Publication

(97) Jeffrey C Hoch*, Kumaran Baskaran, Harrison Burr, John Chin, Hamid R Eghbalnia, Toshimichi Fujiwara, Michael R Gryk, Takeshi Iwata, Chojiro Kojima, Genji Kurisu, Dmitri Maziuk, Yohei Miyanoiri, Jonathan R Wedell, Colin Wilburn, Hongyang Yao, Masashi Yokochi. Biological Magnetic Resonance Data Bank. Nucleic Acids Res, 51, D368-D376 (2023). 2023 Jan 6;51(D1):D368-D376.
DOI:10.1093/nar/gkac1050

(96) Ken-ichiro Taoka*, Ikumi Kawahara, Shoko Shinya, Ken-ichi Harada, Eiki Yamashita, Zenpei Shimatani, Kyoko Furuita, Tomoaki Muranaka, Tokitaka Oyama, Rie Terada, Atsushi Nakagawa, Toshimichi Fujiwara, Hiroyuki Tsuji*, Chojiro Kojima*. Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening. Plant J, 112, 1337-1349 (2022). 2022 Dec;112(6):1337-1349.
DOI:10.1111/tpj.16008

(95) Kyoko Furuita, Kouki Inomata, Toshihiko Sugiki, Naohiro Kobayashi, Toshimich Fujiwara, Chojiro Kojima*. 1H, 13C, and 15N resonance assignments of human glutathione peroxidase 4. Biomol NMR Assign, 16, 267-271 (2022). 2022 Oct;16(2):267-271.
DOI:10.1007/s12104-022-10090-7

(94) Yoshiyuki Tanaka*, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Masayuki Morikawa, Takashi S. Kodama, Vladimir Sychrovsky, Chojiro Kojima, Yoshikazu Hattori. Physicochemical Characterization of the Catalytic Unit of Hammerhead Ribozyme and Its Relationship with the Catalytic Activity. Biophysica, 2, 221-239 (2022). 2022 Aug 25. 2(3):221-239
DOI:10.3390/biophysica2030022

(93) Takeshi Yamada, Kyoko Furuita, Shuhei Sakurabayashi, Makoto Nomura, Chojiro Kojima, Kazuhiko Nakatani*. NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA. Nucleic Acids Res, 50, 9621-9631 (2022). 2022 Sep 23;50(17):9621-9631.
DOI:10.1093/nar/gkac740

(92) Shoko Shinya, Ritsuko Katahira, Kyoko Furuita, Toshihiko Sugiki, Young-Ho Lee, Yoshikazu Hattori, Kohei Takeshita, Atsushi Nakagawa, Aoi Kokago, Ken-ichi Akagi, Muneki Oouchi, Fumiaki Hayashi, Takanori Kigawa, Midori Takimoto-Kamimura, Toshimichi Fujiwara, Chojiro Kojima*. 19F chemical library and 19F-NMR for a weakly bound complex structure. RSC Med Chem, 13, 1100-1111 (2022). 2022 Jul 22;13(9):1100-1111.
DOI:10.1039/d2md00170e

(91) Ken-ichi Harada, Kyoko Furuita, Eiki Yamashita, Ken-ichiro Taoka, Hiroyuki Tsuji, Toshimichi Fujiwara, Atsushi Nakagawa, Chojiro Kojima*. Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition. Sci Rep, 12, 11596 (2022). 2022 Jul 8;12(1):11596.
DOI:10.1038/s41598-022-15505-y

(90) Kota Ichimaru, Koji Yamaguchi, Kenichi Harada, Yusaku Nishio, Momoka Hori, Kazuya Ishikawa, Haruhiko Inoue, Shusuke Shigeta, Kento Inoue, Keita Shimada, Satomi Yoshimura, Takumi Takeda, Eiki Yamashita, Toshimichi Fujiwara, Atsushi Nakagawa, Chojiro Kojima*, Tsutomu Kawasaki*. Cooperative regulation of PBI1 and MAPKs controls WRKY45 transcription factor in rice immunity. Nat Commun, 13, 2397 (2022). 2022 May 16;13(1):2397.
DOI:10.1038/s41467-022-30131-y

(89) Kazuya Jibiki, Mo-yan Liu, Chao-sen Lei, Takashi S. Kodama, Chojiro Kojima, Toshimichi Fujiwara, Noriko Yasuhara*. Biochemical propensity mapping for structural and functional anatomy of importin alpha IBB domain. Genes Cells, 27, 173-191 (2022). 2022 Mar;27(3):173-191.
DOI:10.1111/gtc.12917

(88) Toshihiko Sugiki*, Young-Ho Lee, Nesreen Alsanousi, Kaito Murata, Izuru Kawamura, Toshimichi Fujiwara, Kentaro Hanada, Chojiro Kojima*. A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction. Anal Biochem, 639, 114521 (2022). 2022 Feb 15;639:114521.
DOI:10.1016/j.ab.2021.114521

(87) Kyoko Furuita*, Marina Hiraoka, Kentaro Hanada, Toshimichi Fujiwara, Chojiro Kojima*. Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR. FEBS Lett, 595, 2248-2256 (2021). 2021 Sep;595(17):2248-2256.
DOI:10.1002/1873-3468.14166

(86) Kyoko Furuita*, Toshihiko Sugiki, Mika Takamuku, Yoshikazu Hattori, Masatomo So, Yasushi Kawata, Takahisa Ikegami, Toshimichi Fujiwara, Chojiro Kojima*. Sensitivity enhancement by sequential data acquisition for 13 C-direct detection NMR. J Magn Reson, 322, 106878 (2021). 2021 Jan;322:106878.
DOI:10.1016/j.jmr.2020.106878

