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Kawai Unit

Gota Kawai - Professor

Achievement

  • Okui, S., Ushida, C., Kiyosawa, H., and Kawai, G., Sequence and structure analysis of a mirror tRNA located upstream of the cytochrome oxidase I mRNA in mouse mitochondria, J. Biochem. in press.
  • Kanagawa, M., Baba, S., Watanabe, Y., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Sampei, G., and Kawai, G., Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus, J. Biochem. in press.
  • A new entropy model for RNA: part V, Incorporating the Flory-Huggins model in structure prediction and folding, Dawson, W. and Kawai, G., Journal of Nucleic Acids Investigation, in press.
  • A new entropy model for RNA: part IV, The minimum free energy and the thermodynamically most-probable folding pathway, Dawson, W. and Kawai, G., Journal of Nucleic Acids Investigation, in press.
  • Kiyosawa, H., Okumura, A., Okui, S., Ushida, C., and Kawai, G., Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing, Genomics 106, 122-128 (2015).
  • Tsukimoto, A., Sugiyama, R., Abe, M., Nishitsuji, H., Shimizu, Y., Shimotohno, K., Kawai, G. and Takaku, H., A new role for PGA1 in inhibiting hepatitis C virus-IRES-mediated translation by targeting viral translation factors, Antiviral Res. 117, 1-9 (2015).
  • Okui, S. and Kawai, G., In NMR tube transcription for rapid screening of RNA conformation. Nucleosides, Nucleotides, and Nucleic Acids 34, 103-113 (2015).
  • Zhang, F., Hoque, M. M., Jiang, J., Suzuki, K., Tsunoda, M., Takeda, Y., Ito, Y., Kawai, G., Tanaka, H., Takénaka, A., The Characteristic Structure of Anti-HIV Actinohivin in Complex with Three HMTG D1 Chains of HIV-gp120, Chembiochem 15, 2766-2773 (2014).
  • Hashi, Y., Kawai, G. and Kotani, S., Microtubule-associated protein (MAP) 4 interacts with microtubules in an intrinsically disordered manner, Biosci Biotechnol Biochem. 78, 1864-1870, (2014).
  • A new entropy model for RNA: part III, Is the folding free energy landscape of RNA funnel shaped?, Dawson, W., Takai, T., Ito, I., Shimizu, K. and Kawai, G., Journal of Nucleic Acids Investigation 5, 2652 (2014).
  • Structures and reaction mechanisms of the two related enzymes, PurN and PurU, Sampei, G., Kanagawa, M., Baba, S., Shimasaki, T., Taka, H., Mitsui, S., Fujiwara, S., Yanagida, Y., Kusano, M., Suzuki, S., Terao, K., Kawai, H., Fukai, Y., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S. and Kawai, G., J. Biochem. 154, 569-579 (2013).
  • Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain, Nomura, Y., Tanaka, Y., Fukunaga, J., Fujiwara, K., Chiba M., Iibuchi, H., Tanaka, T., Nakamura, Y., Kawai, G., Kozu, T. and Sakamoto, T., J. Biochem. 154, 513-519 (2013). [JB˜_•śÜ]
  • The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element, Fukunaga, J., Nomura, Y., Tanaka, Y., Amano, R., Tanaka, T., Nakamura, Y., Kawai, G., Sakamoto, T. and Kozu, T., RNA 19, 927-936 (2013).
  • A new entropy model for RNA: part II, persistence-related entropic contributions to RNA secondary structure free energy calculation, Dawson, W., Yamamoto, K., Shimizu, K. and Kawai, G., Journal of Nucleic Acids Investigation 4, e2 (2013).
  • Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond, Hatano, A., Okada, M. and Kawai, G., Org. Biomol. Chem., 10, 7327-7333 (2012).
  • A new entropy model for RNA: part I, a critique of the standard Jacobson-Stockmayer model applied to multiple cross links, Dawson, W., Yamamoto, K. and Kawai, G., Journal of Nucleic Acids Investigation 3, e3 (2012).
  • Crystal Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8, Suzuki, S., Yanai, H., Kanagawa, M., Tamura, S., Watanabe, Y., a Fuse, K., Baba, S., Sampei, G. and Kawai, G., Acta Cryst. F 68, 14-19 (2012) .
  • Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq, Someya, T., Baba, S., Fujimoto, M., Kawai, G., Kumasaka, T. and Nakamura, K., Nucl. Acids Res. 40, 1856-1867 (2012) .
  • Crystal Structures of Glycinamide Ribonucleotide Synthetase, PurD, from Thermophilic Eubacteria, Sampei, G., Baba, S., Kanagawa, M., Yanai, H., Ishii, T., Kawai, H., Fukai, Y., Ebihara, A., Nakagawa, N., and Kawai, G., J. Biochem. 148, 429-438 (2010) .
