発表論文
2022年度
1. | Heme binding to cold shock protein D, CspD, from Vibrio cholerae Dayeon Nam, Wataru Motegi, Koichiro Ishimori, Takeshi Uchida Biochem. Biophys. Res. Commun., 2022, 624, 151-156 |
2. | Converting cytochrome c into a DyP-like metalloenzyme Issei Omura, Koichiro Ishimori, Takeshi Uchida Dalton Trans., 2022, 51, 12641-12649 |
3. | Metal sensing by a glycine–histidine repeat sequence regulates the heme degradation activity of PM0042 from Pasteurella multocida Takeshi Uchida, Kazuki Ota, Akinobu Tatsumi, Syota Takeuchi, Koichiro Ishimori Inorg. Chem., 2022, 61, 13543-13553 |
2021年度
1. | Radical transfer but not heme distal residues is essential for pH dependence of dye-decolorizing activity of peroxidase from Vibrio cholerae Takeshi Uchida, Issei Omura, Sayaka Umetsu, Koichiro Ishimori J. Inorg. Biochem., 2021, 219, 111422 (8 pages) |
2. | Conformational ensemble of a multidomain protein explored by Gd3+ electron paramagnetic resonance Tomohide Saio, Soya Hiramatsu, Mizue Asada, Hiroshi Nakagawa, Kazumi Shimizu, Hiroyuki Kumeta, Toshikazu Nakamura, Koichiro Ishimori Biophys. J., 2021, 120, 2943-2951 |
3. | Zinc-dependent oligomerization of thermus thermophilus trigger factor chaperone Haojie Zhu, Motonori Matsusaki, Taiga Sugawara, Koichiro Ishimori, Tomohide Saio Biology, 2021, 10, 1106-1106 (13 pages) |
4. | Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex Kamran Rizzolo, Angela Yeou Hsiung Yu, Adedeji Ologbenla, Sa Rang Kim, Haojie Zhu, Koichiro Ishimori, Guillaume Thibault, Elisa Leung, Yi Wen Zhang, Mona Teng, Marta Haniszewski, Noha Miah, Sadhna Phanse, Zoran Minic, Sukyeong Lee, Julio Diaz Caballero, Mohan Babu, Francis T. F. Tsai, Tomohide Saio, Walid A. Houry Nat. Commun., 2021, 12, 281 (18 pages) |
5. | C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers Hitoki Nanaura, Honoka Kawamukai, Ayano Fujiwara, Takeru Uehara, Yuichiro Aiba, Mari Nakanishi, Tomo Shiota, Masaki Hibino, Pattama Wiriyasermkul, Sotaro Kikuchi, Riko Nagata, Masaya Matsubayashi, Yoichi Shinkai, Tatsuya Niwa, Taro Mannen, Naritaka Morikawa, Naohiko Iguchi, Takao Kiriyama, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Takashi Oda, Noriyuki Kodera, Sachiko Toma-Fukai, Mamoru Sato, Hideki Taguchi, Shushi Nagamori, Osami Shoji, Koichiro Ishimori, Hiroyoshi Matsumura, Kazuma Sugie, Tomohide Saio, Takuya Yoshizawa, Eiichiro Mori Nat. Commun., 2021, 12, 531 (12 pages) |
6. | Regulation of the expression of the nickel uptake system in Vibrio cholerae by iron and heme via Fur Kazuyoshi Muranishi, Koichiro Ishimori, Takeshi Uchida J. Inorg. Biochem., 2022, 228, 111713 (9 pages) |
7. | Structural and kinetic views of molecular chaperones in multidomain protein folding Soichiro Kawagoe, Koichiro Ishimori, Tomohide Saio Int. J. Mol. Sci., 2022, 23, 2485 (13 pages) |
2020年度
1. | Biophysical research in Hokkaido University, Japan Tomoyasu Aizawa, Makoto Demura, Kazutoshi Gohara, Hisashi Haga, Koichiro Ishimori, Masataka Kinjo, Tamiki Komatsuzaki, Katsumi Maenaka, Min Yao Biophys. Rev., 2020, 12, 233-236 |
