Publication

  1. Hattori Y, Furuita K, Ohki I#, Ikegami T, Fukada H, Shirakawa M, Fujiwara T, Kojima C# (#corresponding authors). Utilization of lysine 13C-methylation NMR for protein-protein interaction studies. J Biomol NMR, Dec 6 (2012). [Epub ahead of print] .
  2. Kawasaki K, Kanaba T, Yoneyama M, Murata-Kamiya N, Kojima C, Ito Y, Kamiya H and Mishima M, Insights into substrate recognition by the Escherichia coli Orf135 protein through its solution structure, Biochem Biophys Res Commun, 420, 263-268 (2012)
  3. 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)
  4. Kawahara I, Haruta K, Ashihara Y, Yamanaka D, Kuriyama M, Toki N, Kondo Y, Teruya K, Ishikawa J, Furuta H, Ikawa Y, Kojima C and Tanaka Y, Site-specific isotope labeling of long RNA for structural and mechanistic studies, Nucleic Acids Res 40, e7 (2012)
  5. Sudo Y, Tanaka R, Kobayashi T, Kamo N, Kohno T and Kojima C, Functional expression of a two-transmembrane HtrII protein using cell-free synthesis, Biophysics, 7, 51-58 (2011)
  6. Taoka K*, Ohki I*, Tsuji H*, Furuita K, Hayashi K, Yanase T, Yamaguchi M, Nakashima C, Purwestri YA, Tamaki S, Ogaki Y, Shimada C, Nakagawa A, Kojima C, Shimamoto K (*equally contributed), 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature 476,332-5 (2011). [PubMed]
  7. Furuita K, Murata S, Jee J-G, Ichikawa S, Matsuda A and Kojima C, Structural feature of bent DNA recognized by HMGB1, J. Am. Chem. Soc.,133, 5788-5790 (2011)
  8. Hayashi K and Kojima C, Efficient protein production method for NMR using soluble protein tags with cold shock expression vector, J. Biomol. NMR, 48, 147-155 (2010)
  9. Ohki I, Amida H, Yamada R, Sugihara M, Ishigaki T, Tate S, Surface plasmon resonance study on functional significance of clustered organization of lectin-like oxidized LDL receptor (LOX-1). Biochim Biophys Acta. 1814, 345-54 (2010). [PubMed]
  10. Furuita K, Jee JG, Fukada H, Mishima M and Kojima C, Electrostatic interaction between oxysterol binding protein and VAMP-associated protein-A revealed by NMR and mutagenesis studies, J. Biol. Chem., 285, 12961-12970 (2010)
  11. 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)
  12. 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)
  13. Inomata K, Ohki I, Tochio H, Fujiwara K, Hiroaki H, Shirakawa M, Kinetic and thermodynamic evidence for flipping of a methyl-CpG binding domain on methylated DNA. Biochemistry 47, 3266-71 (2008). [PubMed]
  14. 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).
  15. 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., F 64, 867?869 (2008).
  16. 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., 95, 753-760 (2008).
  17. 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)
  18. Ishigaki T, Ohki I, Utsunomiya-Tate N, Tate SI, Chimeric structural stabilities in the coiled-coil structure of the NECK domain in human lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1). J Biochem. 141, 855-66 (2007). [PubMed]
  19. 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).
  20. 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).
  21. 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).
  22. 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).
  23. 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).
  24. Kyoko Furuita, Masaki Mishima, and Chojiro Kojima. 1H, 13C and 15N resonance assignments of the VAP-A: OSBP complex. J. Biomol. NMR., 36 Suppl 5, 69 (2006).
  25. 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).
  26. Ohki I, Ishigaki T, Oyama T, Matsunaga S, Xie Q, Ohnishi-Kameyama M, Murata T, Tsuchiya D, Machida S, Morikawa K, Tate S, Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL.Structure 13, 905-17 (2005). [PubMed]
  27. 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).
  28. 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).
  29. Masaki Mishima, Ken-ichi Kato, Toshio Shida, 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. 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).
  37. 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. Functional roles of the metal ion at the A9/G10.1 site in hammerhead ribozymes. J. Am. Chem. Soc., 126, 744-752 (2004).
  38. Watanabe S, Ichimura T, Fujita N, Tsuruzoe S, Ohki I, Shirakawa M, Kawasuji M, Nakao M, Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin. Proc Natl Acad Sci U S A. 100, 12859-64 (2003).[PubMed]
  39. Kato Z, Jee J, Shikano H, Mishima M, Ohki I, Ohnishi H, Li A, Hashimoto K, Matsukuma E, Omoya K, Yamamoto Y, Yoneda T, Hara T, Kondo N, Shirakawa M, The structure and binding mode of interleukin-18. Nat Struct Biol. 10, 966-71 (2003). [PubMed]
  40. 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. Chem. Act., 86, 3265-3273 (2003).
  41. 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).
  42. 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).
  43. 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).
  44. Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M, Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 105, 487-97 (2001). [PubMed]
  45. 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).
  46. 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.
  47. 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).
  48. 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).
  49. Fujita N, Shimotake N, Ohki I, Chiba T, Saya H, Shirakawa M, Nakao M, Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1. Mol Cell Biol. 20, 5107-18 (2000). [PubMed]
  50. 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).
  51. 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).
  52. Chojiro Kojima and Masatsune Kainosho. Simple Suppression of Spurious Peaks in TROSY Experiments. J. Magn. Reson., 143, 417-422 (2000).
  53. Ohki I, Shimotake N, Fujita N, Nakao M, Shirakawa M, Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1. EMBO J. 18, 6653-61 (1999). [PubMed]
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