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Presented papers

2017

1.	HmuS from Yersinia pseudotuberculosis is a non-canonical heme-degrading enzyme to acquire iron from heme Masato Onzuka, Yukari Sekine, Takeshi Uchida, Koichiro Ishimori, and Shin-ichi Ozaki Biochimica et Biophysica Acta (BBA) 2017, in press
2.	*The Iron Chaperone Protein CyaY from Vibrio cholerae* is a Heme-Binding Protein** Takeshi Uchida, Noriyuki Kobayashi, Souichiro Muneta, and Koichiro Ishimori Biochemistry 2017, 56, 2425
3.	Heme iron coordination structure of heme transport protein HutB from Vibrio cholerae Takeshi Uchida,Takumi, Funamizu, Mariko Ogura, and Koichiro Ishimori Bull. Chem. Soc. Jpn., 2017, in press
4.	Heme Proximal Hydrogen Bonding between His170 and Asp132 Plays an Essential Role in the Heme Degradation Reaction by HutZ from Vibrio cholerae Uchida Takeshi, Dojun Nobuhiko, Sekine Yukari, Ishimori Koichiro Biochemistry 2017, in press
5.

2016

1.	Energetic Mechanism of Cytochrome c – Cytochrome c Oxidase Electron Transfer Complex Formation under Turnover Conditions Revealed by Mutational Effects and Docking Simulation Wataru Sato, Seiji Hitaoka, Kaoru Inoue, Mizue Imai, Tomohide Saio,Takeshi Uchida, Kyoko Shinzawa-Itoh, Shinya Yoshikawa,Kazunari Yoshizawa and Koichiro Ishimori J. Biol. Chem., 2016, 291, 15320
2.	Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters Norifumi Muraki, Chihiro Kitatsuji, Mariko Ogura, Takeshi Uchida, Koichiro Ishimori, and Shigetoshi Aono Int. J. Mol. Sci. 2016, 17(6), 829
3.	Redox-Dependent Dynamics in Heme-Bound Bacterial Iron Response Regulator (Irr) Protein Kazuo Kobayashi, Megumi Nakagaki, Haruto Ishikawa, Kazuhiro Iwai, Mark R. O’Brian and Koichiro Ishimori Biochemistry, 2016, 55(29), 4047
4.	Energetic basis on interactions between ferredoxin and ferredoxin NADP⁺ reductase at varying physiological conditions Misaki Kinoshita, Ju Yaen Kim, Satoshi Kume, Yuxi Lin, K. Hun Mok, Yosky Kataoka, Koichiro Ishimori, Natalia Markova, Genji Kurisu, Toshiharu Hase, Young-Ho Lee Biochem. Biophys. Res. Commun., 2017, 428, 909
5.	Dual role of the active-center cysteine in human peroxiredoxin 1: Peroxidase activity and heme binding Yuta Watanabe, Koichiro Ishimori, Takeshi Uchida Biochem. Biophys. Res. Commun., 2017, 483, 930
6.	Iron Chelators Inhibit the Heme-Degradation Reaction by HutZ from Vibrio cholerae Nobuhiko Dojun, Yukari Sekine, Koichiro Ishimori and Takeshi Uchida Dalton Trans., 2017,46, 5147