2. | Spectroscopic characterization of Halorhodopsin reconstituted into nanodisks using native lipids Ayumi Yamamoto, Takashi Tsukamoto, Kenshiro Suzuki, Eri Hashimoto, Yoshihiro Kobashigawa, Kousuke Shibasaki, Takeshi Uchida, Fuyuhiko Inagaki, Makoto Demura, Koichiro Ishimori Biophys. J., 2020, 118, 2853-2865 |
3. | Osmotic pressure effects identify dehydration upon cytochrome c-cytochrome c oxidase complex formation contributing to a specific electron pathway formation Wataru Sato, Seiji Hitaoka, Takeshi Uchida, Kyoko Shinzawa-Itoh, Kazunari Yoshizawa, Shinya Yoshikawa, Koichiro Ishimori Biochem. J., 2020, 477, 1565-1578 |
4. | Mechanistic insights into heme-mediated transcriptional regulation via a bacterial manganese-binding iron regulator, iron response regulator (Irr) Dayeon Nam, Yuki Matsumoto, Takeshi Uchida, Mark R. O’Brian, Koichiro Ishimori J. Biol. Chem., 2020, 295, 11316-11325 |
5. | Distance distribution between two iodine atoms derived from small-angle x-ray scattering interferometry for analyzing a conformational ensemble of heavy atom-labeled small molecules Yuya Taguchi, Tomohide Saio, Daisuke Kohda J. Phys. Chem. Lett., 2020, 25, 5451-5456 |
6. | Dynamics of proteins with different molecular structures under solution condition Rintaro Inoue, Takashi Oda, Hiroshi Nakagawa, Taiki Tominaga, Tomohide Saio, Yukinobu Kawakita, Masahiro Shimizu, Aya Okuda, Ken Morishima, Nobuhiro Sato, Reiko Urade, Mamoru Sato, Masaaki Sugiyama Sci. Rep., 2020, 10, 21678 (10 pages) |
7. | Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex Kamran Rizzolo, Angela Yeou Hsiung Yu, Adedeji Ologbenla, Sa Rang Kim, Haojie Zhu, Koichiro Ishimori, Guillaume Thibault, Elisa Leung, Yi Wen Zhang, Mona Teng, Marta Haniszewski, Noha Miah, Sadhna Phanse, Zoran Minic, Sukyeong Lee, Julio Diaz Caballero, Mohan Babu, Francis T. F. Tsai, Tomohide Saio, Walid A. Houry Nat. Commun., 2021, 12, 281 (18 pages) |
8. | Deuteration aiming for neutron scattering Aya Okuda, Rintaro Inoue, Ken Morishima, Tomohide Saio, Yasuhiro Yunoki, Maho Yagi-Utsumi, Hirokazu Yagi, Masahiro Shimizu, Nobuhiro Sato, Reiko Urade, Koichi Kato, Masaaki Sugiyama Biophys. Physicobiol., 2021, 18, 16-27 |
9. | A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization Masaki Okumura, Shingo Kanemura, Motonori Matsusaki, Misaki Kinoshita, Tomohide Saio, Dai Ito, Chihiro Hirayama, Hiroyuki Kumeta, Mai Watabe, Yuta Amagai, Young-Ho Lee, Shuji Akiyama, Kenji Inaba Structure, 2021, 29, 1-14 |
10. | 金属センシング 石森浩一郎 生命金属ダイナミクス 第4章 第3節、株式会社エヌ・ティー・エス (2021) |
11. | Biological phase separation: cell biology meets biophysics
Biophys. Rev., 2020, 12, 519-539 |
12. | Solution NMR spectroscopy for investigation of liquid-liquid phase separation Tomohide Saio, M. Okumura, Y.Ho. Lee
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13. | 相分離生物学:相分離メガネのススメ 検出技術:天然変性タンパク質の構造生物学 小田隆, 齋尾智英 生物工学会誌, 2020, 98, 232-235 |
14. | 中性子溶液散乱-現在・過去・未来- 杉山正明, 井上倫太郎, 中川洋, 齋尾智英 波紋, 2020, 30, 16-25 |
2019年度
1. | Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding Masaki Okumura, Kentaro Noi, Shingo Kanemura, Misaki Kinoshita, Tomohide Saio, Yuichi Inoue, Takaaki Hikima, Shuji Akiyama, Teru Ogura, and Kenji Inaba Nat. Chem. Biol., 2019, 15, 499-509 |