  • Crystal Structures of Hypoxanthine-Guanine Phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8, Kanagawa, M, Baba, S., Ebihara, A., Shinkai, A., Hirotsu, K., Mega, R., Kim, K., Kuramitsu, S., Sampei, G., and Kawai, G., Acta Cryst. F66, 893-898 (2010) .
  • Expression, crystallization and preliminary crystallographic analysis of RNA binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer, Baba, S., Someya, T., Kawai, G., Nakamura, K., and Kumasaka, T., Acta Cryst. F66, 563-566 (2010) .
  • Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus, Kanai, A., Sato, A., Fukuda, Y., Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G., and Tomita, M., RNA 15, 420-431 (2009) .
  • Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework, Dawson, W., Kawai, G., J. Comput. Sci. Syst. Biol. 2, 1-23 (2009). Feb.
  • Selective structural change of bulged-out region of double-stranded RNA containing bulged nucleotides by spermidine, Higashi, K., Terui, Y., Inomata, E., Katagiri, D., Nomura, Y., Someya, T., Nishimura, K., Kashiwagi, K., Kawai, G., Igarashi, K., Biochem. Biophys. Res. Commun. 370, 572-577 (2008)  13 June
  • Recognition of a bulged RNA by peptides derived from the influenza NS1 protein, Someya, T., Hosono, K., Morimura, K., Takaku, H., and Kawai, G., J. Biochem. 143, 339-347 (2008)  (Advance Access published November 26, 2007). March
  • Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding, Dawson, W., Fujiwara, K., Kawai, G., PLoS ONE 2, e905 (2007) . Sep
  • Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2, Nomura, Y., Kajikawa, M., Baba, S., Nakazato, S., Imai, T., Sakamoto, T., Okada, N., and Kawai, G., Nucleic Acids Res. 34, 5184-5193 (2006) . Sep
  • 1H, 13C and 15N resonance assignments of the 2L-5L RNA ligase-like protein from Pyrococcus furiosus, Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A. and Kawai, G., J. Biomol. NMR 36, 16 (2006) . (Published online: 02 February 2006.)
  • Structural Analysis of a Mutant of the HIV-1 Integrase Zinc Finger Domain that Forms a Single Conformation, Nomura, Y., Masuda, T. and Kawai, G. J. Biochem. 139, 753-759 (2006) D apr
  • Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus, Okada, K., Takahashi, M., Sakamoto, T., Nakamura, K., Kanai, A. and Kawai, G., Nucleosides, Nucleotides and Nucleic Acids 25, 383-395 (2006) .
  • Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering, Kashida, H., Tanaka, M., Baba, S., Sakamoto, T., Kawai, G., Asanuma, H. and Komiyama, M., Chem. Eur. J. 12, 777-784 (2006) . jan
  • A method for finding optimal RNA secondary structures using a new entropy model (vsfold), Dawson, W., Fujiwara, K., Futamura, Y., Yamamoto, K. and Kawai, G., Nucleosides, Nucleotides and Nucleic Acids 25, 171-189 (2006) . jan.
  • Interaction analysis between tmRNA and SmpB from Thermus Thermophilus, Nameki, N., Someya, T., Okano, S., Suemasa, R., Kimoto, M., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Hirao, I., Takaku, H., Himeno, H., Muto, A., Kuramitsu, S., Yokoyama, S. and Kawai, G., J. Biochem. 138, 729-739 (2005) . dec
  • Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers, Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N. and Kawai, G., J. Biochem. 138, 583-592 (2005) . nov
  • NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A, Sakamoto, T., Oguro, A., Kawai, G., Ohtsu, T. and Nakamura, Y., Nucl. Acids Res. 33, 745-754 (2005)  feb
  • Solution structure of an RNA stem-loop derived from the 3f conserved region of eel LINE UnaL2, Baba, S., Kajikawa, K., Okada, N., and Kawai, G., RNA 10, 1380-1387 (2004) .@Sep
  • Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA, Someya, T., Sakamoto, T., Takasu, A. and Kawai, G., Nucleosides, Nucleotides and Nucleic Acids 23, 691-700 (2004) . june
  • Role of the Zinc Fingers of HIV-1 Nucleocapsid Protein for Maturation of Genomic RNA, Baba, S., Takahashi, K., Koyanagi, Y., Yamamoto, N., Takaku, H., Gorelick, R. J. and Kawai, G., J. Biochem. 134, 637 - 639 (2003)  nov
