Details of a Researcher - KOJIMA Chojiro

Papers - KOJIMA Chojiro

about 191

NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA

Shuhei Sakurabayashi, Kyoko Furuita, Takeshi Yamada, Noriaki Sugiura, Makoto Nomura, Takanori Nakan … Show more authors

Journal of the American Chemical Society 147 ( 17 ) 14254 - 14269 2025.4 [Reviewed]

DOI

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

Small molecules that bind to mismatched DNA have been applied in various fields, including nanotechnology, bioimaging, and therapeutics. However, the intrinsic dynamic nature of mismatched DNA complicates the prediction of structural changes upon ligand binding, hindering rational ligand design. In this study, NMR was used for structure-based drug design, with a focus on the G:G mismatch binder ND and the structural dynamics of the DNA-ND complex. Through comprehensive NMR analysis with isotope labeling, two complex structures, the transient and stable complexes, were successfully determined. The nucleobase flip-outs and the distortion of the phosphate backbone of the complex structures were characterized by residual dipolar coupling (RDC) and 31P NMR, respectively. The RDC-refined stable complex structure suggested that the ligand linker–nucleobase interaction allosterically regulates a structural transition. This interaction was experimentally validated by 1H–15N HSQC spectra using a 15N-labeled ligand. Disruption of this key allosteric interaction facilitated the design of a new ligand, sND, that traps the transient complex structure. In conclusion, comprehensive NMR analysis using a weak binder aids in designing nucleic acid-binding ligands based on transient complex structures.

Other Link： https://doi.org/10.1021/jacs.4c17538

An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function

Li, YY; Wang, Q; Jia, HM; Ishikawa, K; Kosami, K; Ueba, T; Tsujimoto, A; Yamanaka, M; Yabumoto, Y; … Show more authors

NATURE COMMUNICATIONS 15 ( 1 ) 2024.5 [Reviewed]

DOI Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal) Joint Work

Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening

Ken-ichiro Taoka, Ikumi Kawahara, Shoko Shinya, Ken-ichi Harada, Eiki Yamashita, Zenpei Shimatani, … Show more authors

Plant J 112 ( 6 ) 1337 - 1349 2022.12 [Reviewed]

DOI Web of Science PubMed

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

19F chemical library and 19F-NMR for a weakly bound complex structure

Shoko Shinya, Ritsuko Katahira, Kyoko Furuita, Toshihiko Sugiki, Young-Ho Lee, Yoshikazu Hattori, K … Show more authors

RSC Medicinal Chemistry 13 ( 9 ) 1100 - 1111 2022.7 [Reviewed] [Invited]

DOI Web of Science PubMed CiNii Research

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Single Work

Cooperative regulation of PBI1 and MAPKs controls WRKY45 transcription factor in rice immunity

NATURE COMMUNICATIONS 13 ( 1 ) 2397 2022.5 [Reviewed]

DOI Web of Science PubMed CiNii Research

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli

Toshihiko Sugiki, Yoshihiro Yamaguchi, Toshimichi Fujiwara, Masayori Inouye,Yutaka Ito, Chojiro Koj … Show more authors

Scientific Reports (Nature Publisher Group) 10 ( 1 ) 2466 2020.2 [Reviewed]

DOI Web of Science PubMed CiNii Research

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

Current NMR Techniques for Structure-Based Drug Discovery

Toshihiko Sugiki, Kyoko Furuita, Toshimichi Fujiwara, Chojiro Kojima

Molecules 23 ( 1 ) 148 2018.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit

Hisashi Tatebe, Shinichi Murayama, Toshiya Yonekura, Tomoyuki Hatano, David Richter, Tomomi Furuya, … Show more authors

eLife 6 e19594 2017.3 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：ELIFE SCIENCES PUBLICATIONS LTD Joint Work

The target of rapamycin (TOR) protein kinase forms multi-subunit TOR complex 1 (TORC1) and TOR complex 2 (TORC2), which exhibit distinct substrate specificities. Sin1 is one of the TORC2-specific subunit essential for phosphorylation and activation of certain AGC-family kinases. Here, we show that Sin1 is dispensable for the catalytic activity of TORC2, but its conserved region in the middle (Sin1CRIM) forms a discrete domain that specifically binds the TORC2 substrate kinases. Sin1CRIM fused to a different TORC2 subunit can recruit the TORC2 substrate Gad8 for phosphorylation even in the sin1 null mutant of fission yeast. The solution structure of Sin1CRIM shows a ubiquitin-like fold with a characteristic acidic loop, which is essential for interaction with the TORC2 substrates. The specific substrate-recognition function is conserved in human Sin1CRIM, which may represent a potential target for novel anticancer drugs that prevent activation of the mTORC2 substrates such as AKT.

Other Link： https://elifesciences.org/content/6/e19594

Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice

Kazuya Ishikawa, Koji Yamaguchi, Kazuaki Sakamoto, Satomi Yoshimura, Kento Inoue, Seiji Tsuge, Choj … Show more authors

NATURE COMMUNICATIONS 5 ( 1 ) 5430 2014.11 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP Joint Work

14-3-3 proteins act as intracellular receptors for rice Hd3a florigen

Ken-ichiro Taoka, Izuru Ohki, Hiroyuki Tsuji, Kyoko Furuita, Kokoro Hayashi, Tomoko Yanase, Midori … Show more authors

Nature 476 ( 7360 ) 332 - 335 2011.7 [Reviewed]

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Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

Structural feature of bent DNA recognized by HMGB1

Kyoko Furuita, Shunpei Murata, JunGoo Jee, Satoshi Ichikawa, Akira Matsuda, and Chojiro Kojima

J. Am. Chem. Soc. 133 ( 15 ) 5788 - 5790 2011.4 [Reviewed]

DOI Web of Science PubMed CiNii Research

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

Small-molecule ligand induces nucleotide flipping in (CAG)(n) trinucleotide repeats

Nakatani K, Hagihara S, Goto Y, Kobori A, Hagihara M, Hayashi G, Kyo M, Nomura M, Mishima M, Kojima … Show more authors

NATURE CHEMICAL BIOLOGY 1 ( 1 ) 39 - 43 2005.6 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

DNA trinucleotide repeats, particularly CXG, are common within the human genome. However, expansion of trinucleotide repeats is associated with a number of disorders, including Huntington disease, spinobulbar muscular atrophy and spinocerebellar ataxia. In these cases, the repeat length is known to correlate with decreased age of onset and disease severity. Repeat expansion of (CAG)n, (CTG)n and (CGG)n trinucleotides may be related to the increased stability of alternative DNA hairpin structures consisting of CXG-CXG triads with X-X mismatches. Small-molecule ligands that selectively bound to CAG repeats could provide an important probe for determining repeat length and an important tool for investigating the in vivo repeat extension mechanism. Here we report that napthyridine-azaquinolone (NA, 1) is a ligand for CAG repeats and can be used as a diagnostic tool for determining repeat length. We show by NMR spectroscopy that binding of NA to CAG repeats induces the extrusion of a cytidine nucleotide from the DNA helix.

A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO

302 ( 5643 ) 286 - 290 2003.10 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Joint Work

Beyond Static Tethering at Membrane Contact Sites: Structural Dynamics and Functional Implications of VAP Proteins

Takashi S. Kodama,Kyoko Furuita and Chojiro Kojima

Molecules 30 ( 6 ) 2025.3 [Reviewed]

DOI

Language：English Publishing type：Research paper (scientific journal) Joint Work

Improved analysis of NMR chemical shift perturbations through an error estimation method

Furuita, K; Kojima, C

BIOPHYSICAL CHEMISTRY 310 2024.7 [Reviewed]

DOI Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal) Joint Work

Hydrogen bonds connecting the N-terminal region and the DE loop stabilize the monomeric structure of transthyretin

Inada Yuki, Ono Yuichiro, Okazaki Kyo, Yamashita Takuma, Kawaguchi Tomoyuki, Kawano Shingo, Kobashi … Show more authors

JOURNAL OF BIOCHEMISTRY 174 ( 4 ) 355 - 370 2023.7 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Biological Magnetic Resonance Data Bank

Jeffrey C Hoch, Kumaran Baskaran, Harrison Burr, John Chin, Hamid R Eghbalnia, Toshimichi Fujiwara, … Show more authors

Nucleic Acids Res 51 ( D1 ) D368 - D376 2023.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Single Work

NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA

Takeshi Yamada, Kyoko Furuita, Shuhei Sakurabayashi, Makoto Nomura, Chojiro Kojima, Kazuhiko Nakata … Show more authors

Nucleic Acids Research 50 ( 17 ) 9621 - 9631 2022.9 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Single Work

Physicochemical Characterization of the Catalytic Unit of Hammerhead Ribozyme and Its Relationship with the Catalytic Activity

Yoshiyuki Tanaka, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Masayuki Morikawa, Takashi S. K … Show more authors

Biophysica 2 ( 3 ) 221 - 239 2022.8 [Reviewed]

DOI Web of Science CiNii Research

Language：English Publishing type：Research paper (scientific journal) Single Work

Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition

Ken-ichi Harada, Kyoko Furuita, Eiki Yamashita, Ken-ichiro Taoka, Hiroyuki Tsuji, Toshimichi Fujiwa … Show more authors

Scientific Reports 12 ( 1 ) 2022.7 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Single Work

1H, 13C, and 15N resonance assignments of human glutathione peroxidase 4

Kyoko Furuita, Kouki Inomata, Toshihiko Sugiki, Naohiro Kobayashi, Toshimich Fujiwara, Chojiro Koji … Show more authors

Biomolecular NMR Assignments 16 ( 2 ) 267 - 271 2022.5 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Single Work

A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction

Toshihiko Sugikia, Young-HoLee, Nesreen Alsanousi, Kaito Murata, Izuru Kawamura, Toshimichi Fujiwar … Show more authors

Analytical biochemistry 639 114521 2022.2 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Joint Work

Biochemical propensity mapping for structural and functional anatomy of importin alpha IBB domain

Jibiki Kazuya, Liu Mo-yan, Lei Chao-sen, Kodama Takashi S., Kojima Chojiro, Fujiwara Toshimichi, Ya … Show more authors

GENES TO CELLS 27 ( 3 ) 173 - 191 2022.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR

Furuita Kyoko, Hiraoka Marina, Hanada Kentaro, Fujiwara Toshimichi, Kojima Chojiro

FEBS LETTERS 595 ( 17 ) 2248 - 2256 2021.9 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Sensitivity enhancement by sequential data acquisition for C-13-direct detection NMR

Furuita Kyoko, Sugiki Toshihiko, Takamuku Mika, Hattori Yoshikazu, So Masatomo, Kawata Yasushi, Ike … Show more authors

JOURNAL OF MAGNETIC RESONANCE 322 106878-1 - 106878-7 2021.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Joint Work

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

Siqin Bala, Shoko Shinya, Arpita Srivastava, Marie Ishikawa, Atsushi Shimada, Naohiro Kobayashi, C … Show more authors

Biochimica et Biophysica Acta (BBA) - General Subjects 1864 ( 2 ) 2019.8 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Science Direct Joint Work

Other Link： https://doi.org/10.1016/j.bbagen.2019.129418

Structural characterization of the N-terminal kinase-interacting domain of an Hsp90-cochaperone Cdc37 by CD and solution NMR spectroscopy

Futoshi Ihama, Mami Yamamoto, Chojiro Kojima, Toshimichi Fujiwara, Katsumi Matsuzaki, Yoshihiko Miy … Show more authors

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Vol.1867 ( 9 ) 813 - 820 2019.6 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Science Direct Joint Work

Other Link： https://doi.org/10.1016/j.bbapap.2019.06.007

Structural instability of lamin A tail domain modulates its assembly and higher order function in Emery-Dreifuss muscular dystrophy

Mio Muneyo, Sugiki Toshihiko, Matsuda Chie, Mitsuhashi Hiroaki, Kojima Chojiro, Chan Siu Yuen, Haya … Show more authors

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 512 ( 1 ) 22 - 28 2019.4 [Reviewed]

DOI Web of Science PubMed

Language：Japanese Publishing type：Research paper (scientific journal) Joint Work

Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks

Naohiro Kobayashi, Yoshikazu Hattori, Takashi Nagata, Shoko Shinya, Peter Güntert, Chojiro Kojima, … Show more authors

Bioinformatics 34 ( 24 ) 4300 - 4301 2018.12 [Reviewed]

DOI

Language：English Publishing type：Research paper (scientific journal) Joint Work

Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks

Kobayashi Naohiro, Hattori Yoshikazu, Nagata Takashi, Shinya Shoko, Guntert Peter, Kojima Chojiro, … Show more authors

BIOINFORMATICS 34 ( 24 ) 4300 - 4301 2018.12 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

The helix rearrangement in the periplasmic domain of the flagellar stator B-subunit activates peptidoglycan binding and ion influx

Seiji Kojima, Masato Takao, Gaby Almira, Ikumi Kawahara, Mayuko Sakuma, Michio Homma, Chojiro Kojim … Show more authors

Struture 26 ( 4 ) 1 - 9 2018.4 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：CELL PRESS Joint Work

The stator of the bacterial flagellar motor couples ion flow with torque generation. The ion-conducting stator channel opens only when incorporated into and anchored around the rotor via the peptidoglycan (PG) binding domain of the B subunit (MotBC). However, no direct evidence of PG-binding coupled with channel activation has been presented. Here, we report the structural rearrangements of MotBC responsible for this coupling process. A MotBC fragment with the L119P replacement, which is known to cause channel activation, was able to bind PG. NMR analysis of MotBC and the crystal structure of the MotBC-L119P dimer revealed major structural changes in helix α1. In vivo crosslinking results confirm that a major rearrangement occurs. Our results suggest that, upon stator incorporation into the motor, helix α1 of MotBC changes into an extended non-helical structure. We propose that this change allows the stator both to bind PG and to open its proton channel.