2. | Accelerating structural life science by paramagnetic lanthanide probe methods Tomohide Saio and Koichiro Ishimori Biochim. Biophys. Acta. Gen. Subj., in press. |
3. | 立体構造から明らかにする分子シャペロンの作用機序 斉尾智英, 石森 浩一郎 生物物理, 2019, 59, 197-201 |
4. | コレラ菌のヘム獲得機構と生合成系 内田 毅 生化学, 2019, 91, 404-408 |
5. | Specific heme binding to heme regulatory motifs in iron regulatory proteins and its functional significance Yudai Nishitani, Hirotaka Okutani, Yukiko Takeda, Takeshi Uchida, Kazuhiro Iwai, and Koichiro Ishimori J. Inorg. Biochem., 2019, 198, 110726 (11 pages) |
6. | Structural basis for heme transfer reaction in heme uptake machinery from Corynebacteria Norifumi Muraki, Chihiro Kitatsuji, Yasunori Okamoto, Takeshi Uchida, Koichiro Ishimori, and Shigetoshi Aono Chem. Commun., 2019, 55, 13864-13867 |
7. | Role of conserved arginine in the heme distal site of HutZ from Vibrio cholerae in the heme degradation reaction Takeshi Uchida, Nobuhiko Dojun, Kazuki Ota, Yukari Sekine, Yuina Nakamura, Sayaka Umetsu, and Koichiro Ishimori Arch. Biochem. Biophys., 2019, 677, 108165 (15 pages) |
8. | A single mutation converts Alr5027 from cyanobacteria Nostoc sp. PCC 7120 to a heme-binding protein with heme-degrading ability Nobuhiko Dojun, Kazuyoshi Muranishi, Koichiro Ishimori, and Takeshi Uchida J. Inorg. Biochem, 2020, 203, 110916 (11 pages) |
2018年度
1. | Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA Kentaro Miyazaki and Kei Kitahara Sci. Rep., 2018, 8, 5179 |
2. | Oligomerization of a molecular chaperone modulates its activity Tomohide Saio, Soichiro Kawagoe, Koichiro Ishimori, and Charalampos G. Kalodimos eLife, 2018, 7, e35731 |
3. | Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy Shohei Konno, Kentaro Doi, and Koichiro Ishimori Biophys. Physicobiol., 2019, 16, 18-27 |
4. | Subunit-subunit interactions play a key role in the heme-degradation reaction of HutZ from Vibrio cholerae Takeshi Uchida, Kazuki Ota, Yukari Sekine, Nobuhiko Dojun, and Koichiro Ishimori Dalton. Trans., 2019, 48, 3973-3983 |
5. | Role of His63 in HutZ from Vibrio cholerae in the heme degradation reaction and heme binding Takeshi Uchida, Nobuhiko Dojun, Yukari Sekine, and Koichiro Ishimori Dalton. Trans., 2019, 48, 5408-5416 |
2017年度
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) 1861, (2017), 1870-1878 |
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, 90, 924-930 |
4. | Heme Proximal Hydrogen Bonding between His170 and Asp132 Plays an Essential Role in the Heme Degradation Reaction by HutZ from Vibrio cholerae Takeshi Uchida, Nobuhiko Dojun, Yukari Sekine, and Koichiro Ishimori Biochemistry 2017, 56, 2723-2734 |
5. | Reaction intermediates in the heme degradation reaction by HutZ from Vibrio cholerae Takeshi Uchida, Yukari Sekine, Nobuhiko Dojun, Ariel Lewis, Izumi Ishigami, Toshitaka Matsui, Syun-Ru Yeh, and Koichiro Ishimori Dalton Trans., 2017, 46, 8104-8109 |
6. | Heme binding to porphobilinogen deaminase from Vibrio cholerae decelerates the formation of 1-hydroxymethylbilane Takeshi Uchida, Takumi Funamizu, Minghao Chen, Yoshikazu Tanaka,and Koichiro Ishimori ACS Chem. Biol., 2018, 13, 750-760 |