(85) Toshihiko Sugiki, Yoshihiro Yamaguchi, Toshimichi Fujiwara, Masayori Inouye, Yutaka Ito, Chojiro Kojima*. In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli. Sci Rep, 10, 2466 (2020). 2020 Feb 12;10(1):2466.
DOI:10.1038/s41598-020-59076-2

(84) Siqin Bala, Shoko Shinya, Arpita Srivastava, Marie Ishikawa, Atsushi Shimada, Naohiro Kobayashi, Chojiro Kojima, Florence Tama, Osamu Miyashita, Daisuke Kohda*. Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study. Biochim Biophys Acta Gen Subj, 1864, 129418 (2020). 2020 Feb;1864(2):129418.
DOI:10.1016/j.bbagen.2019.129418

(83) Futoshi Ihama, Mami Yamamoto, Chojiro Kojima, Toshimichi Fujiwara, Katsumi Matsuzaki, Yoshihiko Miyata, Masaru Hoshino*. Structural characterization of the N-terminal kinase-interacting domain of an Hsp90-cochaperone Cdc37 by CD and solution NMR spectroscopy. Biochim Biophys Acta Proteins Proteom, 1867, 813-820 (2019). 2019 Sep;1867(9):813-820.
DOI:10.1016/j.bbapap.2019.06.007

(82) Muneyo Mio, Toshihiko Sugiki, Chie Matsuda, Hiroaki Mitsuhashi, Chojiro Kojima, Siu Yuen Chan, Yukiko K Hayashi, and Kazuhiro Mio*. Structural instability of lamin A tail domain modulates its assembly and higher order function in Emery-Dreifuss muscular dystrophy. Biochem Biophys Res Commun, 512, 22-28 (2019). 2019 Apr 23;512(1):22-28.
DOI:10.1016/j.bbrc.2019.02.138 Epub 2019 Mar 7.

(81) Naohiro Kobayashi, Yoshikazu Hattori, Takashi Nagata, Shoko Shinya, Peter G_ntert, Chojiro Kojima, and Toshimichi Fujiwara*. Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks. Bioinformatics, 34, 4300-4301 (2018). 2018 Dec 15;34(24):4300-4301.
DOI:10.1093/bioinformatics/bty581

(80) Yoshikazu Hattori, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Honoka Tomonari, Chojiro Kojima, and Yoshiyuki Tanaka*. NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes. Nucleos. Nucleot. Nucleic Acids, 37, 383-396 (2018). 2018;37(7):383-396.
DOI:10.1080/15257770.2018.1473877 Epub 2018 Jun 28

(79) Toshihiko Sugiki, Daichi Egawa, Keigo Kumagai, Chojiro Kojima, Toshimichi Fujiwara, Koh Takeuchi, Ichio Shimada, Kentaro Hanada*, and Hideo Takahashi*. Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif. J. Biol. Chem., 293, 11206-11217 (2018). 2018 Jul 13;293(28):11206-11217.
DOI:10.1074/jbc.RA118.002465 Epub 2018 May 30.

(78) Toshihiko Sugiki, Kyoko Furuita, Toshimichi Fujiwara, and Chojiro Kojima*. Amino acid selective 13C-labeling and 13C-scrambling profile analysis of protein alpha and side-chain carbons in E. coli utilized for protein NMR. Biochemistry, 57, 3576-3589 (2018). 2018 Jul 3;57(26):3576-3589.
DOI:10.1021/acs.biochem.8b00182 Epub 2018 Jun 20.

(77) Seiji Kojima*, Masato Takao, Gaby Almira, Ikumi Kawahara, Mayuko Sakuma, Michio Homma, Chojiro Kojima*, and Katsumi Imada*. The helix rearrangement in the periplasmic domain of the flagellar stator B-subunit activates peptidoglycan binding and ion influx. Structure, 26, 1-9 (2018). 2018 Apr 3;26(4):590-598.e5. Top 10% paper in Biophysics.
DOI:10.1016/j.str.2018.02.016 Epub 2018 Mar 22.

(76) Miho Kaneko-Suzuki, Rie Ishikawa, Chiaki Terakawa, Chojiro Kojima, Misa Fujiwara, Izuru Ohki, Hiroyuki Tsuji, Ko Shimamoto, and Ken-ichiro Taoka*. TFL1-like proteins in rice antagonize rice FT-like protein in inflorescence development by competition for complex formation with 14-3-3 and FD. Plant Cell Physiol., 59, 458-468 (2018). 2018 Mar 1;59(3):458-468. Top 1% paper in Plant Sciences.
DOI:10.1093/pcp/pcy021

(75) Natsuki Fukuda, Kentaro Noi, Lidong Weng, Yoshihiro Kobashigawa, Hiromi Miyazaki, Yukari Wakeyama, Michiyo Takaki, Yusuke Nakahara, Yuka Tatsuno, Makiyo Uchida-Kamekura, Yoshiaki Suwa, Takashi Sato, Naoki Ichikawa-Tomikawa, Motoyoshi Nomizu, Yukio Fujiwara, Fumina Ohsaka, Takashi Saito, Katsumi Maenaka, Hiroyuki Kumeta, Shoko Shinya, Chojiro Kojima, Teru Ogura, Hiroshi Morioka. Production of single-chain Fv antibodies specific for GA-pyridine, an advanced glycation end-product (AGE), with reduced inter-domain motion for structural analysis. Molecules, 22, 1695 (2017). 2017 Oct 10;22(10)
DOI:10.3390/molecules22101695

(74) Yohei Miyanoiri, Atsushi Hijikata, Yuuki Nishino, Mizuki Gohara, Yasuhiro Onoue, Seiji Kojima, Chojiro Kojima, Tsuyoshi Shirai, Masatsune Kainosho, Michio Homma. Structural and functional analysis of the C-terminal region of FliG, an essential motor component of Vibrio Na+-driven flagella. Structure, 25, 1540-1548 (2017). 2017 Oct 3;25(10):1540-1548.e3.
DOI:10.1016/j.str.2017.08.010 Epub 2017 Sep 14.