2015

1.	A dye-decolorizing peroxidase from Vibrio cholerae T. Uchida, M. Sasaki, Y. Tanaka, K. Ishimori Biochemistry, 2015, 54, 6610
2.	Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c M. Imai, T. Saio, H. Kumeta, T. Uchida, F. Inagaki, K. Ishimori Biochem. Biophys. Res. Commun., 2016, 469, 978
3.	Conformational disorder of the most immature Cu,Zn-superoxide dismutase leading to amyotrophic lateral sclerosis Y. Furukawa, I. Anzai, S. Akiyama, M. Imai, F. J. C. Cruz, T. Saio, K. Nagasawa, T. Nomura, K. Ishimori J. Biol. Chem., 2016, 291, 4144. DOI: 10.1074/jbc.M115.683763
4.	Protein oxidation mediated by heme-induced active site conversion specific for heme-regulated transcription factor, iron response regulator C. Kitatsuji, K. Izumi, S. Nambu, M. Kurogochi, T. Uchida, S. Nishimura, K. Iwai, M. R. O’Brian, M. Ikeda-Saito, K. Ishimori Sci. Rep., 2016, 6:18703, 1
5.	Cytoplasmic heme-binding protein (HutX) from Vibrio cholerae is an intracellular heme transport protein for the heme-degrading enzyme, HutZ Yukari Sekine, Takehito Tanzawa, Yoshikazu Tanaka, Koichiro Ishimori, Takeshi Uchida Biochemistry, 2016, 55(6), 884 DOI: 10.1021/acs.biochem.5b01273
6.	Amorphous aggregation of cytochrome c with inherently low amyloidogenicity is characterized by the metastability of supersaturation and the phase diagram Yuxi Lin, József Kardos, Mizue Imai, Tatsuya Ikenoue, Misaki Kinoshita, Toshihiko Sugiki, Koichiro Ishimori,Yuji Goto, and Young-Ho Lee Langmuir, 2016, 32(8), 2010
7.	Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance Yasuaki Kabe,Takanori Nakane,Ikko Koike,Tatsuya Yamamoto,Yuki Sugiura,Erisa Harada,Kenji Sugase,Tatsuro Shimamura,Mitsuyo Ohmura,Kazumi Muraoka,Ayumi Yamamoto,Takeshi Uchida,So Iwata,Yuki Yamaguchi,Elena Krayukhina,Masanori Noda,Hiroshi Handa,Koichiro Ishimori,Susumu Uchiyama,Takuya Kobayashi& Makoto Suematsu Nature Communications, 2016, 7, 11030

2014

1.	Spectroscopic studies on HasA from Yersinia pseudotuberculosis S. Ozaki, T. Sato, Y. Sekine, C. T. Migita, T. Uchida and K. Ishimori J. Inorg. Biochem., Vol. 138, 31-38 (2014).
2.	Molecular Mechanism for Heme-Mediated Inhibition of 5-Aminolevulinic Acid Synthase 1 C. Kitatsuji, M. Ogura, T. Uchida, K. Ishimori and S. Aono Bull. Chem. Soc. Jpn., Vol. 87, 997-1004 (2014)
3.	Heme-binding properties of HupD functioning as a substrate-binding protein in a heme-uptake ABC-transporter system in Listeria monocytogenes Y. Okamoto, H. Sawai, M. Ogura, T. Uchida, K. Ishimori, T. Hayashi and S. Aono Bull. Chem. Soc. Jpn.,
4.	Unique Heme Environmental Structures in Heme-regulated Proteins Using Heme as the Signaling Molecule K. Ishimori and Y. Watanabe Chem. Lett., in press

2013

1.	Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA T. Uzawa, T. Isoshima, Y. Ito, K. Ishimori, D. E. Makarov and K. W. Plaxco Biophys. J., Vol. 104, 2485-2492 (2013).

2012

1.	Effects of the bHLH Domain on Axial Coordination of heme in the PAS-A Domain of Neuronal PAS Domain Protein 2 (NPAS2): Conversion from His119/Cys170 Coordination to His119/His171 Coordination T. Uchida, I. Sagami, T. Shimizu, K. Ishimori, and T. Kitagawa J. Inorg. Biochem., Vol. 108, 188-195 (2012).
2.	The Structural Investigation on Small Methane Clusters Described by Two Different Potentials H. Takeuchi Comput. Theor. Chem., Vol. 986, 48-56 (2012).
3.	Function of Heme Regulatory Motif in the Oxidative Modification for Transcriptional Regulation T. Tatsukawa, T. Uchida, and K. Ishimori Peptide Sci., Vol. 2011, 191-192 (2012).
4.	A Heme Degradation Enzyme, HutZ, from Vibrio cholerae T. Uchida, Y. Sekine, T. Matsui, M. Ikeda-Saito, and K. Ishimori Chem. Commun., Vol. 48, 6741-6743 (2012).
5.	Structural Features of Small Benzene Clusters (C6H6)n (n ≤ 30) As Investigated with the All-Atom OPLS Potential H. Takeuchi J. Phys. Chem. A, Vol. 116, 10172-10181 (2012).
6.	The Structural Investigation on Small Methane Clusters Described by Two Different Potentials H. Takeuchi Comput. Theor. Chem., Vol. 986, 48-56 (2012).