TFL1-like proteins in rice antagonize rice FT-like protein in inflorescence development by competition for complex formation with 14-3-3 and FD

Miho Kaneko-Suzuki, Rie Ishikawa, Chiaki Terakawa, Chojiro Kojima, Misa Fujiwara, Izuru Ohki, Hiroy … Show more authors

Plant Cell Physiol 59 ( 3 ) 458 - 468 2018.3 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS Joint Work

Hd3a, a rice homolog of FLOWERING LOCUS T (FT), is a florigen that induces flowering. Hd3a forms a ternary `florigen activation complex' (FAC) with 14-3-3 protein and OsFD1 transcription factor, a rice homolog of FD that induces transcription of OsMADS15, a rice homolog of APETALA1 (AP1), which leads to flowering. TERMINAL FLOWER 1 (TFL1) represses flowering and controls inflorescence architecture. However, the molecular basis for floral repression by TFL1 remains poorly understood. Here we show that RICE CENTRORADIALIS (RCN), rice TFL1-like proteins, compete with Hd3a for 14-3-3 binding. All four RCN genes are predominantly expressed in the vasculature, and RCN proteins are transported to the shoot apex to antagonize florigen activity and regulate inflorescence development. The antagonistic function of RCN to Hd3a is dependent on its 14-3-3 binding activity. Our results suggest a molecular basis for regulation of the balance between florigen FT and anti-florigen TFL1.

NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes

Yoshikazu Hattori, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Honoka Tomonari, Chojiro Kojim … Show more authors

Nucleosides, Nucleotides and Nucleic Acids 2018 [Reviewed]

Language：English Publishing type：Research paper (scientific journal) Joint Work

Hammerhead ribozymes are a model system for studying molecular mechanism of RNA catalysis. Physicochemical data-driven mechanistic studies are an indispensable step towards understanding the catalysis of hammerhead ribozymes. Here we characterized a model RNA duplex with catalytically important sheared-type G12-A9 base pair and A9-G10.1 metal ion-binding motif in hammerhead ribozymes. By using high magnetic field NMR, all base proton signals, including catalytic residues, were unambiguously assigned. We further characterized structural features of this RNA molecule and found that it reflects the structural features of the A9-G10.1 motif of hammerhead ribozymes. Therefore, this RNA molecule is suitable for extracting an intrinsic physicochemical properties of catalytically important residues.

Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif

Toshihiko Sugiki, Daichi Egawa, Keigo Kumagai, Chojiro Kojima, Toshimichi Fujiwara, Koh Takeuchi, I … Show more authors

J Biol Chem 2018 [Reviewed]

Language：English Publishing type：Research paper (scientific journal) Joint Work

Sphingolipids such as ceramide are important constituents of cell membranes. The ceramide transfer protein (CERT) moves ceramide from the endoplasmic reticulum to the Golgi apparatus in a non-vesicular manner. Hyperphosphorylation of the serine-repeat motif (SRM) adjacent to the pleckstrin homology (PH) domain of CERT down-regulates the inter-organelle ceramide transport function of CERT. However, the mechanistic details of this down-regulation remain elusive. Using solution NMR and binding assays, we herein show that a hyperphosphorylation-mimetic CERT variant in which 10 serine/threonine residues of SRM had been replaced with glutamate residues (the 10E variant) displays an intramolecular interaction between SRM and positively charged regions of the PH domain, which are involved in the binding of this domain to phosphatidylinositol 4-monophosphate (PI4P). Of note, the binding of the PH domain to PI4P-embedded membranes was attenuated by the SRM 10E substitutions in cell-free assays. Moreover, the 10E substitutions reduced the Golgi-targeting activity of the PH-SRM construct in living cells. These results indicate that hyperphosphorylated SRM directly interacts with the surface of the PH domain in an intramolecular manner, thereby decreasing the PI4P-binding activity of the PH domain. In light of these findings, we propose that the hyperphosphorylation of SRM may trigger the dissociation of CERT from the Golgi apparatus, resulting in a functionally less active conformation of CERT.

Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif

Journal of Biological Chemistry 293 ( 28 ) 11206 - 11217 2018 [Reviewed]

DOI Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal)

Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance

Toshihiko Sugiki,Kyoko Furuita,Toshimichi Fujiwara,Chojiro Kojima

Biochemistry 57 ( 26 ) 3576 - 3589 2018 [Reviewed]

DOI Web of Science PubMed CiNii Research

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work

NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes

Hattori Yoshikazu, Yamanaka Daichi, Morioka Saori, Yamaguchi Taishi, Tomonari Honoka, Kojima Chojir … Show more authors

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 37 ( 7 ) 383 - 396 2018 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Production of single-chain Fv antibodies specific for GA-pyridine, an advanced glycation end-product (AGE), with reduced inter-domain motion for structural analysis

Natsuki Fukuda, Kentaro Noi, Lidong Weng, Yoshihiro Kobashigawa, Hiromi Miyazaki, Yukari Wakeyama, … Show more authors

Molecules 22 ( 10 ) 1695 2017.10 [Reviewed] [Invited]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Structural and functional analysis of the C-terminal region of FliG, an essential motor component of Vibrio Na+-driven flagella

Yohei Miyanoiri, Atsushi Hijikata, Yuuki Nishino, Mizuki Gohara, Yasuhiro Onoue, Seiji Kojima, Choj … Show more authors

Structure 25 ( 10 ) 1540 - 1548 2017.10 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：CELL PRESS Joint Work

Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions

Yoshikazu Hattori, David Heidenreich, Yuki Ono, Toshihiko Sugiki, Kei-ichi Yokoyama, Ei-ichiro Suzu … Show more authors

J Biomol NMR 68 ( 4 ) 271 - 279 2017.8 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic 15N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. 19F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, 19F- labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic 19F-labeling readily provided NMR detection of protein-drug and protein-protein interactions with complexes of about 100kDa since the surface residues provided a good substrate for TGase. The 19F-labeling method was 3.5-fold more sensitive than 15N-labeling, and could be combined with other chemical modification techniques such as lysine 13C-methylation. 13C-dimethylated-19F-labeled FKBP12 provided more accurate information concerning the FK506 binding site.

The Mechanism of the Glycosylase Reaction with hOGG1 Base-Excision Repair Enzyme: Concerted Effect of Lys249 and Asp268 During Excision of 8-Oxoguanine

Jakub Sebera, Yoshikazu Hattori, Daichi Sato, David Reha, Radim Nencka, Takashi Kohno, Chojiro Koji … Show more authors

Nucleic Acids Res 45 ( 9 ) 5231 - 5242 2017.5 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS Joint Work

The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme-substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2-(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.

Cold-Shock Expression System in E. coli for Protein NMR Studies

Toshihiko Sugiki, Toshimichi Fujiwara, and Chojiro Kojima

Methods Mol Biol 1586 345 - 357 2017.5 [Reviewed] [Invited]

Language：English Publishing type：Research paper (scientific journal) Joint Work

NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase

Shoko Shinya, Mariana G. Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evg … Show more authors

J Biomol NMR 67 ( 4 ) 309 - 319 2017.4 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：SPRINGER Joint Work

Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction. Equilibrium parameters of the three-state model agreed with the overall thermodynamic dissociation constant determined by ITC. This study presented the first kinetic evidence of the induced-fit mechanism in the glycoside hydrolases.

Noncovalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity

Ju Yaen Kim, Misaki Kinoshita, Satoshi Kume, Guy T. Hanke, Toshihiko Sugiki, John E. Ladbury, Choji … Show more authors

Biochem J 473 ( 21 ) 3837 - 3854 2016.11 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Although electrostatic interactions between negatively charged ferredoxin (Fd) and positively charged sulfite reductase (SiR) have been predominantly highlighted to characterize complex formation, the detailed nature of intermolecular forces remains to be fully elucidated. We investigated interprotein forces for the formation of an electron transfer complex between Fd and SiR and their relationship to SiR activity using various approaches over NaCl concentrations between 0 and 400 mM. Fd-dependent SiR activity assays revealed a bell-shaped activity curve with a maximum ~40-70 mM NaCl and a reverse bell-shaped dependence of interprotein affinity. Meanwhile, intrinsic SiR activity, as measured in a methyl viologen-dependent assay, exhibited saturation above 100 mM NaCl. Thus, two assays suggested that interprotein interaction is crucial in controlling Fd-dependent SiR activity. Calorimetric analyses showed the monotonic decrease in interprotein affinity on increasing NaCl concentrations, distinguished from a reverse bell-shaped interprotein affinity observed from Fd-dependent SiR activity assay. Furthermore, Fd:SiR complex formation and interprotein affinity were thermodynamically adjusted by both enthalpy and entropy through electrostatic and non-electrostatic interactions. A residue-based NMR investigation on the addition of SiR to 15N-labeled Fd at the various NaCl concentrations also demonstrated that a combination of electrostatic and non-electrostatic forces stabilized the complex with similar interfaces and modulated the binding affinity and mode. Our findings elucidate that non-electrostatic forces are also essential for the formation and modulation of the Fd:SiR complex. We suggest that a complex configuration optimized for maximum enzymatic activity near physiological salt conditions is achieved by structural rearrangement through controlled non-covalent interprotein interactions.

HgII/AgI-mediated base pairs and their NMR spectroscopic studies

Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Šebera, Katsuyuki Nakashima, Akira Ono, Vladimí … Show more authors

Inorganica Chimica Acta 452 34 - 42 2016.10 [Reviewed]

DOI Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

The Structure Determination of AgI-mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy

Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Šebera, Katsuyuki Nakashima, Jiro Kondo, Daichi … Show more authors

Chemistry 22 ( 37 ) 13028 - 13031 2016.9 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

The structure of an Ag(I)-mediated cytosine-cytosine base pair, C-Ag(I)-C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15)N-(109)Ag J-coupling ((1)J((15)N,(109)Ag): 83 and 84 Hz) recorded within the C-Ag(I)-C base pair evidenced the N3-Ag(I)-N3 linkage in C-Ag(I)-C. The triplet resonances of the N4 atoms in C-Ag(I)-C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I)-DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I)-C (-18.3 +- 3.0 degree). The (109)Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (delta((109)Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I)-C base pair.

Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

Nesreen Alsanousi, Toshihiko Sugiki, Kyoko Furuita, Masatomo So, Young-Ho Lee, Toshimichi Fujiwara, … Show more authors

Biochem. Biophys. Res. Commun. 477 ( 4 ) 647 - 653 2016.9 [Reviewed]

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Expression, purification, and crystallization of a plant-specific DUF1110 protein from Oryza sativa

Kenichi Harada, Eiki Yamashita, Kento Inoue, Koji Yamaguchi, Toshimichi Fujiwara, Atsushi Nakagawa, … Show more authors

Acta Crystallogr. F Struct. Biol. Commun. 72 ( 6 ) 480 - 484 2016.6 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：INT UNION CRYSTALLOGRAPHY Joint Work

The Os01T0156300 protein from Oryza sativa has been classified into the domain of unknown function (DUF) family DUF1110. DUF1110 family members exist in monocotyledons but not in dicotyledons, and share no sequence identity with proteins for which structures have been reported. In this study, the Os01T0156300 protein was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.84 angstrom resolution. The crystal belonged to space group P2(1), with unit-cell parameters a = 89.9, b = 89.8, c = 107.1 angstrom, beta = 106.6 degrees. The asymmetric unit was estimated to contain 6-11 molecules.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioann … Show more authors

J. Biomed. Semant. 7 ( 1 ) 16 2016.5 [Reviewed]

DOI Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal) Publisher：BIOMED CENTRAL LTD Joint Work

Background: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases.