(73) Yoshikazu Hattori, David Heidenreich, Yuki Ono, Toshihiko Sugiki, Kei-ichi Yokoyama, Ei-ichiro Suzuki, Toshimichi Fujiwara, Chojiro Kojima. Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions. J. Biomol. NMR, 68, 271-279 (2017). 2017 Aug;68(4):271-279.
DOI:10.1007/s10858-017-0125-6 Epub 2017 Jul 29.

(72) Jakub Sebera, Yoshikazu Hattori, Daichi Sato, David Reha, Radim Nencka, Takashi Kohno, Chojiro Kojima, Yoshiyuki Tanaka, and Vladimir Sychrovsky. The Mechanism of the Glycosylase Reaction with hOGG1 Base-Excision Repair Enzyme: Concerted Effect of Lys249 and Asp268 During Excision of 8-Oxoguanine. Nucleic Acids Res., 45, 5231-5242 (2017). 2017 May 19;45(9):5231-5242.
DOI:10.1093/nar/gkx157

(71) Shoko Shinya, Mariana G. Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L. Kovrigin, Tamo Fukamizo. NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase. J. Biomol. NMR, 64, 309-319 (2017). 2017 Apr;67(4):309-319.

(70) Hisashi Tatebe, Shinichi Murayama, Toshiya Yonekura, Tomoyuki Hatano, David Richter, Tomomi Furuya, Saori Kataoka, Kyoko Furuita, Chojiro Kojima, and Kazuhiro Shiozaki. Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit. eLife, 6, e19594 (2017). 2017 Mar 7;6.
DOI:10.7554/eLife.19594

(69) Ju Yaen Kim, Misaki Kinoshita, Satoshi Kume, Guy T. Hanke, Toshihiko Sugiki, John E. Ladbury, Chojiro Kojima, Takahisa Ikegami, Genji Kurisu, Yuji Goto, Toshiharu Hase, and Young-Ho Lee. Noncovalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity. Biochem. J, 473, 3837-3854 (2016). 2016 Nov 1;473(21):3837-3854.
Epub 2016 Aug 22.

(68) Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub _ebera, Katsuyuki Nakashima, Jiro Kondo, Daichi Yamanaka, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Vladim_r Sychrovsk_, Chojiro Kojima, and Yoshiyuki Tanaka. The Structure Determination of AgI-mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy. Chemistry, 22, 13028-13031 (2016). 2016 Sep 5;22(37):13028-31.
DOI:10.1002/chem.201603048 Epub 2016 Aug 9.

(67) Nesreen Alsanousi, Toshihiko Sugiki, Kyoko Furuita, Masatomo So, Young-Ho Lee, Toshimichi Fujiwara, and Chojiro Kojima. Solution NMR structure and inhibitory effect against amyloid-� fibrillation of Humanin containing a D-isomerized serine residue. Biochem. Biophys. Res. Commun., 477, 647-653 (2016). 2016 Sep 2;477(4):647-53.
DOI:10.1016/j.bbrc.2016.06.114 Epub 2016 Jun 25.

(66) Kenichi Harada, Eiki Yamashita, Kento Inoue, Koji Yamaguchi, Toshimichi Fujiwara, Atsushi Nakagawa, Tsutomu Kawasaki, and Chojiro Kojima*. Expression, purification, and crystallization of a plant-specific DUF1110 protein from Oryza sativa. Acta Crystallogr. F Struct. Biol. Commun., 72, 480-484 (2016). 2016 Jun 1;72(Pt 6):480-4.
DOI:10.1107/S2053230X16007573 Epub 2016 May 23.

(65) Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, and Toshimichi Fujiwara*. Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J. Biomed. Semant., 7, 16 (2016). 2016 May 5;7(1):16.
DOI:10.1186/s13326-016-0057-1

(64) Takenori Dairaku, Kyoko Furuita, Hajime Sato, Yoshinori Kondo, Chojiro Kojima, Akira Ono and Yoshiyuki Tanaka*. 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. Nucleosides Nucleotides Nucleic Acids, 34, 877-900 (2015). 2015 Dec 2;34(12):877-900.
DOI:10.1080/15257770.2015.1088160

(63) Misaki Kinoshita, Ju yaen Kim, Satoshi Kume, Yukiko Sakakibara, Toshihiko Sugiki, Chojiro Kojima, Genji Kurisu, Takahisa Ikegami, Toshiharu Hase, Yoko Kimata-Ariga, and Young-Ho Lee*. Physicochemical natures of interfaces control activity of ferredoxin NADP+ reductase through its interprotein interactions with ferredoxin. BBA - Bioenergetics, 1847, 1200-1211 (2015). 2015 Oct;1847(10):1200-11.
DOI:10.1016/j.bbabio.2015.05.023

(62) Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub _ebera, Daichi Yamanaka, Hiroyuki Otaki, Shoko Kikkawa, Yoshinori Kondo, Ritsuko Katahira, F. Matthias Bickelhaupt, C_lia Fonseca Guerra, Akira Ono, Vladimir Sychrovsky*, Chojiro Kojima* and Yoshiyuki Tanaka*. Direct Detection of the Mercury_Nitrogen Bond in the Thymine_HgII_Thymine Base-pair with 199Hg NMR Spectroscopy. Chem. Commun., 51, 8488-8491 (2015). 2015 May 5;51(40):8488-91.
DOI:10.1039/c5cc02423d

(61) Saori Kataoka, Kyoko Furuita*, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikegami, Kazuhiro Shiozaki, Toshimichi Fujiwara and Chojiro Kojima*. 1H, 15N and 13C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein. Biomol. NMR Assign., 9, 89-92 (2015). 2015 Apr;9(1):89-92.
DOI:10.1007/s12104-014-9550-6 Epub 2014 Mar 8.

