-3616 (2015)
  • T. Tsuge, S. Sato, A. Hiroe, K. Ishizuka, H. Kanazawa, Y. Shiro, T. Hisano: “Contribution of the Distal Pocket Residue to the Acyl-chain-length Substrate Specificity of (R)-specific Enoyl-CoA Hydratases from Pseudomonas: Site-directed Mutagenesis, Chimeragenesis, X-ray Crystallographic Analysis, and Homology Modeling” Appl. Environ. Microbiol. 81, 8076-8083 (2015)
  • M. Sakaguchi, T. Kimura, T. Nishida, T. Tosha, Y. Yamaguchi, S. Yanagisawa, G. Ueno, H. Murakami, H. Ago, M. Yamamoto, T. Ogura, Y. Shiro, M. Kubo: “A Nearly On-axis Spectroscopic System for Simultaneously Measuring UV-visible Absorption and X-ray Diffraction in the SPring-8 Structural Genomics Beamline” J. Synch. Rad. 23, 334-338 (2016)
  • A. Doi, H. Nakamura, Y. Shiro, H. Sugimoto: “Crystal Structure of Response Regulator ChrA in the Heme-Sensing Two-Component System of Corynebacterium diphtheriaeActa Cryst. F71, 966-971 (2015)
  • Yano N, Muramoto K, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yoshikawa S, Tsukihara T. “X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 Å resolution.” Acta Cryst. F71, 726-730 (2015)

2014年度 研究報告書

  • E. Terasaka, N. Okada, N. Sato, Y. Sako, Y. Shiro, T. Tosha: “Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: Enzymatic activity and active site structure.” Biochim. Biophys. Acta 1837, 1019-1026 (2014)
  • S. Takahashi, S. Nagano, T. Nogawa, N. Kanoh, M. Uramoto, M. Kawatani, T. Shimizu, T. Miyazawa, Y. Shiro, H. Osada: “Structure-function analyses of cytochrome P450revI involved in reveromycin A biosynthesis and evaluation of the biological activity of its substrate, reveromycin T.” J. Biol. Chem. 289, 32446-32458 (2014)
  • K. Takagi, M. Al-Amin, N. Hoshiya, J. Wouters, H. Sugimoto, Y. Shiro, H. Fukuda, S. Shuto, M. Arisawa: “Palladium-nanoparticle-catalyzed 1,7-palladium migration involving C-H activation, followed by intramolecular amination: regioselective synthesis of N1-arylbenzotriazoles and an evaluation of their inhibitory activity toward indoleamine 2,3-dioxygenase.” J. Org. Chem. 79, 6366-6371 (2014)
  • Z. Cong, O. Shoji, C. Kasai, N. Kawakami, H. Sugimoto, Y. Shiro, Y. Watanabe: “Activation of Wild-Type Cytochrome P450BM3 by the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence.” ACS Catalysis 5, 150-156 (2014)
  • C. Shirataki, O. Shoji, M. Terada, S. Ozaki, H. Sugimoto, Y. Shiro, Y. Watanabe: “Inhibition of Heme Uptake in Pseudomonas aeruginosa by its Hemophore (HasAp) Bound to Synthetic Metal Complexes.” Angew. Chem. Int. Ed. 53, 2862-2866 (2014)
  • Y. Okamoto, H. Sawai, M. Ogura, T. Uchida, K. Ishimori, T. Hayashi, S. Aono: “Heme-binding properties of HupD functioning as a substrate-binding protein in a heme-uptake ABC-transporter system in Listeria monocytogenes” Bull. Chem. Soc. Japan 87, 1140-1146 (2014)
  • N. Sato, S. Ishii, H. Sugimoto, T. Hino, Y. Fukumori, Y. Sako, Y. Shiro, T. Tosha: "Structures of Reduced and Ligand-Bound Nitric Oxide Reductase Provide Insights into Functional Differences in Respiratory Enzymes" PROTEINS: Structure, Function, and Bioinformatics 82, 1258-1271 (2014)
  • Y. Okamoto, A. Onoda, H. Sugimoto, Y. Takano, S. Hirota, D. Kurtz, Y. Shiro, T. Hayashi: “H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin.” Chem. Comm. 50, 3421-3423 (2014)
  • H. Tsujino, T. Yamashita, A. Nose, K. Kukino, H. Sawai, Y. Shiro, T. Uno: Disulfide bonds regulate binding of exogenous ligand to human cytoglobin. J. Inorg. Biochem. 135, 20-27 (2014)
  • K. Hirata, K. Shinzawa-Itoh, N. Yano, S. Takemura, K. Kato, M. Hatanaka, K. Muramoto, T. Kawahara, T Tsukihara, E. Yamashita, K. Tono, G. Ueno, T. Hikima, H. Murakami, Y. Inubushi, M. Yabashi, T. Ishikawa, M. Yamamoto, T. Ogura, H. Sugimoto, J.-R. Shen, S. Yoshikawa, H. Ago: “Determination of damage-free crystal structure of an X-ray sensitive protein using an XFEL" Nature Methods 11, 734–736 (2014)

2013年度 研究報告書

  • Y. Okamoto, A. Onoda, H. Sugimoto, Y. Takano, S. Hirota, D. Kurtz, Y. Shiro, T. Hayashi: “Crystal Structure, Exogenous Ligand Binding and Redox Properties of an Engineered Diiron Active Site in a Bacterial Hemerythrin” Inorg Chem. 52, 13014-13020 (2013)
  • T. Tosha, Y. Shiro: “Crystal Structures of Nitric Oxide Reductases Provide Key Insights into Functional Conversion of Respiratory Enzymes” IUBMB (International Union of Biochemistry and Molecular Biology) Life 65, 217-226 (2013)
  • S. Yanagisawa, M. Hara, H. Sugimoto, Y. Shiro, T. Ogura: “Resonance Raman Study on Indoleamine 2,3-Dioxygenase: Control of Reactivity by Substrate-binding” Chem. Phys. 419, 178-183 (2013)
  • S. Yano, H. Ishikawa, M. Mizuno, H. Nakamura, Y. Shiro, Y. Mizutani: “Ultraviolet Resonance Raman Observation of the Structural Dynamics of FixL on Ligand Recognition” J. Phys. Chem. B, 117, 15786-15791 (2013)
  • 日野智也、松本悠史、當舍武彦、杉本 宏、永野真吾、城 宜嗣:「一酸化窒素還元酵素の結晶構造と呼吸酵素の分子進化」化学と生物、10月号(2013)
  • 澤井仁美、城宜嗣 サイトグロビンの分子構造 細胞 45 (13), 9-12 (2013)

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