HgII/AgI-mediated base pairs and their NMR spectroscopic studies

古板恭子, 児嶋長次郎

Inorg. Chim. Acta 452 34 - 42 2016 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Lysine 13C-Methylation NMR for Analyses of Interactions and Structural Changes

HATTORI Yoshikazu, KOJIMA Chojiro

Seibutsu Butsuri 56 ( 5 ) 288 - 289 2016

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

小林直宏, 児嶋長次郎

J. Biomed. Semant. 7 16 2016 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Noncovalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity

杉木俊彦, 児嶋長次郎

Biochem. J. 473 3837 - 3854 2016 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Noncovalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity

杉木俊彦, 児嶋長次郎

Biochem. J. 473 3837 - 3854 2016 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Exploring a DNA sequence for 3-dimensional structure determination of a silver(I)-mediated C-C base pair in a DNA duplex with 1H NMR spectroscopy

Takenori Dairaku, Kyoko Furuita, Hajime Sato, Yoshinori Kondo, Chojiro Kojima, Akira Ono and Yoshiy … Show more authors

Nucleosides Nucleotides Nucleic Acids 34 ( 12 ) 877 - 900 2015.12 [Reviewed]

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Physicochemical natures of interfaces control activity of ferredoxin NADP+ reductase through its interprotein interactions with ferredoxin

Misaki Kinoshita, Ju yaen Kim, Satoshi Kume, Yukiko Sakakibara, Toshihiko Sugiki, Chojiro Kojima, G … Show more authors

BBA - Bioenergetics 1847 ( 10 ) 1200 - 1211 2015.10 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER Joint Work

Direct Detection of the Mercury-Nitrogen Bond in the Thymine-HgII-Thymine Base-pair with 199Hg NMR Spectroscopy

Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Šebera, Daichi Yamanaka, Hiroyuki Otaki, Shoko … Show more authors

Chem. Commun. 51 ( 40 ) 8488 - 8491 2015.5 [Reviewed]

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1H, 15N and 13C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein

Saori Kataoka, Kyoko Furuita, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikegami, Kazuhiro Shio … Show more authors

Biomol. NMR Assign. 9 ( 1 ) 89 - 92 2015.4 [Reviewed]

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Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

Kyoko Furuita, Saori Kataoka, Toshihiko Sugiki, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikeg … Show more authors

J. Biomol. NMR 61 ( 1 ) 55 - 64 2015.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：SPRINGER Joint Work

The crystal structure of the plant small GTPase OsRac1 reveals its mode of binding to NADPH oxidase

Ken-ichi Kosami, Izuru Ohki, Minoru Nagano, Kyoko Furuita, Toshihiko Sugiki, Yoji Kawano, Tsutomu K … Show more authors

J. Biol. Chem. 289 ( 41 ) 28569 - 28578 2014.10 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY Joint Work

Latest approaches for efficient protein production in drug discovery

Toshihiko Sugiki, Toshimichi Fujiwara, Chojiro Kojima

Expert Opin. Drug Discov 9 ( 10 ) 1189 - 1204 2014.10 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Joint Work

The crystal structure of the plant small GTPase OsRac1 reveals its mode of binding to NADPH oxidase

Kosami Ken-Ichi, Ohki Izuru, Nagano Minoru, Furuita Kyoko, Sugiki Toshihiko, Kawano Yoji, Kawasaki … Show more authors

Journal of Biological Chemistry 289 ( 41 ) 28569 - 28578 2014.10 [Reviewed]

CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：American Society for Biochemistry and Molecular Biology Joint Work

This research was originally published in Journal of Biological Chemistry. Ken-ichi Kosami, Izuru Ohki, Minoru Nagano, Kyoko Furuita, Toshihiko Sugiki, Yoji Kawano, Tsutomu Kawasaki, Toshimichi Fujiwara, Atsushi Nakagawa, Ko Shimamoto and Chojiro Kojima. The crystal structure of the plant small GTPase OsRac1 reveals its mode of binding to NADPH oxidase. Journal of Biological Chemistry. 2014; 289, 28569-28578. © the American Society for Biochemistry and Molecular Biology.

NMR spectroscopic studies on metallo-base-pair in DNA duplex

Tanaka Yoshiyuki, Okamoto Itaru, Furuita Kyoko, Sebera Jakub, Kondo Jiro, Torigoe Hidetaka, Urata H … Show more authors

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 19 S732 - S733 2014.8 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Proton and nitrogen-15 NMR spectroscopic studies of Ag-I-mediated C-C base-pairs

Dairaku Takenori, Okamoto Itaru, Furuita Kyoko, Oda Shuji, Yamanaka Daichi, Torigoe Hidetaka, Kozas … Show more authors

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 19 S825 - S826 2014.8 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Invited lectures

田中好幸, 小野晶, 児嶋長次郎

JBIC Journal of Biological Inorganic Chemistry 19 ( S2 ) 725 - 747 2014.7

DOI CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

Metal–nucleic acid interactions

小野晶, 児嶋長次郎, 田中好幸

JBIC Journal of Biological Inorganic Chemistry 19 ( S2 ) 815 - 832 2014.7

DOI CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

The structure of metallo-DNA with consecutive T-HgII-T base-pairs explains positive entropy for the metallo-base-pair formation

Hiroshi Yamaguchi, Jakub Šebera, Jiro Kondo, Shuji Oda, Tomoyuki Komuro, Takuya Kawamura, Takenori … Show more authors

Nucleic Acids Res. 42 ( 6 ) 4094 - 4099 2014.4 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Purification, crystallization and preliminary X-ray crystallographic analysis of a rice Rac/Rop GTPase, OsRac1

Ken-ichi Kosami, Izuru Ohki, Kokoro Hayashi, Ryo Tabata, Sayaka Usugi, Tsutomu Kawasaki, Toshimichi … Show more authors

Acta Crystallogr F Struct Biol Commun. 70 ( 1 ) 113 - 115 2014.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-BLACKWELL Joint Work

The structure of metallo-DNA with consecutive T-Hg^<II>-T base-pairs explains positive entropy for the metallo-base-pair formation

児嶋長次郎

Nucleic Acids Res. 42 4094 - 4099 2014 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

The structure of metallo-DNA with consecutive T-HgII-T base-pairs explains positive entropy for the metallo-base-pair formation

児嶋長次郎

Nucleic Acids Res 42 4094 - 4099 2014 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Formation of the T-HgII-T Metal-Mediated DNA Base Pair; Proposal and Theoretical Calculation of the Reaction Pathway

Jakub Šebera, Jaroslav Burda, Michal Straka, Akira Ono, Chojiro Kojima, Yoshiyuki Tanaka, and Vladi … Show more authors

Chemistry 19 ( 30 ) 9884 - 9894 2013.7 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Structure and function of florigen and the receptor complex

Ken-ichiro Taoka, Izuru Ohki, Hiroyuki Tsuji, Chojiro Kojima, Ko Shimamoto

Trends Plant Sci. 18 ( 5 ) 287 - 294 2013.5 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Joint Work

Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na+ driven flagellar motor

Rei Abe-Yoshizumi, Shiori Kobayashi, Mizuki Gohara, Kokoro Hayashi, Chojiro Kojima, Seiji Kojima, Y … Show more authors

Biophysics 9 ( 0 ) 21 - 29 2013.2 [Reviewed]

DOI PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan Joint Work

Utilization of lysine 13C-methylation NMR for protein-protein interaction studies

Yoshikazu Hattori, Kyoko Furuita, Izuru Ohki, Takahisa Ikegami, Harumi Fukada, Masahiro Shirakawa, … Show more authors

J. Biomol. NMR 55 ( 1 ) 19 - 31 2013.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

Formation of the T-HgII-T Metal-Mediated DNA Base Pair; Proposal and Theoretical Calculation of the Reaction Pathway

児嶋長次郎

Chem.-Eur. J 19 9884 - 9894 2013 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

NMR滴定実験と蛋白質の化学修飾

児嶋長次郎

NMR 4 93 - 98 2013 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

In vivo imaging of Florigen Activation Complex (FAC) comprising Hd3a, 14-3-3 and OsFD1 in rice

Tsuji Hiroyuki, Nakashima Chika, Taoka Ken-ichiro, Ohki Izuru, Kojima Chojiro, Inada Noriko, Shimam … Show more authors

GENES & GENETIC SYSTEMS 87 ( 6 ) 392 - 392 2012.12 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Insights into substrate recognition by the Escherichia coli Orf135 protein through its solution structure

Kumiko Kawasaki, Teppei Kanaba, Momoko Yoneyama, Naoko Murata-Kamiya, Chojiro Kojima, Yutaka Ito, H … Show more authors

Biochem Biophys Res Commun 420 ( 2 ) 263 - 268 2012.4 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

1H, 13C and 15N NMR assignments of the Escherichia coli Orf135 protein

Kumiko Kawasaki, Momoko Yoneyama, Naoko Murata-Kamiya, Hideyoshi Harashima, Chojiro Kojima, Yutaka … Show more authors

Biomol NMR Assign 6 ( 1 ) 1 - 4 2012.4 [Reviewed]

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Site-specific isotope labeling of long RNA for structural and mechanistic studies

Ikumi Kawahara, Kaichiro Haruta, Yuta Ashihara, Daichi Yamanaka, Mituhiro Kuriyama, Naoko Toki, Yos … Show more authors

Nucleic Acids Res. 40 ( 1 ) e7 - e7 2012.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Joint Work

^1H, ^<13>C and^<15>N NMR assignments of the Escherichia coli Orf135 protein

児嶋長次郎, 三島正規

Biomol NMR Assign 286 1 - 4 2012 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Molecular Basis of Florigen Function Revealed by Structural Analysis of Florigen Activation Complex

TAOKA Ken-ichiro, OHKI Izuru, TSUJI Hiroyuki, KOJIMA Chojiro, SHIMAMOTO Ko

KAGAKU TO SEIBUTSU 50 ( 9 ) 654 - 659 2012

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry Joint Work

花成ホルモン-フロリゲン-とその受容体の構造解析からみえてきたフロリゲン機能の分子基盤

田岡健一郎, 大木出, 辻寛之, 児島長次郎, 島本功

化学と生物 50 654 - 659 2012 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

フロリゲン(花成ホルモン)の細胞内受容体の発見

大木出, 児嶋長次郎

SPring-8 利用者情報 17 3 - 8 2012 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Insights into substrate recognition by the Escherichia coli Orf135 protein through its solution structure

児嶋長次郎

Biochem Biophys Res Commun 420 263 - 268 2012 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Functional expression of a two-transmembrane HtrII protein using cell-free synthesis

Yuki Sudo, Rikou Tanaka, Toshitatsu Kobayashi, Naoki Kamo, Toshiyuki Kohno, and Chojiro Kojima

Biophysics 7 51 - 58 2011.6 [Reviewed]

DOI PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan Joint Work

1H, 13C and 15N NMR assignments of the Escherichia coli Orf135 protein.

児嶋長次郎

Biomol.NMR Assign. in press 2011 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Structural feature of bent DNA recognized by HMGB1

児嶋長次郎

J. Am. Chem. Soc 133 5788 - 5790 2011 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Structural basis for floral induction by rice florigen Hd3a

Ohki Izuru, Furuita Kyoko, Hayashi Kokoro, Taoka Ken-ichiro, Tsuji Hiroyuki, Nakagawa Atsushi, Shim … Show more authors

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 67 C351 - C351 2011 [Reviewed]

DOI Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Functional expression of a two-transmembrane HtrII protein using cell-free synthesis.

児嶋長次郎

Biophysics (accepted) 2011 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Efficient protein production method for NMR using soluble protein tags with cold shock expression vector

Hayashi Kokoro, Kojima Chojiro

JOURNAL OF BIOMOLECULAR NMR 48 ( 3 ) 147 - 155 2010.11 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

The E. coli protein expression system is one of the most useful methods employed for NMR sample preparation. However, the production of some recombinant proteins in E. coli is often hampered by difficulties such as low expression level and low solubility. To address these problems, a modified cold-shock expression system containing a glutathione S-transferase (GST) tag, the pCold-GST system, was investigated. The pCold-GST system successfully expressed 9 out of 10 proteins that otherwise could not be expressed using a conventional E. coli expression system. Here, we applied the pCold-GST system to 84 proteins and 78 proteins were successfully expressed in the soluble fraction. Three other cold-shock expression systems containing a maltose binding protein tag (pCold-MBP), protein G B1 domain tag (pCold-GB1) or thioredoxin tag (pCold-Trx) were also developed to improve the yield. Additionally, we show that a C-terminal proline tag, which is invisible in ¹H-¹⁵N HSQC spectra, inhibits protein degradation and increases the final yield of unstable proteins. The purified proteins were amenable to NMR analyses. These data suggest that pCold expression systems combined with soluble protein tags can be utilized to improve the expression and purification of various proteins for NMR analysis.

Electrostatic Interaction between Oxysterol-binding Protein and VAMP-associated Protein A Revealed by NMR and Mutagenesis Studies

Furuita Kyoko, Jee JunGoo, Fukada Harumi, Mishima Masaki, Kojima Chojiro

JOURNAL OF BIOLOGICAL CHEMISTRY 285 ( 17 ) 12961 - 12970 2010.4 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Oxysterol-binding protein (OSBP), a cytosolic receptor of cholesterol and oxysterols, is recruited to the endoplasmic reticulum by binding to the cytoplasmic major sperm protein (MSP) domain of integral endoplasmic reticulum protein VAMP-associated protein-A (VAP-A), a process essential for the stimulation of sphingomyelin synthesis by 25-hydroxycholesterol. To delineate the interaction mechanism between VAP-A and OSBP, we determined the complex structure between the VAP-A MSP domain (VAP-A(MSP)) and the OSBP fragment containing a VAP-A binding motif FFAT (OSBP(F)) by NMR. This solution structure explained that five of six conserved residues in the FFAT motif are required for the stable complex formation, and three of five, including three critical intermolecular electrostatic interactions, were not explained before. By combining NMR relaxation and titration, isothermal titration calorimetry, and mutagenesis experiments with structural information, we further elucidated the detailed roles of the FFAT motif and underlying motions of VAP-A(MSP), OSBP(F), and the complex. Our results show that OSBP(F) is disordered in the free state, and VAP-A(MSP) and OSBP(F) form a final complex by means of intermediates, where electrostatic interactions through acidic residues, including an acid patch preceding the FFAT motif, probably play a collective role. Additionally, we report that the mutation that causes the familial motor neuron disease decreases the stability of the MSP domain.

Structure of the N-terminal Regulatory Domain of a Plant NADPH Oxidase and Its Functional Implications

Oda Takashi, Hashimoto Hiroshi, Kuwabara Naoyuki, Akashi Satoko, Hayashi Kokoro, Kojima Chojiro, Wo … Show more authors

JOURNAL OF BIOLOGICAL CHEMISTRY 285 ( 2 ) 1435 - 1445 2010.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Plant NADPH oxidases (Rboh, for respiratory burst oxidase homolog) produce reactive oxygen species that are key regulators of various cellular events including plant innate immunity. Rbohs possess a highly conserved cytoplasmic N-terminal region containing two EF-hand motifs that regulate Rboh activity. Rice (Oryza sativa) RbohB (OsRbohB) is regulated by the direct binding of a small GTPase (Rac1) to this regulatory region as well as by Ca(2+) binding to the EF-hands. Here, we present the atomic structure of the N-terminal region of OsRbohB. The structure reveals that OsRbohB forms a unique dimer stabilized by swapping the EF-hand motifs. We identified two additional EF-hand-like motifs that were not predicted from sequence data so far. These EF-hand-like motifs together with the swapped EF-hands form a structure similar to that found in calcineurin B. We observed conformational changes mediated by Ca(2+) binding to only one EF-hand. Structure-based in vitro pulldown assays and NMR titration experiments defined the OsRac1 binding interface within the coiled-coil region created by swapping the EF-hands. In addition, we demonstrate a direct intramolecular interaction between the N and C terminus, and that the complete N-terminal cytoplasmic region is required for this interaction. The structural features and intramolecular interactions characterized here might be common elements shared by Rbohs that contribute to the regulation of reactive oxygen species production.