(60) Kyoko Furuita, Saori Kataoka, Toshihiko Sugiki, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikegami, Kazuhiro Shiozaki, Toshimichi Fujiwara and Chojiro Kojima*. Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints. J. Biomol. NMR, 61, 55-64 (2015). 2015 Jan;61(1):55-64.
DOI:10.1007/s10858-014-9882-7 Epub 2014 Nov 27.

(59) Kazuya Ishikawa, Koji Yamaguchi, Kazuaki Sakamoto, Satomi Yoshimura, Kento Inoue, Seiji Tsuge, Chojiro Kojima and Tsutomu Kawasaki*. Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice. Nat. Commun., 5, 5430 (2014). 2014 Nov 12;5:5430. Top 10% paper in Biochemistry & Molecular Biology.
DOI:10.1038/ncomms6430

(58) 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. J. Biol. Chem., 289, 28569-28578 (2014). 2014 Oct 10;289(41):28569-78.
DOI:10.1074/jbc.M114.603282 Epub 2014 Aug 15.

(57) Hiroshi Yamaguchi, Jakub Jakub _ebera, Jiro Kondo, Shuji Oda, Tomoyuki Komuro, Takuya Kawamura, Takenori Dairaku, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Jaroslav V. Burda, Chojiro Kojima, Vladimir Sychrovsky*, and Yoshiyuki Tanaka*. The structure of metallo-DNA with consecutive T-HgII-T base-pairs explains positive entropy for the metallo-base-pair formation. Nucleic Acids Res., 42, 4094-4099 (2014). 2014 Apr;42(6):4094-9. Top 10% paper in Biochemistry & Molecular Biology.
DOI:10.1093/nar/gkt1344 Epub 2013 Dec 26.

(56) Ken-ichi Kosami, Izuru Ohki*, Kokoro Hayashi, Ryo Tabata, Sayaka Usugi, Tsutomu Kawasaki, Toshimichi Fujiwara, Atsushi Nakagawa, Ko Shimamoto, and Chojiro Kojima*. Purification, crystallization and preliminary X-ray crystallographic analysis of a rice Rac/Rop GTPase, OsRac1. Acta Cryst. F70, 113-115 (2014). 2013 Jul 22;19(30):9884-94.
DOI:10.1002/chem.201300460 Epub 2013 Jun 13.

(55) Jakub _ebera, Jaroslav Burda, Michal Straka, Akira Ono, Chojiro Kojima, Yoshiyuki Tanaka, and Vladimir Sychrovsky*. Formation of the T-HgII-T Metal-Mediated DNA Base Pair; Proposal and Theoretical Calculation of the Reaction Pathway. Chemistry, 19, 9884-9894 (2013). 2013 Jul 22;19(30):9884-94.
DOI:10.1002/chem.201300460 Epub 2013 Jun 13.

(54) Rei Abe-Yoshizumi, Shiori Kobayashi, Mizuki Gohara, Kokoro Hayashi, Chojiro Kojima, Seiji Kojima, Yuki Sudo, Yasuo Asami and Michio Homma*. Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na+ driven flagellar motor. Biophysics, 9, 21-29 (2013). 2013 Feb 05;9:21-9.
DOI:10.2142/biophysics.9.21

(53) Yoshikazu Hattori, Kyoko Furuita, Izuru Ohki*, Takahisa Ikegami, Harumi Fukada, Masahiro Shirakawa, Toshimichi Fujiwara and Chojiro Kojima*. Utilization of lysine 13C-methylation NMR for protein-protein interaction studies. J. Biomol. NMR, 55, 19-31 (2013). 2013 Jan;55(1):19-31.
DOI:10.1007/s10858-012-9675-9 Epub 2012 Dec 6.

(52) Kumiko Kawasaki, Teppei Kanaba, Momoko Yoneyama, Naoko Murata-Kamiya, Chojiro Kojima, Yutaka Ito, Hiroyuki Kamiya and Masaki Mishima. Insights into substrate recognition by the Escherichia coli Orf135 protein through its solution structure. Biochem Biophys Res Commun, 420, 263-268 (2012). 2012 Apr 6;420(2):263-8.
DOI:10.1016/j.bbrc.2012.02.146 Epub 2012 Mar 5.

(51) Kumiko Kawasaki, Momoko Yoneyama, Naoko Murata-Kamiya, Hideyoshi Harashima, Chojiro Kojima, Yutaka Ito, Hiroyuki Kamiya and Masaki Mishima. 1H, 13C and 15N NMR assignments of the Escherichia coli Orf135 protein. Biomol NMR Assign, 6, 1-4 (2012). 2012 Apr;6(1):1-4.
DOI:10.1007/s12104-011-9312-7 Epub 2011 May 7.

(50) Ikumi Kawahara, Kaichiro Haruta, Yuta Ashihara, Daichi Yamanaka, Mituhiro Kuriyama, Naoko Toki, Yoshinori Kondo, Kenta Teruya, Junya Ishikawa, Hiroyuki Furuta, Yoshiya Ikawa, Chojiro Kojima and Yoshiyuki Tanaka. Site-specific isotope labeling of long RNA for structural and mechanistic studies. Nucleic Acids Res., 40, e7 (2012). 2012 Jan;40(1):e7.
DOI:10.1093/nar/gkr951 Epub 2011 Nov 12.