7. | Redox-dependent axial ligand replacement and its functional significance in heme-bound iron regulatory proteins Mariko Ogura, Ryosuke Endo, Haruto Ishikawa, Yukiko Takeda, Takeshi Uchida, Kazuhiro Iwai, Kazuo Kobayashi, and Koichiro Ishimori J. Inorg. Biochem., 2018, 182, 238-248 |
8. | Polyethylene Glycol Promotes Autoxidation of Cytochrome c Wataru Sato, Takeshi Uchida, Tomohide Saio, and Koichiro Ishimori Biochim. Biophys. Acta., Gen. Subj., 2018, 1862, 1339-1349 |
2016年度
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年度
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
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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
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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年
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., 2014, 138, 31 |
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., 2014, 87, 997 |
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., 2014, 43, 1680 (Chem. Lett. 誌の表紙を飾りました!) |
2013年
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., 2013, 104, 2485 |
2012年
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., 2012, 108, 188 |
2. | The Structural Investigation on Small Methane Clusters Described by Two Different Potentials H. Takeuchi Comput. Theor. Chem., 2012, 986, 48 |
3. | Function of Heme Regulatory Motif in the Oxidative Modification for Transcriptional Regulation T. Tatsukawa, T. Uchida, and K. Ishimori Peptide Sci., 2012, 2011, 191 |
4. | A Heme Degradation Enzyme, HutZ, from Vibrio cholerae T. Uchida, Y. Sekine, T. Matsui, M. Ikeda-Saito, and K. Ishimori Chem. Commun., 2012, 48, 6741 |
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, 2012, 116, 10172 |
6. | The Structural Investigation on Small Methane Clusters Described by Two Different Potentials H. Takeuchi Comput. Theor. Chem., 2012, 986, 48 |
2011年
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, 2011, 95, 410 |
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., 2011, 32, 1345 |
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, 2011, 50, 1016 |
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., 2011, 108, 12271 |
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., 2011, 286, 35522 |
6. | Theoretical Investigation on Structural Properties of Ethylene Clusters (C2H4)n (n ≤ 25) H. Takeuchi Comput.Theor. Chem., 2011, 970, 48 |
2010年
1. | Molecular Oxygen Regulates the Enzymatic Activity of a Heme-containing Diguanylate Cyclase (HemDGC) for the Synthesis of Cyclic Di-GMP |
2. | Global Minimum Geometries of Acetylene Clusters (HCCH)n with n ≤ 55 Obtained by a Heuristic Method Combined with Geometrical Perturbations |
3. | Redox-controlled Backbone Dynamics of Human Cytochrome c Revealed by 15N NMR Relaxation Measurements |
4. | Global Minimum Geometries of Acetylene Clusters (HCCH)n with n ≤ 55 Obtained by a Heuristic Method Combined with Geometrical Perturbations |
5. | Molecular Oxygen Regulates the Enzymatic Activity of a Heme-containing Diguanylate Cyclase (HemDGC) for the Synthesis of Cyclic di-GMP |
2009年
1. | Optical Manipulation of Proteins in Aqueous Solution |