Efficient protein production method for NMR using soluble protein tags with cold shock expression vector.

児嶋長次郎

J.Biomol.NMR 48 147 - 155 2010 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Activity of Regional Branch

Seibutsu Butsuri 50 ( 6 ) 310 - 311 2010

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Single Work

Structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications

児嶋長次郎

J Biol Chem 285 1435 - 1445 2010 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Electrostatic interaction between oxysterol binding protein and VAMP- associated protein-A revealed by NMR and mutagenesis studies.

ジージュングー, 児嶋長次郎

J.Biol.Chem. 285 12961 - 12970 2010 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB

Kojima Seiji, Imada Katsumi, Sakuma Mayuko, Sudo Yuki, Kojima Chojiro, Minamino Tohru, Homma Michio … Show more authors

MOLECULAR MICROBIOLOGY 73 ( 4 ) 710 - 718 2009.8 [Reviewed]

DOI Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal) Joint Work

NMR studies of DNA recognition mechanism of HMGB1 protein.

児嶋長次郎

Nucleic Acids Symp.Ser. 53 89 - 90 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

可溶性タンパク質発現のための新規大腸菌大量発現ベクター

児嶋長次郎

実験医学 27 927 - 932 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Protein Expression System Combined with Soluble Protein Tag and Cold-Shock Vector in Escherichia coli

HAYASHI Kokoro, KOJIMA Chojiro

Seibutsu Butsuri 49 ( 4 ) 210 - 211 2009

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

コールドショックベクターと可溶性タグの組み合わせによる大腸菌大量発現系

児嶋長次郎

生物物理 49 210 - 211 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB.

児嶋長次郎

Mol.Microbiol. 73 710 - 718 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Preparations of hammerhead ribozymes for investigations of their cleavable sequences.

児嶋長次郎, 田中好幸

Nucleic Acids Symp.Ser. 53 277 - 278 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

NMR studies of HAC1 mRNA.

児嶋長次郎, 田中好幸

Nucleic Acids Symp.Ser. 53 269 - 270 2009 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

NMR studies of HAC1 mRNA.

Ikumi Kawahara, Yoshiyuki Tanaka, Chojiro Kojima, Kaichiro Haruta

Nucleic Acids Symposium Series 53 269 - 270 2009 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

HAC1 is a transcription factor related to Unfolded Protein Response (UPR) signaling in yeast. Processing of HAC1 mRNA on Endoplasmic reticulum (ER) plays a key role in UPR signaling pathway, but the recognition mechanism of HAC1 mRNA by processing enzyme Ire1p is still unclear. Here, the solution structure of HAC1 mRNA was investigated by Nuclear Magnetic Resonance (NMR) spectroscopy, focusing on the structure of the recognition site of Ire1p in HAC1 mRNA. From the NOESY spectrum, imino proton signals of 5' processing regions of HAC1 mRNA were assigned and it was found that this region forms the stem-loop structure.

Preparations of hammerhead ribozymes for investigations of their cleavable sequences.

Yoshinori Kondo, Yoshiyuki Tanaka, Hisaaki Tateoka, Ikumi Kawahara, Kaichiro Haruta, Satomi Hasegaw … Show more authors

Nucleic Acids Symposium Series 53 277 - 278 2009 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Recently, in hammerhead ribozymes, newly identified loop-loop interaction was found to be important for their activation. Therefore, we chemically synthesized a hammerhead ribozyme with this extra loop sequences and its mutant ribozymes, as well as their substrate RNA strands in order to clarify their cleavable sequences. After purification with an anion exchange column chromatography, we were able to obtain 44mer and 20mer RNA.

pCold-GST vector: A novel cold-shock vector containing GST tag for soluble protein production

Hayashi Kokoro, Kojima Chojiro

PROTEIN EXPRESSION AND PURIFICATION 62 ( 1 ) 120 - 127 2008.11 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

The production of recombinant protein in Escherichia coli is often hampered by low expression levels and low solubility. A variety of methodologies have been developed including protein production at low temperature, and fusion protein expression using soluble protein tags. Here, we present the novel cold-shock vector pCold-GST for high-level expression of soluble proteins in E. coli. This vector is a modified pCold I cold-shock vector that includes the glutathione S-transferase (GST) tag. The pCold-GST expression system developed was applied to 10 proteins that could not be expressed using conventional E. coli expression methodologies, and nine of these proteins were successfully obtained in the soluble fraction. The expression and purification of two unstable protein fragments were also demonstrated by employing a C-terminal hexa-histidine tag for purification purposes. The purified proteins were amenable to NMR analyses. These data suggest that the pCold-GST expression system can be utilized to improve the expression and purification of various proteins.

Crystallographic characterization of the N-terminal domain of a plant NADPH oxidase

Oda Takashi, Hashimoto Hiroshi, Kuwabara Naoyuki, Hayashi Kokoro, Kojima Chojiro, Kawasaki Tsutomu, … Show more authors

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 64 ( 9 ) 867 - 869 2008.9 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：International Union of Crystallography (IUCr) Joint Work

Respiratory burst oxidase homologue (Rboh), which is found in the plasma membrane, is a generator of reactive oxygen species (ROS) in plants. Many studies have indicated that the ROS produced by Rboh play critical roles in various cellular activities, including plant defence against pathogens. Crystals of the N-terminal domain of Oryza sativa RbohB (OsRbohB) have been obtained. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 60.4, b = 72.2, c = 118.9 A. An intensity data set was collected to 2.4 A resolution.

A long-lived M-like state of phoborhodopsin that mimics the active state

Sudo Yuki, Nishihori Tatsuya, Iwamoto Masayuki, Shimono Kazumi, Kojima Chojiro, Kamo Naoki

BIOPHYSICAL JOURNAL 95 ( 2 ) 753 - 760 2008.7 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II) is a seven transmembrane helical retinal protein. ppR forms a signaling complex with pharaonis Halobacterial transducer II (pHtrII) in the membrane that transmits a light signal to the sensory system in the cytoplasm. The M-state during the photocycle of ppR (lambda(max) = 386 nm) is one of the active (signaling) intermediates. However, progress in characterizing the M-state at physiological temperature has been slow because its lifetime is very short (decay half-time is approximately 1 s). In this study, we identify a highly stable photoproduct that can be trapped at room temperature in buffer solution containing n-octyl-beta-d-glucoside, with a decay half-time and an absorption maximum of approximately 2 h and 386 nm, respectively. HPLC analysis revealed that this stable photoproduct contains 13-cis-retinal as a chromophore. Previously, we reported that water-soluble hydroxylamine reacts selectively with the M-state, and we found that this stable photoproduct also reacts selectively with that reagent. These results suggest that the physical properties of the stable photoproduct (named the M-like state) are very similar with the M-state during the photocycle. By utilizing the high stability of the M-like state, we analyzed interactions of the M-like state and directly estimated the pK(a) value of the Schiff base in the M-like state. These results suggest that the dissociation constant of the ppR(M-like)/pHtrII complex greatly increases (to 5 muM) as the pK(a) value greatly decreases (from 12 to 1.5). The proton transfer reaction of ppR from the cytoplasmic to the extracellular side is proposed to be caused by this change in pK(a).

Enzymatic Characterization of 5-Methylthioribulose-1-phosphate Dehydratase of the Methionine Salvage Pathway in Bacillus subtilis

Bioscience, Biotechnology, and Biochemistry 72 ( 4 ) 959 - 967 2008.4

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry Joint Work

A long-lived M-like state of phoborhodopsin that mimics the active state.

児嶋長次郎

Biophys.J. 95 753 - 760 2008 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

The crystal structure of N-terminal domain of plant NADPH oxidase

Oda Takashi, Hashimoto Hiroshi, Kuwabara Naoyuki, Hayashi Kokoro, Kojima Chojiro, Kawasaki Tsutomu, … Show more authors

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 64 C285 - C286 2008 [Reviewed]

DOI Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

pCold-GST vector : A novel cold-shock vector containing GST tag for soluble protein production.

児嶋長次郎

Protein Expr.Purif. 62 120 - 127 2008 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

NMR structural study of DNA oligomers containing alkylene cross-linked cyclic 2'-dioxyuridylate dimmers.

児嶋長次郎

Nucleic Acids Symp.Ser. 52 181 - 182 2008 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Na[+]/H[+]交換輸送体の機能制御機構

林こころ, 児嶋長次郎

生化学 / 日本生化学会編 80 ( 10 ) 925 - 932 2008 [Reviewed]

CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：日本生化学会 Joint Work

Establishment of Primary Culture System of Hepatocellular Carcinoma and Pancreatic Cancer on NanoCulture Plate

Shimomura M., Ozawa F., Kojima C., Kuronuma T., Nakatsura T.

TUMOR BIOLOGY 29 65 - 65 2008 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Crystallographic characterization of the N-terminal domain of plant NADPH oxidase.

児嶋長次郎

Acta Crystallogr. F64 867 - 869 2008 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Single Work

Crystallographic characterization of the N-terminal domain of a plant NADPH oxidase

児嶋長次郎, 島本功

Acta Crystallogr Sect F Struct Biol Cryst Commun 64 867 - 869 2008 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Dust charge in cryogenic environment

Kubota, J; Kojima, C; Sekine, W; Ishihara, O

MULTIFACETS OF DUSTY PLASMA 1041 235 - 236 2008 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Structural analysis of the phototactic transducer protein HtrII linker region from Natronomonas pharaonis

Hayashi Kokoro, Sudo Yuki, Jee JunGoo, Mishima Masaki, Hara Hideyuki, Kamo Naoki, Kojima Chojiro

BIOCHEMISTRY 46 ( 50 ) 14380 - 14390 2007.12 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

Halobacterial pharaonis phoborhodopsin [ppR, also called Natronomonas pharaonis sensory rhodopsin II (NpSRII)] is a phototaxis protein which transmits a light signal to the cytoplasm through its transducer protein (pHtrII). pHtrII, a two-transmembrane protein that interacts with ppR, belongs to the group of methyl-accepting chemotaxis proteins (MCPs). Several mutation studies have indicated that the linker region connecting the transmembrane and methylation regions is necessary for signal transduction. However, the three-dimensional (3D) structure of an MCP linker region has yet to be reported, and hence, details concerning the signal transduction mechanism remain unknown. Here the structure of the pHtrII linker region was investigated biochemically and biophysically. Following limited proteolysis, only one trypsin resistant fragment in the pHtrII linker region was identified. This fragment forms a homodimer with a Kd value of 115 microM. The 3D structure of this fragment was determined by solution NMR, and only one alpha-helix was found between two HAMP domains of the linker region. This alpha-helix was significantly stabilized within transmembrane protein pHtrII as revealed by CW-EPR. The presence of Af1503 HAMP domain-like structures in the linker region was supported by CD, NMR, and ELDOR data. The alpha-helix determined here presumably works as a mechanical joint between two HAMP domains in the linker region to transfer the photoactivated conformational change downstream.

Regulation of rice NADPH oxidase by binding of Rac GTPase to its N-terminal extension

Wong Hann Ling, Pinontoan Reinhard, Hayashi Kokoro, Tabata Ryo, Yaeno Takashi, Hasegawa Kana, Kojim … Show more authors

PLANT CELL 19 ( 12 ) 4022 - 4034 2007.12 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

<jats:title>Abstract</jats:title>
<jats:p>Reactive oxygen species (ROS) produced by NADPH oxidase play critical roles in various cellular activities, including plant innate immunity response. In contrast with the large multiprotein NADPH oxidase complex of phagocytes, in plants, only the homologs of the catalytic subunit gp91phox and the cytosolic regulator small GTPase Rac are found. Plant homologs of the gp91phox subunit are known as Rboh (for respiratory burst oxidase homolog). Although numerous Rboh have been isolated in plants, the regulation of enzymatic activity remains unknown. All rboh genes identified to date possess a conserved N-terminal extension that contains two Ca2+ binding EF-hand motifs. Previously, we ascertained that a small GTPase Rac (Os Rac1) enhanced pathogen-associated molecular pattern–induced ROS production and resistance to pathogens in rice (Oryza sativa). In this study, using yeast two-hybrid assay, we found that interaction between Rac GTPases and the N-terminal extension is ubiquitous and that a substantial part of the N-terminal region of Rboh, including the two EF-hand motifs, is required for the interaction. The direct Rac–Rboh interaction was supported by further studies using in vitro pull-down assay, a nuclear magnetic resonance titration experiment, and in vivo fluorescence resonance energy transfer (FRET) microscopy. The FRET analysis also suggests that cytosolic Ca2+ concentration may regulate Rac–Rboh interaction in a dynamic manner. Furthermore, transient coexpression of Os Rac1 and rbohB enhanced ROS production in Nicotiana benthamiana, suggesting that direct Rac–Rboh interaction may activate NADPH oxidase activity in plants. Taken together, the results suggest that cytosolic Ca2+ concentration may modulate NADPH oxidase activity by regulating the interaction between Rac GTPase and Rboh.</jats:p>

Enzymatic Characterization of 5-Methylthioribose 1-Phosphate Isomerase from Bacillus subtilis

Bioscience, Biotechnology, and Biochemistry 71 ( 8 ) 2021 - 2028 2007.8

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry Joint Work

Solution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1

Mishima Masaki, Wakabayashi Shigeo, Kojima Chojiro

JOURNAL OF BIOLOGICAL CHEMISTRY 282 ( 4 ) 2741 - 2751 2007.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Na+/H+ exchanger 1 (NHE1) regulates intracellular pH, Na+ content, and cell volume. Calcineurin B homologous protein 1 (CHP1) serves as an essential cofactor that facilitates NHE1 exchange activity under physiological conditions by direct binding to the cytoplasmic juxtamembrane region of NHE1. Here we describe the solution structure of the cytoplasmic juxtamembrane region of NHE1 complexed with CHP1. The region of NHE1 forms an amphipathic helix, which is induced by CHP1 binding, and CHP1 possesses a large hydrophobic cleft formed by EF-hand helices. The apolar side of the NHE1 helix participates in extensive hydrophobic interactions with the cleft of CHP1. We suggest that helix formation of the cytoplasmic region of NHE1 by CHP1 is a prerequisite for generating the active form of NHE1. The molecular recognition detailed in this study also provides novel insight into the target binding mechanism of EF-hand proteins.