(49) Ken-ichiro Taoka, Izuru Ohki, Hiroyuki Tsuji, Kyoko Furuita, Kokoro Hayashi, Tomoko Yanase, Midori Yamaguchi, Chika Nakashima, Yekti Asih Purwestri, Shojiro Tamaki, Yuka Ogaki, Chihiro Shimada, Atsushi Nakagawa, Chojiro Kojima and Ko Shimamoto. 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature, 476, 332-335 (2011). 2011 Jul 31;476(7360):332-5. Top 1% paper in Biochemistry & Molecular Biology.
DOI:10.1038/nature10272

(48) Yuki Sudo, Rikou Tanaka, Toshitatsu Kobayashi, Naoki Kamo, Toshiyuki Kohno and Chojiro Kojima. Functional expression of a two-transmembrane HtrII protein using cell-free synthesis. Biophysics, 7, 51-58 (2011). 2011 Jun 18;7:51-8.
DOI:10.2142/biophysics.7.51

(47) Kyoko Furuita, Shunpei Murata, JunGoo Jee, Satoshi Ichikawa, Akira Matsuda and Chojiro Kojima. Structural feature of bent DNA recognized by HMGB1. J. Am. Chem. Soc., 133, 5788-5790 (2011). 2011 Apr 20;133(15):5788-90.
DOI:10.1021/ja2013399 Epub 2011 Mar 28.

(46) Kokoro Hayashi and Chojiro Kojima. Efficient protein production method for NMR using soluble protein tags with cold shock expression vector. J. Biomol. NMR, 48, 147-155 (2010). 2010 Nov;48(3):147-55.
DOI:10.1007/s10858-010-9445-5 Epub 2010 Sep 16.

(45) Kyoko Furuita, JunGoo Jee, Harumi Fukada, Masaki Mishima and Chojiro Kojima. Electrostatic interaction between oxysterol binding protein and VAMP-associated protein-A revealed by NMR and mutagenesis studies. J. Biol. Chem., 285, 12961-12970 (2010). 2010 Apr 23;285(17):12961-70.
DOI:10.1074/jbc.M109.082602 Epub 2010 Feb 23.

(44) Takashi Oda, Hiroshi Hashimoto, Naoyuki Kuwabara, Satoko Akashi, Kokoro Hayashi, Chojiro Kojima, Hann Ling Wong, Tsutomu Kawasaki, Ko Shimamoto, Mamoru Sato and Toshiyuki Shimizu. The structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications. J. Biol. Chem., 285, 1435-1445 (2010). 2010 Jan 8;285(2):1435-45. Top 10% paper in Biochemistry & Molecular Biology.
DOI:10.1074/jbc.M109.058909 Epub 2009 Oct 28.

(43) Seiji Kojima, Katsumi Imada, Mayuko Sakuma, Yuki Sudo, Chojiro Kojima, Tohru Minamino, Michio Homma and Keiichi Namba. Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB. Mol. Microbiol., 73, 710-718 (2009). 2009 Aug;73(4):710-8. Top 10% paper in Microbiology.
DOI:10.1111/j.1365-2958.2009.06802.x Epub 2009 Jul 21.

(42) Kokoro Hayashi and Chojiro Kojima. pCold-GST vector: A novel cold-shock vector containing GST tag for soluble protein production. Protein Expr. Purif., 62, 120-127 (2008). 2008 Nov;62(1):120-7.
DOI:10.1016/j.pep.2008.07.007 Epub 2008 Jul 29.

(41) Takashi Oda, Hiroshi Hashimoto, Naoyuki Kuwabara, Kokoro Hayashi, Chojiro Kojima, Tsutomu Kawasaki, Ko Shimamoto, Mamoru Sato and Toshiyuki Shimizu. Crystallographic characterization of the N-terminal domain of plant NADPH oxidase. Acta Crystallogr., F64, 867-869 (2008). 2008 Sep 1;64(Pt 9):867-9.
DOI:10.1107/S1744309108026535 Epub 2008 Aug 29.

(40) Yuki Sudo, Tatsuya Nishihori, Masayuki Iwamoto, Kazumi Shimono, Chojiro Kojima and Naoki Kamo. A long-lived M-like state of phoborhodopsin that mimics the active state. Biophys. J., 295, 753-760 (2008). 2008 Jul;95(2):753-60.
DOI:10.1529/biophysj.107.125294 Epub 2008 Mar 28.

(39) Hiroki Ashida, Yohtaro Saito, Chojiro Kojima and Akiho Yokota. Enzymatic Characterization of 5-Methylthioribulose-1-phosphate Dehydratase of the Methionine Salvage Pathway from Bacillus subtilis. Biosci. Biotechnol. Biochem., 72, 959-967 (2008). 2008 Apr;72(4):959-67.
Epub 2008 Apr 7.

(38) Hann Ling Wong, Reinhard Pinontoan, Kokoro Hayashi, Ryo Tabata, Takashi Yaeno, Kana Hasegawa, Chojiro Kojima, Hirofumi Yoshioka, Koh Iba, Tsutomu Kawasaki and Ko Shimamoto. Regulation of rice NADPH oxidase by binding of Rac GTPase to its N-terminal extension. Plant Cell, 19, 4022-4034 (2007). 2007 Dec;19(12):4022-34. Top 1% paper in Plant Sciences.
Epub 2007 Dec 21.

(37) Kokoro Hayashi, Yuki Sudo, JunGoo Jee, Masaki Mishima, Hideyuki Hara, Naoki Kamo and Chojiro Kojima. Structural analysis of phototactic transducer protein HtrII linker region from Natronomonas pharaonis. Biochemistry, 46, 14380-14390 (2007). 2007 Dec 18;46(50):14380-90.
Epub 2007 Nov 15.

(36) Yohtaro Saito, Hiroki Ashida, Chojiro Kojima, Haruka Tamura, Hiroyoshi Matsumura, Yasushi Kai and Akiho Yokota. Enzymatic Characterization of 5-Methlthioribose 1-Phosphate Isomerase from Bacillus subtilis. Biosci. Biotechnol. Biochem., 71, 2021-2028 (2007). 2007 Aug;71(8):2021-8.
Epub 2007 Aug 7.