2011

1.	Probing Phenylalanine Environments in Oligomeric Structures with Pentafluorophenylalanine and Cyclohexylalanine T. Nomura, R. Kamada, I. Ito, K. Sakamoto, Y. Chuman, K. Ishimori, Y. Shimohigashi, K. Sakaguchi Biopolymer, Vol. 95, 410-419 (2011).
2.	A Theoretical Investigation on Optimal Structures of Ethane Clusters (C2H6)n with n ≤ 25 and Their Building-up Principle H. Takeuchi J. Comput. Chem., Vol. 32, 1345-1352 (2011).
3.	Unusual Heme Binding in the Bacterial Iron Response Regulator Protein (Irr): Spectral Characterization of Heme Binding to Heme Regulatory Motif H. Ishikawa, M. Nakagaki, A. Bamba, T. Uchida, H. Hori, M. R. O’Brian, K. Iwai, and K. Ishimori Biochemistry, Vol. 50, 1016-1022 (2011).
4.	NMR Basis for Interprotein Electron Transfer Gating between Cytochrome c – Cytochrome c Oxidase K. Sakamoto, M. Kamiya, M. Imai, K. Shinzawa-Ito, T. Uchida, K. Kawano, S. Yoshikawa, and K. Ishimori Proc. Natl. Acad. Sci. U.S.A., Vol. 108, 12271-12276 (2011).
5.	Identification and Functional and Spectral Characterizations of a Novel Globin-Coupled Histidine Kinase from Anaeromixobacter sp. Fw109-5 K. Kitanishi, K. Kobayashi, T. Uchida, K. Ishimori, J. Igarashi, and T. Shimizu J. Biol. Chem., Vol. 286, 35522-35534 (2011).
6.	Theoretical Investigation on Structural Properties of Ethylene Clusters (C2H4)n (n ≤ 25) H. Takeuchi Comput.Theor. Chem., Vol. 970, 48-53 (2011).

2010

1.	Molecular Oxygen Regulates the Enzymatic Activity of a Heme-containing Diguanylate Cyclase (HemDGC) for the Synthesis of Cyclic Di-GMP H. Sawai, S. Yoshioka, T. Uchida, M. Hyodo, Y. Hayakawa, K. Ishimori, and S. Aono Biochimica et Biophysica Acta, Vol. 1804, No. 1, 166-172 (2010).
2.	Global Minimum Geometries of Acetylene Clusters (HCCH)n with n ≤ 55 Obtained by a Heuristic Method Combined with Geometrical Perturbations H. Takeuchi J. Comput. Chem., Vol. 31, No. 8, 1699-1706 (2010).
3.	Redox-controlled Backbone Dynamics of Human Cytochrome c Revealed by 15N NMR Relaxation Measurements K. Sakamoto, M. Kamiya, T. Uchida, K. Kawano, and K. Ishimori Biochem. Biophys. Res. Commun., Vol. 398, 231-236 (2010).
4.	Global Minimum Geometries of Acetylene Clusters (HCCH)n with n ≤ 55 Obtained by a Heuristic Method Combined with Geometrical Perturbations H. Takeuchi J. Comput. Chem., Vol. 31, 1699-1706 (2010).
5.	Molecular Oxygen Regulates the Enzymatic Activity of a Heme-containing Diguanylate Cyclase (HemDGC) for the Synthesis of Cyclic di-GMP H. Sawai, S. Yoshioka, T. Uchida, M. Hyodo, Y. Hayakawa, K. Ishimori, and S. Aono Biochim. Biophys. Acta, Vol. 1804, 166-172 (2010).

2009

1.	Optical Manipulation of Proteins in Aqueous Solution Y. Tsuboi, T. Shoji, M. Nishino, S. Masuda, K. Ishimori, and N. Kitamura App. Sur. Sci., Vol. 255, 9906–9908 (2009)

Hokkaido University Graduate School of Chemical Sciences and Engineering