N-15-N-15 J-coupling across Hg-II: Direct observation of Hg-II-mediated T-T base pairs in a DNA duplex

Tanaka Yoshiyuki, Oda Shuji, Yamaguchi Hiroshi, Kondo Yoshinori, Kojima Chojiro, Ono Akira

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 129 ( 2 ) 244 - 245 2007.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

N−N J-coupling across a metal center (2JNN) was clearly detected in a biological macromolecule (DNA duplex) for the first time. By using 2JNN, the base pairing mode of mercury-mediated T−T pairs (T−HgII−T) was definitely determined. This pairing mode was found to be a novel metal ion-binding mode for DNA and RNA molecules, in which imino proton−metal exchange processes are included. Accordingly, 2JNN is highly important for the determination of the chemical structures of metal-mediated base pairs.

2P190 Purification and crystallization of periplasmic fragments of MotB, a stator component of the bacterial flagellar motor(Cell biological problems-adhesion, motility, cytoskeleton, signaling,and membrane,Poster Presentations)

Kojima Seiji, Sakuma Mayuko, Sudo Yuki, Kojima Chojiro, Minamino Tohru, Imada Katsumi, Namba Keiich … Show more authors

Seibutsu Butsuri 47 ( supplement ) S160 2007

DOI CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Structural analysis of phototactic transducer protein HtrII linker region from Natronomonas pharaonis

須藤雄気, 児嶋長次郎

Biochemistry 46 14380 - 14390 2007 [Reviewed]

CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Joint Work

Regulation of the rice NADPH oxidase by binding of small GTPase Rac and Ca2+ to its N-terminal extension

Wong Hann Ling, Pinontoan Reinhard, Hasegawa Kana, Yaeno Takashi, Iba Koh, Tabata Ryo, Hayashi Koko … Show more authors

BIOTECHNOLOGY AND SUSTAINABLE AGRICULTURE 2006 AND BEYOND 209 - + 2007 [Reviewed]

DOI Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

3P237 Structural studies of juxtamembrane region of a pharaonis transducer protein, pHtrII by NMR and EPR(Photobiology- vision and photoreception,Poster Presentations)

Hayashi Kokoro, Sudo Yuki, JunGoo Jee, Mishima Masaki, Hara Hideyuki, Kamo Naoki, Kojima Chojiro

Seibutsu Butsuri 47 ( supplement ) S262 2007

DOI CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Structural and physicochemical features on the metal-mediated base pairs.

Miura Takashi, Hiroshi Yamaguchi, Hideo Takeuchi, Yoshiyuki Tanaka, Tomomi Uchiyama, Takuya Kawamur … Show more authors

Nucleic Acids Symposium Series 51 75 - 76 2007 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

The chemical structure of the mercury-mediated T-T pair (T-Hg(I)I-T) was determined with (15)N NMR spectroscopy. In order to determine the chemical structure of the T-Hg(I)I-T pair, (15)N-(15)N J-coupling across a metal center (2JNN) was employed. Notably, this is the first observation of (2)J(NN) in a biological macromolecule (DNA duplex). This pairing mode was found to be a irregular metal ion-binding mode for DNA and RNA molecules, in which imino proton-metal exchange processes are included. Accordingly, (2)J(NN) is highly important for the determination of the chemical structures of metal-mediated base pairs.

H-1, C-13 and N-15 resonance assignments of the VAP-A: OSBP complex

Furuita Kyoko, Mishima Masaki, Kojima Chojiro

JOURNAL OF BIOMOLECULAR NMR 36 ( S1 ) 69 - 69 2006 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

Structural studies of phytochrome B using solution NMR spectroscopy

Kobayashi T, Nishigaya Y, Mishima M, Tabata R, Akagi K, Sakai N, Katoh E, Takano M, Yamazaki T, Koj … Show more authors

PLANT AND CELL PHYSIOLOGY 47 S122 - S122 2006 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Plant photoreceptor phytochrome A and B have different dimerization mechanisms

Yamazaki T., Kobayashi T., Mishima M., Tabata R., Suzuki R., Takano M., Kojima C.

JOURNAL OF PEPTIDE SCIENCE 12 97 - 97 2006 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

NMR spectroscopic study of a DNA duplex with mercury-mediated T-T base pairs

Tanaka Yoshiyuki, Yamaguchi Hiroshi, Oda Shuji, Kondo Yoshinori, Nomura Makoto, Kojima Chojiro, Ono … Show more authors

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 25 ( 4-6 ) 613 - 624 2006 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Informa UK Limited Joint Work

Recently, we reported that T-T mismatches can specifically recognize Hg(II) (T-Hg(II)-T pair formation). In order to understand the properties of the T-Hg(II)-T pair, we recorded NMR spectra for a DNA duplex, d(CGCGTTGTCC).d(GGACTTCGCG), with two successive T-T mismatches (Hg (II)-binding sites). We assigned 1H resonances for mercury-free and di-mercurated duplexes, and performed titration experiments with Hg(II) by using 1D 1H NMR spectra. Because of the above mentioned assignments, we could confirm the existence of mono-mercurated species, because individual components gave independent NMR signals in the titration spectra.

Structural analyses on the mercuryII-mediated T-T base pair.

Yoshiyuki Tanaka, Shuji Oda, Hiroshi Yamaguchi, Megumi Kudo, Yoshinori Kondo, Chojiro Kojima, Akira … Show more authors

Nucleic Acids Symposium Series 50 ( 1 ) 47 - 48 2006

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Recently, it was reported that T-T mismatches can specifically recognize Hg(II), and form T-Hg(II)-T pairs. In order to understand the structure and properties of the T-Hg(II)-T pair, we measured NMR spectra for a DNA duplex, d(CGCGTTGTCC) x d(GGACTTCGCG), with two successive T-T mismatches (Hg(II)-binding sites) in the middle of the duplex. We identified imino proton resonances of the T-T mismatches in mercury-free duplex, and performed titration experiments with Hg(II) by using 1-dimensional (1D) (1)H NMR spectra. From the titration spectra, disappearances of imino proton signals were observed upon the addition of Hg(II). Furthermore, we observed additional signals of transient species, most likely mono-mercurated duplexes. This is an evidence that structural transformations between Hg(II)-free and Hg(II)-bound forms are slow enough for each species to give independent signals. These data strongly suggest that the imino protons of thymine bases were substituted with Hg(II), to form T-Hg(II)-T pairs in which one Hg(II) cross-links two N3 atoms of thymines.

Studies of DNA recognition mechanism of transcription factor IRF-4.

Kyoko Furuita, Itsuko Ishizaki, Kazuo Yamamoto, Toshifumi Matsuyama, Harumi Fukada, Makoto Nomura, … Show more authors

Nucleic Acids Symposium Series 50 259 - 260 2006 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Transcription factor IFN regulatory factor-4 (IRF-4) prefers a DNA sequence including CCGAAA, though the consensus DNA-binding sequence of the IRF family proteins is NNGAAA, and the crystal structure of PU.1/IRF-4/DNA (GTGAAA) ternary complex indicates the NN region of DNA does not interact with IRF-4 directly. This suggests that there is an indirect DNA recognition mechanism in IRF-4. In order to account for the sequence preference of IRF-4, we focused on structural properties of DNA duplexes recognized by IRF-4. Here, we performed solution NMR studies on DNA duplexes containing GGGAAA and CCGAAA sequences, and assigned most of proton resonances of DNA 17 mer with GGGAAA. (1)H-(1)H NOESY spectra indicated B-form like structure for GGGAAA. We also assigned imino proton resonances of DNA 17 mer with CCGAAA. For the imino proton region, the (1)H-(1)H NOESY spectra of these two DNA duplexes were similar.

Active repression of IFN regulatory factor-1-mediated transactivation by IFN regulatory factor-4

Yoshida K, Yamamoto K, Kohno T, Hironaka N, Yasui K, Kojima C, Mukae H, Kadota J, Suzuki S, Honma K … Show more authors

INTERNATIONAL IMMUNOLOGY 17 ( 11 ) 1463 - 1471 2005.11 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

IFN regulatory factor-4 (IRF-4) is a transcription factor that is involved in the development and the functions of lymphocytes, macrophages and dendritic cells. Despite their critical roles in immune system regulation, the target genes controlled by IRF-4 are poorly understood. In this study, we determined the consensus DNA-binding sequences preferred for IRF-4 by in vitro binding site selections. IRF-4 preferentially bound to the sequences containing tandem repeats of 5'-GAAA-3', flanked by CpC, in most cases. IRF-4 repressed the promoter bearing tandem copies of the selected binding sequence, while IRF-1 activated the same constructs. Interestingly, the IRF-1-dependent transactivation is inhibited in the presence of IRF-4, but not IRF-2. A series of deletion mutants of IRF-4 revealed that its DNA-binding domain was necessary and sufficient to antagonize the IRF-1-dependent transactivation. This dominant negative action of IRF-4 over IRF-1 was also observed in a natural promoter context, such as the TRAIL gene. These results indicate that IRF-4 acts as a natural antagonist against IRF-1 in immune cells.

Disassembling and bleaching of chloride-free pharaonis halorhodopsin by octyl-beta-glucoside

Kubo M, Sato M, Aizawa T, Kojima C, Kamo N, Mizuguchi M, Kawano K, Demura M

BIOCHEMISTRY 44 ( 39 ) 12923 - 12931 2005.10 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

Natronomonas (Natronobacterium) pharaonis halorhodopsin (NpHR) is a transmembrane, seven-helix retinal protein of the archaeal bacterium and acts as an inward light-driven chloride ion pump in the membrane. The denaturation process of NpHR solubilized with n-octyl-beta-d-glucopyranoside (OG) was investigated to clarify the effects of the chloride ion and pH on the stability and bleaching of the NpHR chromophore. Initially, active NpHR solubilized with n-dodecyl-beta-d-maltopyranoside (DM) was obtained from the recombinant halo-opsin (NpHO), which was expressed in Escherichia coli cells, by adding all-trans retinal to the medium. Apparent molecular weight of the active NpHR solubilized with DM, which was determined by gel-filtration chromatography and dynamic light scattering, indicated the oligomeric state. The bleaching of NpHR in the dark by the addition of 50 mM OG in the presence and absence of chloride was investigated. In the presence of 256 mM NaCl, the bleaching of NpHR was strongly inhibited. On the other hand, in the absence of NaCl, an immediate decrease of absorbance at 600 nm was observed. Stopped-flow rapid-mixing analysis clarified the bleaching process in the absence of chloride as DM-NpHR (oligomeric)--OG-NpHR (disassembled)--intermediate --NpHO and free retinal, and each rate constant were determined. The formation of an intermediate (450 nm) in the dark was found to be strongly dependent on pH, as well as anion and detergent concentrations. The disassembling and protonation of a Schiff base corresponding to the bleaching intermediate is also discussed.

Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR

Mishima M, Shida T, Yabuki K, Kato K, Sekiguchi J, Kojima C

BIOCHEMISTRY 44 ( 30 ) 10153 - 10163 2005.8 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

Bacillus subtilis CwlC is a cell wall lytic N-acetylmuramoyl-l-alanine amidase that plays an important role in mother-cell lysis during sporulation. The enzyme consists of an N-terminal catalytic domain with C-terminal tandem repeats. The repeats [repeat 1 (residues 184-219) and repeat 2 (residues 220-255)] are termed CwlCr. We report on the solution structure of CwlCr as determined by multidimensional NMR, including the use of 36 (h3)J(NC)'-derived hydrogen bond restraints and 64 residual (1)D(NH) dipolar couplings. Two tandem repeats fold into a pseudo-2-fold symmetric single-domain structure consisting of a betaalphabetabetaalphabeta-fold containing numerous contacts between the repeats. Hydrophobic residues important for structural integrity are conserved between the repeats, and are located symmetrically. We also present NMR analysis of the circularly permuted repeat mutant of CwlCr. Secondary structure content from the chemical shifts and hydrogen bonds derived from (h3)J(NC)' show that the mutant folds into a structure similar to that of the wild type, suggesting that the repeats are exchangeable. This implies that conserved hydrophobic residues are crucial for maintaining the folding of the repeats. While monitoring the chemical shift perturbations following the addition of digested soluble peptidoglycan fragments, we identified two peptidoglycan interaction sites of CwlCr at the edges of the protein symmetrically, and they are located approximately 28 A from each other.