(35) Masaki Mishima, Shigeo Wakabayashi and Chojiro Kojima. Solution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1. J. Biol. Chem., 282, 2741-2751 (2007). 2007 Jan 26;282(4):2741-51.
Epub 2006 Oct 18.

(34) Yoshiyuki Tanaka, Shuji Oda, Hiroshi Yamaguchi, Yoshinori Kondo, Chojiro Kojima and Akira Ono. 15N-15N J-coupling across HgII: Direct observation of HgII-mediated T-T base pairs in a DNA duplex. J. Am. Chem. Soc., 129, 244-245 (2007). 2007 Jan 17;129(2):244-5. Top 1% paper in Chemistry, Multidisciplinary.

(33) Kyoko Furuita, Masaki Mishima, and Chojiro Kojima. 1H, 13C and 15N resonance assignments of the VAP-A: OSBP complex. J. Biomol. NMR., 36 Suppl 1, 69 (2006). 2006 Dec;36 Suppl 1:69.
Epub 2006 Sep 20.

(32) Yoshiyuki Tanaka, Hiroshi Yamaguchi, Shuji Oda, Makoto Nomura, Chojiro Kojima, Yoshinori Kondo, and Akira Ono. NMR spectroscopic study of a DNA duplex with mercury-mediated T-T basepairs. Nucleosides Nucleotides Nucleic Acids, 25, 613-624 (2006). 2006 Apr;25(4-6):613-24.
DOI:10.1080/15257770600686154 Epub 2007 Feb 07.

(31) Kayo Yoshida, Kazuo Yamamoto, Tomoko Kohno, Noriko Hironaka, Kiyoshi Yasui, Chojiro Kojima, Hiroshi Mukae, Jun-ichi Kadota, Shoichi Suzuki, Kiri Honma, Shigeru Kohno, and Toshifumi Matsuyama. Active Repression of IFN Regulatory Factor-1-Mediated Transactivation by IFN Regulatory Factor-4. Int. Immunol., 17, 1463-1471 (2005). 2005 Nov;17(11):1463-71.
Epub 2005 Sep 19.

(30) Megumi Kubo, Maki Sato, Tomoyasu Aizawa, Chojiro Kojima, Naoki Kamo, Mineyuki Mizuguchi, Keiichi Kawano, and Makoto Demura. Disassembling and bleaching of chloride-free pharaonis halorhodopsin by octyl-beta-glucoside. Biochemistry, 44, 12923-12931 (2005). 2005 Oct 4;44(39):12923-31.

(29) Masaki Mishima, Toshio Shida, Kazuto Yabuki, Ken-ichi Kato, Junichi Sekiguchi and Chojiro Kojima. Solution structure of the peptidoglycan binding domain of B. subtilis cell wall lyticenzyme CwlC: Characterization of the sporulation-related repeats by NMR. Biochemistry, 44, 10153-10163 (2005). 2005 Aug 2;44(30):10153-63.

(28) Kazuhiko Nakatani, Shinya Hagihara, Yuki Goto, Akio Kobori, Masaki Hagihara, Gosuke Hayashi, Motoki Kyo, Makoto Nomura, Masaki Mishima and Chojiro Kojima. Small molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats. Nat. Chem. Biol., 1, 39-43 (2005). 2005 Jun;1(1):39-43. Top 10% paper in Biochemistry & Molecular Biology.
Epub 2005 May 24.

(27) Yuki Sudo, Hideyasu Okuda, Masaki Yamabi, Yuta Fukuzaki, Masaki Mishima, Naoki Kamo and Chojiro Kojima. Linker region of a Halobacterial transducer protein directly interacts with its sensor retinar protein. Biochemistry, 44, 6144-6152 (2005). 2005 Apr 26;44(16):6144-52.

(26) Emiko Iida, Kazuya Satou, Masaki Mishima, Chojiro Kojima, Hideyoshi Harashima and Hiroyuki Kamiya. Amino acid residues involved in substrate recognition of the Escherichia coli ORF135 protein. Biochemistry, 44, 5683-5689 (2005). 2005 Apr 19;44(15):5683-9.

(25) Toshitatsu Kobayashi, Masaki Mishima, Kayo Akagi, Nobuya Sakai, Etsuko Katoh, Makoto Takano, Toshimasa Yamazaki and Chojiro Kojima. 1H, 15N and 13C backbone and side-chain assignments of the rice phytochrome B PAS1 domain and backbone assignments of the PAS1-PAS2 domain. J. Biomol. NMR, 31, 269-270 (2005). 2005 Mar;31(3):269-70.

(24) Makoto Nomura, Toshitatsu Kobayashi, Toshiyuki Kohno, Ken-ichiro Fujiwara, Takeshi Tenno, Masahiro Shirakawa, Itsuko Ishizaki, Kazuo Yamamoto, Toshifumi Matsuyama, Masaki Mishima and Chojiro Kojima. Paramagnetic NMR study of Cu2+-IDA complex localization on a protein surface and its application to elucidate long distance information. FEBS Lett., 566, 157-161 (2004). 2004 May 21;566(1-3):157-61.

(23) Ken-ichiro Fujiwara, Takeshi Tenno, Kaoru Sugasawa, Jun-Goo Jee, Izuru Ohki, Chojiro Kojima, Hidehito Tochio, Hidekazu Hiroaki, Fumio Hanaoka and Masahiro Shirakawa. Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B. J. Biol. Chem., 279, 4760-4767 (2004). 2004 Feb 6;279(6):4760-7.
Epub 2003 Oct 29.

