発表論文

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. 201617(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

Biochemistry2016, 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

Biochemistry2015, 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
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年

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)

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