Linker region of a halobacterial transducer protein interacts directly with its sensor retinal protein

Sudo Y, Okuda H, Yamabi M, Fukuzaki Y, Mishima M, Kamo N, Kojima C

BIOCHEMISTRY 44 ( 16 ) 6144 - 6152 2005.4 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

pHtrII, a pharaonis halobacterial transducer protein, possesses two transmembrane helices and forms a signaling complex with pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, NpSRII) within the halobacterial membrane. This complex transmits a light signal to the sensory system located in the cytoplasm. It has been suggested that the linker region connecting the transmembrane region and the methylation region of pHtrII is important for binding to ppR and subsequent photosignal transduction. In this study, we present evidence to suggest that the linker region itself interacts directly with ppR in addition to the interaction in the membrane region. An in vitro pull-down assay revealed that the linker region bound to ppR, and its dissociation constant (K(D)) was estimated to be approximately 10 microM using isothermal titration calorimetry (ITC). Solution NMR analyses showed that ppR interacted with the linker region of pHtrII (pHtrII(G83)(-)(Q149)) and resulted in the broadening of many peaks, indicating structural changes within this region. These results suggest that the pHtrII linker region interacts directly with ppR. There was no demonstrable interaction between the C-terminal region of ppR (ppR(Gly224)(-)(His247)) and either the linker region (pHtrII(G83)(-)(Q149)) or the transmembrane region (pHtrII(M1)(-)(E114)) of pHtrII. On the basis of the NMR, CD, and photochemical data, we discuss the structural changes and role of the linker region of pHtrII in relation to photosignal transduction.

Amino acid residues involved in substrate recognition of the Escherichia coli Orf 135 protein

Iida E, Satou K, Mishima M, Kojima C, Harashima H, Kamiya H

BIOCHEMISTRY 44 ( 15 ) 5683 - 5689 2005.4 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

The Escherichia coli Orf135 protein, a MutT-type enzyme, hydrolyzes mutagenic 2-hydroxy-dATP (2-OH-dATP) and 8-hydroxy-dGTP, in addition to dCTP and 5-methyl-dCTP, and its deficiency causes increases in both the spontaneous and H(2)O(2)-induced mutation frequencies. To identify the amino acid residues that interact with these nucleotides, the Glu-33, Arg-72, Arg-77, and Asp-118 residues of Orf135, which are candidates for residues interacting with the base, were substituted, and the enzymatic activities of these mutant proteins were examined. The mutant proteins with a substitution at the 33rd, 72nd, and 118th amino acid residues displayed activities affected to various degrees for each substrate, suggesting the involvement of these residues in substrate binding. On the other hand, the mutant protein with a substitution at the 77th Arg residue had activitiy similar to that of the wild-type protein, excluding the possibility that this Arg side chain is involved in base recognition. In addition, the expression of some Orf135 mutants in orf135(-) E. coli reduced the level of formation of rpoB mutants elicited by H(2)O(2). These results reveal the residues involved in the substrate binding of the E. coli Orf135 protein.

H-1, N-15 and C-13 backbone and side-chain assignments of the rice phytochrome BPAS1 domain and backbone assignments of the PAS1-PAS2 domain

Kobayashi T, Mishima M, Akagi K, Sakai N, Katoh E, Takano M, Yamazaki T, Kojima C

JOURNAL OF BIOMOLECULAR NMR 31 ( 3 ) 269 - 270 2005.3 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

1P267 Structural study of transducer protein pHtrII by NMR

Hayashi K., Sudo Y., Mishima M., Kamo N., Kojima C.

Seibutsu Butsuri 45 ( supplement ) S98 2005

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Structural studies of rice phytochrome BPAS1 domain using multi-dimensional NMR

Kobayashi T, Mishima M, Tabata R, Akagi K, Sakai N, Katoh E, Takano M, Yamazaki T, Kojima C

PLANT AND CELL PHYSIOLOGY 46 S166 - S166 2005 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Solution structure of C-terminal domain of rice phytochrom B

Kojima C

PLANT AND CELL PHYSIOLOGY 46 S2 - S2 2005 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Single Work

2P137 NMR structural analysis of the CGG/CGG containing DNA complexed with the recognition drugs

Nomura M., Hagihara S., Goto Y., Nakatani K., Kojima C.

Seibutsu Butsuri 45 ( supplement ) S154 2005

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

2P133 Spectroscopic analysis of DNA duplex including T-Hg-T base pairs

Oda S., Yamaguchi H., Ono A., Kojima C., Kondo Y., Tanaka Y.

Seibutsu Butsuri 45 ( supplement ) S153 2005

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

NMR spectroscopic analyses of functional nucleic acids-metal interaction and their solution structure analyses.

Kazunari Taira, Yoshiyuki Tanaka, Chojiro Kojima, Yoshinori Kondo, Akira Ono, Shuji Oda, Hiroshi Ya … Show more authors

Nucleic Acids Symposium Series 49 51 - 52 2005 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

We have studied complexations of functional nucleic acids and metal ions, by means of NMR spectroscopy. In the case of hammerhead ribozymes, they have a metal ion-binding motif in their core sequences. Upon the metallation of N7 of a guanosine in an RNA duplex modelled after hammerhead ribozymes, 20 ppm higher field shift of N7 was observed in 1-dimensional (1D) 15N NMR spectra. It was found that metal ion binding to nucleobases were detectable with 15N NMR spectroscopy.

Spectroscopic analyses of DNA duplexes in the presence of mercury ions.

Yoshinori Kondo, Yoshiyuki Tanaka, Chojiro Kojima, Shuji Oda, Akira Ono, Hiroshi Yamaguchi

Nucleic Acids Symposium Series 49 199 - 200 2005 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

The DNA duplex with tandem T x T mismatches in the presence of Hg(II) has been studied by NMR spectroscopy. For this study, we synthesized decamer duplex with two successive T x T mismatches (TT10). From two-dimensional (2D) 1H-1H NOESY spectrum of TT10 in complex with Hg(II), we were able to trace sequential NOE walks between base protons and anomeric protons (H1'), and assigned all of them. Based on these assignments and NOESY spectra, we could assigned all the non-exchangeable protons of TT10 in the presence of Hg(II).

Solution structure of a small-molecular ligand complexed with CAG trinucleotide repeat DNA.

Masaki Mishima, Kazuhiko Nakatani, Motoki Kyo, Gosuke Hayashi, Makoto Nomura, Chojiro Kojima, Yuki … Show more authors

Nucleic Acids Symposium Series 49 49 - 50 2005 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

NMR structure of the first identified ligand, naphthyridine-azaquinolone (NA), complexed with the CAG-CAG triad is reported. The determined structure revealed the invasive ligands binding to the A-A mismatch and flanking G-C base pairs, causing the widowed cytosines to flip out from pi-stack. Hydrogen-bond pairs between NA and DNA, naphthyridine-guanine and azaquinolone-adenine, are well stacked in the right-handed DNA helix, showing structural mimicry of Watson-Crick base pairing. This is the first observation that the small molecular ligand induced the base flipping of the nucleotide base in the Watson-Crick base pair.

NMR structural analysis of the G.G mismatch DNA complexed with naphthyridine-dimer.

Makoto Nomura, Shinya Hagihara, Yuki Goto, Kazuhiko Nakatani, Chojiro Kojima

Nucleic Acids Symposium Series 49 ( 1 ) 213 - 214 2005

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Naphthyridine-dimer (ND) specifically recognizes G.G mismatch DNA (Figure 1). However, its detailed recognition mechanism is not clear. Here a DNA oligomer d(CTAACGGAATG)/d(CATTCGGTTAA) complexed with ND was studied by NMR. The stoichiometry of DNA to ND was determined to be 1:2 at NMR concentration (2.5 mM). Proton resonances were completely assigned including H5' and H5'' using 1H-1H and 1H-13C 2D spectra of the complex. These spectra showed that four naphthyridine rings are staked in the helix and form hydrogen bonds with the four G residues in CGG/CGG region. These results indicate ND can specifically recognize the CGG/CGG sequence.

Paramagnetic NMR study of Cu2+-IDA complex localization on a protein surface and its application to elucidate long distance information

Nomura M, Kobayashi T, Kohno T, Fujiwara K, Tenno T, Shirakawa M, Ishizaki I, Yamamoto K, Matsuyama … Show more authors

FEBS LETTERS 566 ( 1-3 ) 157 - 161 2004.5 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Wiley Joint Work

<jats:p>The paramagnetic metal chelate complex Cu<jats:sup>2+</jats:sup>‐iminodiacetic acid (Cu<jats:sup>2+</jats:sup>–IDA) was mixed with ubiquitin, a small globular protein. Quantitative analyses of <jats:sup>1</jats:sup>H and <jats:sup>15</jats:sup>N chemical shift changes and line broadenings induced by the paramagnetic effects indicated that Cu<jats:sup>2+</jats:sup>–IDA was localized to a histidine residue (His68) on the ubiquitin surface. The distances between the backbone amide proton and the Cu<jats:sup>2+</jats:sup> relaxation center were evaluated from the proton transverse relaxation rates enhanced by the paramagnetic effect. These correlated well with the distances calculated from the crystal structure up to 20 Å. Here, we show that a Cu<jats:sup>2+</jats:sup>–IDA is the first paramagnetic reagent that specifically localizes to a histidine residue on the protein surface and gives the long‐range distance information.</jats:p>

Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B

Fujiwara K, Tenno T, Sugasawa K, Jee JG, Ohki I, Kojima C, Tochio H, Hiroaki H, Hanaoka F, Shirakaw … Show more authors

JOURNAL OF BIOLOGICAL CHEMISTRY 279 ( 6 ) 4760 - 4767 2004.2 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves signaling functions that control several cellular processes. The ubiquitination signal is recognized by downstream effectors, many of which carry a ubiquitin-interacting motif (UIM). Such interactions can be modulated by regulators carrying a ubiquitin-like (UbL) domain, which binds UIM by mimicking ubiquitination. Of them, HR23B regulates the proteasomal targeting of ubiquitinated substrates, DNA repair factors, and other proteins. Here we report the structure of the UIM of the proteasome subunit S5a bound to the UbL domain of HR23B. The UbL domain presents one hydrophobic and two polar contact sites for interaction with UIM. The residues in these contact sites are well conserved in ubiquitin, but ubiquitin also presents a histidine at the interface. The pH-dependent protonation of this residue interferes with the access of ubiquitin to the UIM and the ubiquitin-associated domain (UBA), and its mutation to a smaller residue increases the affinity of ubiquitin for UIM.

Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes

Tanaka Y, Kasai Y, Mochizuki S, Wakisaka A, Morita EH, Kojima C, Toyozawa A, Kondo Y, Taki M, Takag … Show more authors

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126 ( 3 ) 744 - 752 2004.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

We have studied the interaction between metal ions and the metal ion-binding motif in hammerhead ribozymes, as well as the functions of the metal ion at the motif, with heteronuclear NMR spectroscopy. In this study, we employed model RNA systems which mimic the metal ion-binding motif and the altered motif. In Co(NH3)6(III) titrations, we observed large 1H and 31P chemical shift perturbations for the motif and found that outer-sphere complexation of Co(NH3)6(III) is possible for this motif. From the reinvestigation of our previous 15N chemical shift data for Cd(II) binding, in comparison with those of organometallic compounds, we conclude that Cd(II) can form an inner-sphere complex with the nucleobase in the motif. Therefore, the A9/G10.1 site was found to accept both inner-sphere and outer-sphere complexations. The Mg(II) titration for a slightly different motif from the A9/G10.1 site (G10.1-C11.1 to A10.1-U11.1) revealed that its affinity to Mg(II) was drastically reduced, although the ribozyme with this altered motif is known to retain enzymatic activities. This observation suggests that the metal ion at these motifs is not a catalytic center of hammerhead ribozymes.

1P117 Solution NMR Study of Halobacterial Transducer pHtrII Linker Region

Fukuzaki Y., Okuda H., Sudo Y., Yamabi M., Mishima M., Kamo N., Kojima C.

Seibutsu Butsuri 44 ( supplement ) S59 2004

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

NMR structural study of phytochrome BPAS1 and PAS2 domain

Tabata R, Mishima M, Kobayashi T, Akagi K, Katoh E, Takano M, Yamazaki T, Kojima C

PLANT AND CELL PHYSIOLOGY 45 S227 - S227 2004 [Reviewed]

Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

New sequential-assignment routes of nucleic acid NMR signals using a [5 '-C-13]-labeled DNA dodecamer

Kawashima E, Sekine T, Umabe K, Kamaike K, Mizukoshi T, Shimba N, Suzuki E, Kojima C

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 23 ( 1-2 ) 255 - 262 2004 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Informa UK Limited Joint Work

NMR signal assignments for DNA oligomers have been performed by the well-established sequential assignment procedures based on NOESY and COSY. The H4'/H5'/H5'' resonance region is congested and difficult to analyze without the use of isotope-labeled DNA oligomers. Here a DNA dodecamer constructed with 2'-deoxy[5'-(13)C]ribonucleotides, 5'-d(*C*G*C*G*A*A*T*T*C*G*CG)-3' (*N = [5'-(13)C]Nucleotide), was prepared in an effort to analyze the H4'/H5'/H5'' resonance region by 2D 1H-13C HMQC-NOESY. In the C5' and H1' resonance region, weak and strong cross peaks for C5'(i)-H1'(i) and C5'(i)-H1'(i-1), respectively, were found, thus enabling the sequential assignment within this region. A similar sequential assignment route was found between C5' and H2''. Proton pair distances evaluated from the canonical B-DNA as well as A-DNA indicated that these sequential-assignment routes on a 2D 1H-13C HMQC-NOESY spectrum work for most nucleic acid stem regions.