(22) Yoshiyuki Tanaka, Yasuhiro Kasai, Shunsuke Mochizuki, Akihiro Wakisaka, Eugene H. Morita, Chojiro Kojima, Atsushi Toyozawa, Yoshinori Kondo, Masumi Taki, Yasuomi Takagi, Atsushi Inoue, Kazuhiko Yamasaki and Kazunari Taira. Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes. J. Am. Chem. Soc., 126, 744-752 (2004). 2004 Jan 28;126(3):744-52.

(21) Etsuko Kawashima, Takeshi Sekine, Kaoru Umabe, Kazuo Kamaike, Toshimi Mizukoshi, Nobuhisa Shimba, Ei-ichiro Suzuki and Chojiro Kojima. New sequential-assignment routes of nucleic acid NMR signals using a [5'-13C]-labeled DNA dodecamer. Nucleosides Nucleotides Nucleic Acids, 23, 255-262 (2004). 2004 Jan 01;23(1-2):255-62.
DOI:10.1081/NCN-120027832 Epub 2007 Jun 01.

(20) Shun-ichi Kawahara, Chojiro Kojima, Kazunari Taira and Tadafumi Uchimaru. Theoretical study of correlation between hydrogen bond stability and J-coupling through a hydrogen bond. Helv. Chim. Act., 86, 3265-3273 (2003). 2003 Oct;86(10):3265-73.
DOI:10.1002/hlca.200390267

(19) Hiroki Ashida, Yohtaro Saito, Chojiro Kojima, Kazuo Kobayashi, Naotake Ogasawara and Akiho Yokota. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science, 302, 286-290 (2003). 2003 Oct 10;302(5643):286-90. Top 10% paper in Biochemistry & Molecular Biology.

(18) Masaki Mishima, Seiji Takayama, Kei-ichi Sasaki, Jun-goo Jee, Chojiro Kojima, Akira Isogai and Masahiro Shirakawa. Structure of the male determinant factor for Brassica self-incompatibility. J. Biol. Chem., 278, 36389-36395 (2003). 2003 Sep 19;278(38):36389-95.
Epub 2003 Jun 30.

(17) Yoshiyuki Tanaka, Chojiro Kojima, Eugene H. Morita, Yasuhiro Kasai, Kazuhiko Yamasaki, Akira Ono, Masatsune Kainosho and Kazunari Taira. Identification of the Metal Ion Binding Site on an RNA Motif from Hammerhead Ribozymes using 15N-NMR Spectroscopy. J. Am. Chem. Soc., 124, 4595-4601 (2002). 2002 May 1;124(17):4595-601.

(16) Rei Ishikawa, Chojiro Kojima, Akira Ono and Masatsune Kainosho. Developping Model Systems for the NMR Study of Substituent Effects on the N-H_�N Hydrogen Bond in Duplex DNA. Magn. Reson. Chem., 39, S159-S165 (2001). 2001 Dec;39(S1):S159-65
DOI:10.1002/mrc.941 Epub 2001 Nov 5.

(15) Chojiro Kojima, Nikolai. B. Ulyanov, Masatsune Kainosho and Thomas L. James. Slow Motion in the CAA/TTG Sequence of a DNA Decamer Duplex Studied by NMR. Biochemistry, 40, 7239-7246 (2001). 2001 Jun 19;40(24):7239-46.

(14) Chojiro Kojima, Etsuko Kawashima, Takeshi Sekine, Yoshiharu Ishido, Akira Ono, Masatsune Kainosho and Yoshimasa Kyogoku. Sugar Conformation of the Stereospecific 2'-R or 2'-S Deuterium-Labeled DNA Decamer Studied with Proton-Proton J Coupling Constants. J. Biomol. NMR, 19, 19-31 (2001). 2001 Jan;19(1):19-31.

(13) Chojiro Kojima, Akira Ono and Masatsune Kainosho. Studies of Physicochemical Properties of N_H_�N Hydrogen Bonds in DNA, Using Selective 15N-labeling and Direct 15N 1D NMR. J. Biomol. NMR, 18, 269-277 (2000). 2000 Nov;18(3):269-77.

(12) Yoshiyuki Tanaka, Chojiro Kojima, Toshio Yamazaki, Takashi S. Kodama, Kazuhiro Yasuno, Shin Miyashita, Akira (Mei) Ono, Akira (Sho) Ono, Masatsune Kainosho and Yoshimasa Kyogoku. Solution Structure of an RNA Duplex including a C-U Base-Pair. Biochemistry, 39, 7074-7080 (2000). 2000 Jun 20;39(24):7074-80.

(11) Chojiro Kojima and Masatsune Kainosho. Simple Suppression of Spurious Peaks in TROSY Experiments. J. Magn. Reson., 143, 417-422 (2000). 2000 Apr;143(2):417-22.

(10) Etsuko Kawashima, Takeshi Sekine, Kaoru Umabe Yuhki Naito, Kazuo Kamaike, Chojiro Kojima, Toshimi Mizukoshi, Ei-ichiro Suzuki and Yoshiharu Ishido. The Synthesis of 2'-deoxy[5'-13C]ribonucleotides and HMQC-NOESY NMR Study on the Dickerson Dodecamer with 13C-labeling at the 5'-Positions. Nucleoside Nucleotides, 18, 1597-1598 (1999). 1999 Jun;18(6-7):1597-8.
DOI:10.1080/07328319908044794 Epub 2006 Oct 04.

(9) Hidehito Tochio, Chojiro Kojima, Hiroshi Matsuo, Toshio Yamazaki and Yoshimasa Kyogoku. Intermolecular Contacts Between the ?-Cro Repressor and the Operator DNA Characterized by Nuclear Magnetic Resonance Spectroscopy. J. Biomol. Struct. Dyn., 16, 989-1002 (1999). 1999 Apr;16(5):989-1002.

(8) Chojiro Kojima, Akira Ono, Masatsune Kainosho and Thomas L. James. Quantitative Measurement of Transverse and Longitudinal Cross-Correlation between 13C-1H Dipolar Interaction and 13C Chemical Shift Anisotrophy: Application to a 13C-Labeled DNA Duplex. J. Magn. Reson., 136, 169-175 (1999). 1999 Feb;136(2):169-75.

(7) Patrick Furrer, Todd M. Billeci, Alessandro Donati, Chojiro Kojima, Boleslaw Karwowski, Agnieszka Sierzchala, Wojciech Stec and Thomas L. James. Structural Effect of Complete [Rp]-Phosphorothioate and Phosphorodithioate Substitutions in the DNA Strand of a Model Antisense Inhibitor-Target RNA Complex. J. Mol. Biol., 285, 1609-1622 (1999). 1999 Jan 29;285(4):1609-22.

(6) Chojiro Kojima, Akira Ono, Masatsune Kainosho and Thomas L. James. DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly 13C-Labeled Purine Nucleotides. J. Magn. Reson., 135, 310-333 (1998). 1998 Dec;135(2):310-33. Top 10% paper in Spectroscopy.

(5) Chojiro Kojima, Etsuko Kawashima, Keizo Toyama, Kenshiro Ohshima, Yoshiharu Ishido, Masatsune Kainosho and Yoshimasa Kyogoku. Stereospecific Assignment of H5' and H5" in a (5'R)- / (5'S)- Deuterium Labeled DNA Decamer for 3JHH Determination and unambiguous NOE Assignments. J. Biomol. NMR, 11, 103-109 (1998). 1998 Jan;11(1):103-9.
DOI:10.1023/A:1008286925516

(4) Tomoko Nishizaki, Shigenori Iwai, Tadayasu Ohkubo, Chojiro Kojima, Haruki Nakamura, Yoshimasa Kyogoku and Eiko Ohtsuka. Solution Strucutres of DNA Duplexes Containing a DNA x RNA Hybrid Region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Biochemistry, 35, 4016-4025 (1996). 1996 Apr 2;35(13):4016-25.

(3) Bong Jin Lee, Tae Woo Lee, Sang Ho Park, Hiroji Aiba, Chojiro Kojima and Yoshimasa Kyogoku. Nuclear Magnetic Resonance Study of Complexes between CRP and its 22- and 28-Base-Pair Operators. J. Biochem. (Tokyo), 117, 239-243 (1995). 1995 Feb;117(2):239-43.

(2) Chojiro Kojima and Yoshimasa Kyogoku. Filtering Methods for Selection of Singlet and Doublet Signals in NMR Spectra of DNA Oligomers. J. Biomol. NMR, 4, 181-191 (1994). 1994 Mar;4(2):181-91.

(1) Chojiro Kojima and Yoshimasa Kyogoku. HAL Experiment, A Novel Filtering Method and Its Application to DNA Assignment. J. Magn. Reson. B, 102, 214-217 (1993). 1993 Oct;102(2):214-7.
DOI:10.1006/jmrb.1993.1086

(8) Toshihiko Sugiki, Kyoko Furuita, Toshimichi Fujiwara, and Chojiro Kojima*. Current NMR Techniques for Structure-Based Drug Discovery. Molecules, 23, 148 (2018) 2018 Jan 12;23(1). pii: E148. Review.
DOI:10.3390/molecules23010148

(7) Toshihiko Sugiki, Toshimichi Fujiwara and Chojiro Kojima*. Latest approaches for efficient protein production in drug discovery. Expert Opin. Drug Discov., 9, 1189-1204 (2014). 2014 Oct;9(10):1189-204. Review.
DOI:10.1517/17460441.2014.941801 Epub 2014 Jul 21.

(6) Ken-ichiro Taoka, Izuru Ohki, Hiroyuki Tsuji, Chojiro Kojima and Ko Shimamoto. Structure and function of florigen and the receptor complex. Trends Plant Sci., 18, 287-294 (2013). 2013 May;18(5):287-94. Review.
DOI:10.1016/j.tplants.2013.02.002 Epub 2013 Mar 13.

(5) Ken-ichiro Taoka, Izuru Ohki, Hiroyuki Tsuji, Chojiro Kojima and Ko Shimamoto. Discovery of Flowering Hormone (Florigen) Receptor and Its Crystal Structure. Photon Factory Activity Report, Part A "Highlights and Facility Report", 44-45 (2012). Review.

(4) Izuru Ohki, Ko Shimamoto and Chojiro Kojima. Structure of florigen activation complex. SPring-8 Research Frontiers, 2011, 30-31 (2012). Review.

(3) Chojiro Kojima, Akira M. Ono, Akira Ono and Masatsune Kainosho. Solid-Phase Syntheses of the Selectively Labeled DNA: the Application for Multidimensional NMR Spectroscopy. Methods Enzymol., 338, 261-283 (2001). Review.
DOI:10.1016/S0076-6879(02)38224-7

(2) Yoshimasa Kyogoku, Chojiro Kojima, Sang Jeon Lee, Hidehito Tochio, Nobuaki Suzuki, Hiroshi Matsuo and Masahiro Shirakawa. Induced Structural Changes in Protein-DNA Complexes. Methods Enzymol., 261, 524-541 (1995). Review.

(1) Masahiro Shirakawa, Hiroshi Matsuo, Yasuharu Serikawa, Nobuaki Suzuki, Chojiro Kojima, Tadayasu Ohkubo and Yoshimasa Kyogoku. Conformational Changes of Proteins and DNA Induced by Their Interactions. Molecular Structure and Life, Y. Kyogoku and Y. Nishimura eds., pp. 129-140, Japan Sci. Soc. Press, CRC Press, Tokyo (1992). Book.