Solution NMR study of DNA recognition mechanism of IRF4 protein.

Itsuko Ishizaki, Kazuo Yamamoto, Toshifumi Matsuyama, Masaki Mishima, Makoto Nomura, Chojiro Kojima

Nucleic Acids Symposium Series 48 105 - 106 2004 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was investigated by NMR and fluorescence antisotropy as an example of the indirect sequence recognition. The 1H-15N HSQC spectra of the IRF-4/DNA complex containing the CCGAAA sequence indicated that the 1:1 complex was formed. The dissociation constants (Kd) for two DNA oligomers containing CCGAAA and GGGAAA were determined by fluorescence antistropy, but their difference was very small.

Structure of the male determinant factor for Brassica self-incompatibility

Mishima M, Takayama S, Sasaki K, Jee J, Kojima C, Isogai A, Shirakawa M

JOURNAL OF BIOLOGICAL CHEMISTRY 278 ( 38 ) 36389 - 36395 2003.9 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Many flowering plants possess a self-incompatibility system to prevent inbreeding. In Brassica rapa, self/non-self recognition in mating is established through S-haplotype-specific interactions between stigma receptors and S-locus protein 11 (SP11, also called S-locus cysteine-rich protein) that is encoded at the highly polymorphic S-locus. Here we describe the solution structure of the SP11 protein of the S8-haplotype (S8-SP11), which specifically binds to the stigma factor of the same haplotype. It folds into an alpha/beta sandwich structure that resembles those of plant defensins. Residues important for structural integrity are highly conserved among the allelic SP11s, suggesting the existence of a common folding pattern. Structure-based sequence alignment and homology modeling of allelic SP11 identified a hyper-variable (HV) region, which is thought to form a loop that bulges out from the body of the protein that is amenable to solvent exposure. We suggest that the HV region could serve as a specific binding site for the stigma receptor.

NMR spectroscopic investigations of the roles of the metal ion at A9/G10.1 site in hammerhead ribozymes

Atsushi Toyozawa, Yoshiyuki Tanaka, Yoshinori Kondo, Yasuhiro Kasai, Kazuhiko Yamasaki, Kazunari Ta … Show more authors

Nucleic Acids Symposium Series 3 45 - 46 2003.9 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Most hammerhead ribozymes have metal ion-binding sequences which are composed of the sheared type G12-A9 pair and the G10.1-C11.1 base-pair. However, in some hammerhead ribozymes, the G10.1-C11.1 base-pair is substituted with the A10.1-U11.1 base-pair. Here, we studied structural features of this altered motif, by using NMR spectroscopy. For this purpose, we have synthesized a model RNA oligomer, UGAA10:rGGAUGAAUCC which mimics the altered motif. From a 2-dimensional (2D) 1H-1H NOESY spectrum, we were able to trace sequential NOEs between base protons and anomeric protons (H1'), and assigned these resonances. It was also found that G5 and A6 formed a sheared type G-A pair from the imino proton resonance of G5. Observation of the imino proton resonance of U4 suggested that U4 forms a base-pair with A7. These structural features of the altered motif of UGAA10 are similar to the common metal ion-binding motif with G12-A9 and G10.1-C11.1.

NMR spectroscopic investigations of the roles of the metal ion at A9/G10.1 site in hammerhead ribozymes

Atsushi Toyozawa, Yoshiyuki Tanaka, Yoshinori Kondo, Yasuhiro Kasai, Kazuhiko Yamasaki, Kazunari Ta … Show more authors

Nucleic Acids Symposium Series 3 45 - 46 2003.9 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Solution NMR of seven transmembrane protein, phR and ppR

Okuda H., Sudo Y., Mishima M., Sato M., Demura M., Nitta K., Kamo N., Kojima C.

Seibutsu Butsuri 43 ( supplement ) S183 2003

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Solution NMR of gel-phase protein and transmembrane protein

Kojima C.

Seibutsu Butsuri 43 ( supplement ) S21 2003

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Single Work

Metal ion recognition of the metal-binding motif in hammerhead ribozymes

Tanaka Y., Kasai Y., Kojima C., Yamasaki K., Morita H., Taira K.

Seibutsu Butsuri 43 ( supplement ) S28 2003

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

A theoretical study of correlation between hydrogen-bond stability and J-coupling through a hydrogen bond

Kawahara S, Kojima C, Taira K, Uchimaru T

HELVETICA CHIMICA ACTA 86 ( 10 ) 3265 - 3273 2003 [Reviewed]

DOI Web of Science

Language：English Publishing type：Research paper (scientific journal) Joint Work

Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using N-15 NMR spectroscopy

Tanaka Y, Kojima C, Morita EH, Kasai Y, Yamasaki K, Ono A, Kainosho M, Taira K

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 ( 17 ) 4595 - 4601 2002.5 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

An RNA oligomer, r(GGACGAGUCC), which mimics the metal ion-binding motif of hammerhead ribozymes, was shown to fold by itself into a conformation possessing a metal ion binding property which is similar to that of the intact ribozyme (Tanaka, et al. J. Am. Chem. Soc. 2000, 122, 11303-11310). To determine the metal ion-binding site of this motif at an atomic level, we synthesized a series of RNA oligomers which were selectively labeled with a (15)N-labeled guanosine at each of the four guanosine residues. The (15)N-chemical shift perturbation with Cd(II) ions by one-dimensional (1D) (15)N NMR spectra showed that the chemical shift of the N7 of the G7 residue, N7/G7, in the metal ion-binding motif was specifically perturbed. This is the first experimental evidence to prove that the N7/G7 binds with a Cd(II) ion.

2H1400 Structural analysis of transmembrane helical halobacterial transducer protein and its interaction with pharaonis phoborhodopsin

Sudo Y., Misima M., Kamo N., Kojima C.

Seibutsu Butsuri 42 ( supplement2 ) S119 2002

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

ChemInform Abstract: Solid‐Phase Synthesis of Selectively Labeled DNA — Applications for Multidimensional Nuclear Magnetic Resonance Spectroscopy

Chojiro Kojima, Akira Ono, Masatsune Kainosho

ChemInform 32 2001.12 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Wiley Joint Work

<jats:title>Abstract</jats:title><jats:p>ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.</jats:p>

ChemInform Abstract: Solid‐Phase Synthesis of Selectively Labeled DNA — Applications for Multidimensional Nuclear Magnetic Resonance Spectroscopy

Chojiro Kojima, Akira Ono, Masatsune Kainosho

ChemInform 32 2001.12 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Wiley Joint Work

ChemInform Abstract: Solid‐Phase Synthesis of Selectively Labeled DNA — Applications for Multidimensional Nuclear Magnetic Resonance Spectroscopy

Chojiro Kojima, Akira Ono, Masatsune Kainosho

ChemInform 32 2001.12 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Wiley Joint Work

Synthesis of 5-substituted [N3-15N]-pyrimidine nucleosides: Developing model systems for NMR studies of substituent effects on the N-H{middle dot}{middle dot}{middle dot}N hydrogen bond in duplex DNA

Chojiro Kojima, Rei Ishikawa, Masatsune Kainosho, Akira Ono

Nucleic Acids Symposium Series 1 9 - 10 2001.11 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

The effects on various NMR parameters of substitutions, which may influence the hydrogen bond strengths of Watson-Crick-type base pairs, were investigated for DNA dodecamers containing 5-substituted-2'-deoxyuridine derivatives in oligomers, 5'-d(CGCGAATXCGCG)-3', where A and X were [ul-15N]-2'-deoxyadenosine and [3(-15)N]-2'-deoxyuridine derivatives. The substitution effects on the NMR parameters were linearly correlated with the pKa values of the 2'-deoxyuridine derivatives.

Synthesis of 5-substituted [N3-15N]-pyrimidine nucleosides: Developing model systems for NMR studies of substituent effects on the N-H{middle dot}{middle dot}{middle dot}N hydrogen bond in duplex DNA

Chojiro Kojima, Rei Ishikawa, Masatsune Kainosho, Akira Ono

Nucleic Acids Symposium Series 1 9 - 10 2001.11 [Reviewed]

DOI PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP) Joint Work

Slow motion in the CAA center dot TTG sequence of a DNA decamer duplex studied by NMR

Kojima C, Ulyanov NB, Kainosho M, James TL

BIOCHEMISTRY 40 ( 24 ) 7239 - 7246 2001.6 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

In DNA duplexes, pyrimidine-purine steps are believed to be flexible or conformationally unstable. Indeed, several DNA crystal structures exhibit a multitude of conformations for CpA*TpG steps. The question arises of whether this structural flexibility is accompanied by dynamical flexibility, i.e., a question pertaining to the energy barrier between conformations. Except for TpA steps, slow motions on the microsecond-to-millisecond time scale have not been detected in duplexes until now. In the present study, such slow motion was investigated by 1H, 13C, and 15N NMR relaxation measurements on a DNA decamer d(CATTTGCATC)*d(GATGCAAATG). The DNA decamer was enriched with 15% 13C and 98% 15N isotopes for each adenosine and guanosine residue. Three lines of evidence support the notion of slow motion in the CAA*TTG moiety. Analysis of (15)N relaxation showed that the order parameter, S2, of guanosine imino NH groups was about 0.8, similar to that of CH groups for this oligomer. The strong temperature dependence of guanosine NH S2 in the CAA*TTG sequence indicated the presence of a large-amplitude motion. Signals of adenosine H8 protons in the CAA*TTG sequence were broadened in 2D 1H NOESY spectra, which also suggested the existence of slow motion. As well as being smaller than for other adenine residues, the 1H T2 values exhibited a magnetic field strength dependence for all adenosine H8 signals in the ATTTG*CAAAT region, suggesting slow motions more pronounced at the first adenosine in the CAA*TTG sequence but extending over the CAAAT*ATTTG region. This phenomenon was further examined by the pulse field strength dependence of the 1H, 13C, and 15N T1rho values. 1H and 13C T1rho values showed a pulse field strength dependence, but 15N T1rho did not. Assuming a two-site exchange process, an exchange time constant of 20-300 micros was estimated for the first adenosine in the CAA sequence. The exact nature of this motion remains unknown.

Sugar conformation of a stereospecific 2 '-R or 2 '-S deuterium-labeled DNA decamer studied with proton-proton J coupling constants

Kojima C, Kawashima E, Sekine T, Ishido Y, Ono A, Kainosho M, Kyogoku Y

JOURNAL OF BIOMOLECULAR NMR 19 ( 1 ) 19 - 31 2001.1 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

The sugar conformation of a DNA decamer was studied with proton-proton 3J coupling constants. Two samples, one comprising stereospecifically labeled 2'-R-2H for all residues and the other 2'-S-2H, were prepared by the method of Kawashima et al. [J. Org. Chem. (1995) 60, 6980-6986; Nucleosides Nucleotides (1995) 14, 333-336], the deuterium labeling being highly stereospecific (or = 99% for all 2''-2H,or = 98% for 2'-2H of A, C, and T, andor = 93% for 2'-2H of G). The 3J values of all H1'-H2' and H1'-H2'' pairs, and several H2'-H3' and H2''-H3' pairs were determined by line fitting of 1D spectra with 0.1-0.2 Hz precision. The observed J coupling constants were explained by the rigid sugar conformation model, and the sugar conformations were found to be between C3'-exo and C2'-endo with phi(m) values of 26 degrees to 44 degrees, except for the second and 3' terminal residues C2 and C10. For the C2 and C10 residues, the lower fraction of S-type conformation was estimated from JH1'H2' and JH1'H2'' values. For C10, the N-S two-site jump model or Gaussian distribution of the torsion angle model could explain the observed J values, and 68% S-type conformation or C1'-exo conformation with 27 degrees distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-coupling constants.

Solid-phase synthesis of selectively labeled DNA: Applications for multidimensional nuclear magnetic resonance spectroscopy

Kojima C, Ono AM, Ono A, Kainosho M

NUCLEAR MAGNETIC RESONANCE OF BIOLOGICA MACROMOLECULES, PT A 338 261 - 283 2001 [Reviewed]

Web of Science PubMed

Language：English Publishing type：Research paper (scientific journal) Joint Work

Studies of physicochemical properties of N-H center dot center dot center dot N hydrogen bonds in DNA, using selective N-15-labeling and direct N-15 1D NMR

Kojima C, Ono A, Kainosho M

JOURNAL OF BIOMOLECULAR NMR 18 ( 3 ) 269 - 277 2000.11 [Reviewed]

DOI Web of Science PubMed CiNii Research

Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

15N-15N scalar coupling constants across base pair hydrogen bonds (2hJ(NN)) were studied using residue- and atom-specifically 15N labeled DNA oligomers. The N3 atom selectively 15N enriched 2'-deoxycytidine and thymidine, and the uniformly 15N enriched 2'-deoxyadenosine and 2'-deoxyguanosine, were chemically prepared and incorporated into two DNA oligomers, d(CGCGAATTCGCG)2 and d(CGCAAAAAGCG).d(CGCTTTTTGCG). This isotope labeling enabled us to determine the 2hJ(NN) value from the splitting of the 15N 1D spectrum. Additionally, it enabled the determination of 2hJ(NN) in D2O quite easily and highly quantitatively. The temperature and DNA sequence dependence were examined for these oligomers. The sequence dependence was not clear; however, a significant decrease of 2hJ(NN) was observed by elevating the temperature. This temperature dependence was not due to the hydrogen exchange, since the addition of 20 mM NH3 did not change the 2hJ(NN) values. The 2hJ(NN) values in D2O were somewhat smaller than those in H2O. As compared to our 15N 1D method, the quantitative HNN-COSY method gave systematically smaller 2hJ(NN) values in our system, due to the lower 15N fraction of our sample (79 and 88% for dA and the other nucleotides, respectively) and the insufficient power of the 15N RF pulse (B1 = 6.6 kHz). These systematic differences were recovered by theoretical correction of the 15N isotope fraction contribution, by using the composite 15N 180 degrees pulse in a quantitative HNN-COSY experiment.

Solution structure of an RNA duplex including a C-U base pair

Tanaka Y, Kojima C, Yamazaki T, Kodama TS, Yasuno K, Miyashita S, Ono A, Ono A, Kainosho M, Kyogoku … Show more authors

BIOCHEMISTRY 39 ( 24 ) 7074 - 7080 2000.6 [Reviewed]

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Simple suppression of spurious peaks in TROSY experiments

Kojima C, Kainosho M

JOURNAL OF MAGNETIC RESONANCE 143 ( 2 ) 417 - 422 2000.4 [Reviewed]

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In (1)H-(15)N TROSY experiments of proteins and nucleic acids, where the second coherence transfer delay time tau' has been fixed as 5.6 ms, 1/(2(1)J(NH)), in order to achieve complete spin-state selection, spurious negative peaks are observed along the (15)N axes. These peaks are often annoyingly large, especially for nucleic acids. A simple product operator calculation, however, indicated that the shortening of the second delay time tau', which is next to the t1 period, would efficiently suppress these spurious peaks, without sacrificing the sensitivities of the TROSY peaks too much. We have shown for three systems, two 11- and 17-kDa proteins and one 8-kDa DNA duplex, that these spurious peaks can be effectively suppressed with delay times of 3.3 ms for the two proteins and 2.3 ms for the DNA. These delay times, optimized by trial and error, for the spurious peak suppression did not depend on the magnetic field strength and the temperature very much. Although the shortened tau' delay times attenuate the TROSY peak intensities by about 10 and 20% for the two proteins and the DNA, respectively, this simple modification will be useful for the quantitative uses of TROSY peaks and will result in cleaner spectra for various TROSY-based multiple resonance experiments.

13C-NMR Relaxation Analysis of Nucleic Acid Structure and Dynamics

KOJIMA Chojiro, KAINOSHO Masatsune

Seibutsu Butsuri 40 ( 3 ) 191 - 194 2000

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Direct Observation of Hydrogen Bonding in Biomolecules by NMR

KOJIMA Chojiro, KAINOSHO Masatsune

Seibutsu Butsuri 40 ( 6 ) 379 - 384 2000

DOI CiNii Research

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Intermolecular contacts between the λ-Cro repressor and the operator DNA characterized by nuclear magnetic resonance spectroscopy

Tochio, H; Kojima, C; Matsuo, H; Yamazaki, T; Kyogoku, Y

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 16 ( 5 ) 989 - + 1999.4 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Informa UK Limited Joint Work

The specific interaction between lambda phage Cro repressor and the DNA fragment bearing the consensus sequence of operators has been studied using nuclear magnetic resonance (NMR). Using both 15N- and 13C/15N- labeled lambda-Cro in complex with unlabeled DNA, chemical shift assignments of the lambda-Cro-DNA complex were obtained using heteronuclear NMR experiments. Inter-molecular contacts between the protein and DNA were identified using heteronuclear filtered NOESY experiments. The inter-molecular contacts were supplemented with intra-protein and intra-DNA NOE constraints to dock lambda-Cro to the bent B-form DNA using restrained molecular dynamics. The structure of one of the subunits of lambda-Cro in the complex is essentially the same as that of the unbound form. In the complex, inter-molecular NOEs were observed between the "helix-turn-helix" region comprising the alpha2 and alpha3 helices of the lambda-Cro protein and the major groove of the DNA. The methyl group of Thr17 forms a hydrophobic contact with the methyl group of the thymine at base pair 1 in the DNA, and Val25 and Ala29 make hydrophobic contacts with the methyl group of the thymine at base pair 5. The presence and the absence of these contacts can explain the difference in the affinity of lambda-Cro to several variants of the operator sequence.

Quantitative measurement of transverse and longitudinal cross-correlation between C-13-H-1 dipolar interaction and C-13 chemical shift anisotropy: Application to a C-13-labeled DNA duplex

Kojima C, Ono A, Kainosho M, James TL

JOURNAL OF MAGNETIC RESONANCE 136 ( 2 ) 169 - 175 1999.2 [Reviewed]

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Measurement of both longitudinal and transverse relaxation interference (cross-correlation) between 13C chemical shift anisotropy and 13C-1H dipolar interactions is described. The ratio of the transverse to longitudinal cross-correlation rates readily yields the ratio of spectral densities J(0)/J(omegaC), independent of any structural attributes such as internuclear distance or chemical shift tensor. The spectral density at zero frequency J(0) is also independent of chemical exchange effects. With limited internal motions, the ratio also enables an accurate evaluation of the correlation time for overall molecular tumbling. Applicability of this approach to investigating dynamics has been demonstrated by measurements made at three temperatures using a DNA decamer duplex with purines randomly enriched to 15% in 13C.

Structural effect of complete [Rp]-phosphorothioate and phosphorodithioate substitutions in the DNA strand of a model antisense inhibitor-target RNA complex

Furrer P, Billeci TM, Donati A, Kojima C, Karwowski B, Sierzchala A, Stec W, James TL

JOURNAL OF MOLECULAR BIOLOGY 285 ( 4 ) 1609 - 1622 1999.1 [Reviewed]

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Synthesis of 2 '-deoxy[5 '-C-13]ribonucleotides and HMQC-NOESY NMR study of the Dickerson's dodecamer with C-13 labeling at the 5 ' positions

Kawashima E, Sekine T, Umabe K, Naito Y, Kamaike K, Kojima C, Mizukoshi T, Suzuki E, Ishido Y

NUCLEOSIDES & NUCLEOTIDES 18 ( 6-7 ) 1597 - 1598 1999 [Reviewed]

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DNA duplex dynamics: NMR relaxation studies of a decamer with uniformly C-13-labeled purine nucleotides

Kojima C, Ono A, Kainosho M, James TL

JOURNAL OF MAGNETIC RESONANCE 135 ( 2 ) 310 - 333 1998.12 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier BV Joint Work

Dynamics in a DNA decamer duplex, d(CATTTGCATC). d(GATGCAAATG), were investigated via a detailed 13C NMR relaxation study. Every 2'-deoxyadenosine and 2'-deoxyguanidine was chemically enriched with 15% 13C and 98% 15N isotopes. Six nuclear relaxation parameters [R(13Cz), R(1Hz), R(2(1)Hz13Cz), R(13Cx), R(2(1)Hz13Cx) and steady-state 13C¿1H¿ NOE] were measured at 600 MHz and three were measured at 500 MHz (1H frequency) for the CH spin systems of sugar 1', 3', and 4' as well as base 8 and 2 positions. A dependence of relaxation parameter values on chemical position was clearly observed; however, no sequence-specific variation was readily evident within our experimental error of approximately 5-10%, except for 3' and 5' termini. It was demonstrated that the random 15% 13C enrichment effectively suppressed both scalar and dipolar contributions of the neighboring carbons and protons on the relaxation parameters. To analyze dynamics via all observed relaxation parameters, full spectral density mapping (1992, J. W. Peng and G. Wagner, J. Magn. Reson. 98, 308) and the "model-free" approach (1982, Lipari and Szabo, J. Am. Chem. Soc. 104, 4546) were applied complementarily. A linear correlation between three spectral density values, J(omegaC), J(omegaH - omegaC), and J(omegaH + omegaC) was observed in plots containing all measured values, but not for the other spectral density terms including J(0). These linear correlations reflect the effect of overall motion and similar internal motions for each CH vector in the decamer. The correlations yielded two correlation times, 3-4 ns and 10-200 ps. One value, 3-4 ns, corresponds to the value of 3.3 ns obtained for the overall isotropic tumbling correlation time determined from analysis of 13C T1/T2 ratios. The possibility of overall anisotropic tumbling was examined, but statistical analysis showed no advantage over the assumption of simple isotropic tumbling. Lack of correlations entailing J(0) implies that a relatively slow chemical exchange contributes to yielding of effective Jeff(0) values. Based on spectral density mapping and the T1/T2 ratio analysis, three basic assumptions were initially employed (and subsequently justified) for the model-free calculation: isotropic overall tumbling, one internal motion, and the presence of chemical exchange terms. Except for terminal residues, the order parameter S2 and the corresponding fast internal motion correlation time were determined to be about 0.8 +/- 0.1 and 20 +/- 20 ps, respectively, for the various CH vectors. Only a few differences were observed between or within sugars and bases. The internal motion is very fast (ps-ns time scale) and its amplitude restricted; e.g., assuming a simple wobble-in-a-cone model, the internal motion is restricted to an angular amplitude of +/-22. 5 degrees for each of the 1', 3', 4', 2, and 8 positions in the purine nucleotides in the entire duplex.

Stereospecific assignment of H5 ' and H5 '' in a (5 ' R)-/(5 ' S)-deuterium-labeled DNA decamer for (3)J(HH) determination and unambiguous NOE assignments

Kojima C, Kawashima E, Toyama K, Ohshima K, Ishido Y, Kainosho M, Kyogoku Y

JOURNAL OF BIOMOLECULAR NMR 11 ( 1 ) 103 - 109 1998.1 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

The stereoselective deuterium labeling at the 5' methylene protons of the ribose ring recently developed by Kawashima et al. [1995, Tetrahedron Lett., 36, 6699-6700] enabled the assignment of pro-R and pro-S protons at the 5' position. The deuterium-labeled nucleotides, [(5'S)-(2)H]- and [(5'R)-(2)H]-diastereomers, in an approximate ratio of 2:1, were incorporated in the decamer 5'-d(GCATTAATGC)-3'. Thus, both pro-R and pro-S methylene proton signals without geminal coupling appeared in the NOESY and DQF-COSY spectra. Complete stereospecific assignments and simplified spin systems enabled the determination of 15 (3)J coupling constants between H4' and H5'/H5", and the unambiguous assignment of 135 NOESY cross peaks originating from H4'/H5'/H5" resonances.

NMR study of solution structure of lambda-Cro-DNA complex

TOCHIO H., KOJIMA C., YAMAZAKI T., KYOGOKU Y.

Biophysics 37 S14 1997.10 [Reviewed]

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Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Biophysical Society of Japan General Incorporated Association Joint Work

Solution structures of DNA duplexes containing a DNA center dot RNA hybrid region, d(GG)r(AGAU)d(GAC)center dot d(GTCATCTCC) and d(GGAGA)r(UGAC)d(GTCATCTCC)

Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E

BIOCHEMISTRY 35 ( 13 ) 4016 - 4025 1996.4 [Reviewed]

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Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS) Joint Work

The solution structures of two DNA duplexes containing a DNA*RNA hybrid region at different sites, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) (DHD, where D and H represent the DNA and DNA x RNA hybrid segments, respectively) and d(GGAGA)r(UGAC) x d(GTCATCTCC) (DDH), were determined by nuclear magnetic resonance spectroscopy to clarify the structural features of the D-H and H-D junctions. All proton-proton distances were derived from the NOESY spectra, with mixing times of 45 ms, and the restrained molecular dynamics were carried out starting from the typical A- and B-form conformations. Both duplexes were converged from the respective initial structures into structures with RMSD values of less than 1.0 angstrom. These structures were subjected to full relaxation matrix refinement to produce the final structures. In the case of the D-H junction, where the ribonucleotide was linked to the 3'-end of the DNA, the H2' and H2" signals of the deoxynucleotide overlapped completely, and the ribonucleotide had a H1'-H2' coupling constant larger than that of the normal C3'-endo sugar pucker. The dihedral angles, the pseudorotation phase angles, and the helical parameters changed at the H-D junction, but not at the D-H junction. A detailed comparison of the two duplexes revealed the structural heterogeneity between the DNA segment and the DNA x RNA hybrid region and the transitions at the junctions.

Filtering methods for selection of singlet and doublet signals in NMR spectra of DNA oligomers

Chojiro Kojima, Yoshimasa Kyogoku

Journal of Biomolecular NMR 4 1994.3 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

The base proton (purine H8 and pyrimidine H6) resonances are key signals for the assignment of the proton resonances of DNA oligomers. They are classified into two groups, i.e., cytosine H6 signals, observed as doublets, and the other base proton signals, observed as singlets. Here we propose some experiments for distinguishing the cytosine H6 signals from the other base proton signals. Moreover, the ability of signal selection and the sensitivity as to signal detection were compared for all experiments, and the optimum conditions for spectral measurements were surveyed. Some of the experiments were employed as the NOESY detection pulse. Previously proposed experiments, such as HOENOE and HAL, were also used in the comparison.

Filtering methods for selection of singlet and doublet signals in NMR spectra of DNA oligomers

Chojiro Kojima, Yoshimasa Kyogoku

Journal of Biomolecular NMR 4 1994.3 [Reviewed]

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Language：The in addition, foreign language Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC Joint Work

FILTERING METHODS FOR SELECTION OF SINGLET AND DOUBLET SIGNALS IN NMR-SPECTRA OF DNA OLIGOMERS

KOJIMA C, KYOGOKU Y

JOURNAL OF BIOMOLECULAR NMR 4 ( 2 ) 181 - 191 1994.3 [Reviewed]

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