  • NMR study on the Photo-responsive DNA Tethering an Azobenzene. Assignment of the Absolute Configuration of Two Diastereomers and Structure Determination of their Duplexes in the trans-Form, Liang, X., Asanuma, H., Kashida, H., Takasu, A., Sakamoto, T., Kawai, G. and Komiyama, M., J. Am. Chem. Soc. 125, 16408-16415 (2003) . dec
  • RNA LEGO: Magnesium-dependent formation of specific RNA assemblies through kissing interactions, Horiya, S., Li, X., Kawai, G., Saito, R., Katoh, A., Kobayashi, K. and Harada, K., Chem. & Biol. 10, 645-654 (2003)  july
  • Conformational properties of 2f,5f linked Rp- and Sp-phosphorothioate oligoadenylates studied by circular dichroism and NMR, Shimizu, M., Kawai, G., Okutsu, T., Shinozuka, K., and Sawai, H., Biopolymers 72, 48-58 (2003)  jan
  • Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus, Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S. and Kawai, G., FEBS lett. 535, 94-100 (2003) . jan
  • Polyamines Enhance Synthesis of the RNA polymerase s38 Subunit by Suppression of an Amber Termination Codon in the Open Reading Frame, Yoshida, E., Kashiwagi, K., Kawai, G., Ishihama, A., and Igarashi, K., J. Biol. Chem. 277, 37139-37146 (2002)  Oct
  • Binding of ribosome recycling factor (RRF) to ribosomes - Comparison with tRNA, Hirokawa, G., Kiel, M. C., Muto, A., Kawai, G., Igarashi, K., Kaji, H., and Kaji, A., J. Biol. Chem. 277, 35847-35852 (2002)  Sep
  • Analysis of Relative Positions of Ribonucleotide Bases in a Crystal Structure of Ribosome, Takasu, A., Watanabe, K. and Kawai, G., Nucleosides, Nucleotides and Nucleic Acids@21 449-462@(2002)  june
  • Classification of RNA Structures Based on Hydrogen Bond and Base-Base Stacking Patterns: Application for NMR structures, Takasu, A., Watanabe, K. and Kawai, G., J. Biochem. 132, 211-215 (2002)  Aug
  • Solution structure of a SRP19 binding domain in human SRP RNA, Sakamoto, T., Morita, S., Tabata, K., Nakamura, K. and Kawai, G., J. Biochem., 132, 177-182 (2002)  Aug
  • Redox-coupled Conformational Alternations in Cytochrome c(3) from D. vulgaris Miyazaki F on the Basis of its Reduced Solution Structure., Harada E., Fukuoka Y., Ohmura T., Fukunishi A., Kawai G., Fujiwara T., Akutsu H., J. Mol. Biol. 319, 767-778 (2002)  June 7
  • Solution Structure of an RNA fragment with the P7/P9.0 region and the 3f-terminal guanosine of the Tetrahymena group I intron, Kitamura, A., Muto, Y., Watanabe, S., Kim, I., Ito, T., Nishiya, Y., Sakamoto, K., Ohtsuki, T., Kawai, G., Watanabe, K., Hosono, K., Takaku, H., Katoh, E., Yamazaki, T., Inoue T. and Yokoyama, S., RNA 8, 440-451 (2002)  Apr
  • Inhibition of human immunodeficiency virus type 1 activity in vitro by a new self-stabilized oligonucleotide with guanosine-thymidine quadruplex motifs, Suzuki, J., Miyano-Kurosaki, N., Kuwasaki, T., Takeuchi, H., Kawai, G. and Takaku, H., J. Virology 76, 3015-3022 (2002)  Mar
  • The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNASerUCU having a short T arm and lacking the entire D arm, Ohtsuki, T., Kawai, G., and Watanabe, K., FEBS lett. 514, 37-43 (2002)  Mar 6
  • Two basic regions of NCp7 are sufficient for conformational conversion of HIV-1 dimerization initiation site from kissing-loop dimer to extended-duplex dimer, Takahashi, K., Baba, S., Koyanagi, Y., Yamamoto, N., Takaku, H., and Kawai, G., J. Biol. Chem. 276, 31274-31278 (2001)  Aug 17
  • Minimal functional structure of Escherichia coli 4.5S RNA required for binding EF-G, Nakamura, K., Miyamoto, H., Suzuma, S., Sakamoto, T., Kawai, G., Yamane, K., J. Biol. Chem. 276, 22844-22849 (2001)  June 22
  • An "Elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria, Ohtsuki, T., Watanabe, Yi. Y., Takemoto, C., Kawai, G., Ueda, T., Kita, K., Kojima, S., Kaziro, Y., Nyborg, J., Watanabe, K., J. Biol. Chem. 276, 21571-21577 (2001)  June 15
  • Polyamine enhancement of the synthesis of adenylate cyclase at the translational level and the consequential stimulation of the synthesis of the RNA polymerase s28 subunit, Yoshida, M., Kashiwagi, K., Kawai, G., Ishihama, A., Igarashi, K., J. Biol. Chem. 276, 16289-16295 (2001)  Jan 30
  • Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions, Kim, I., Muto, Y., Watanabe, S., Kitamura, A., Futamura, Y., Yokoyama, S., Hosono, K., Kawai, G., Takaku, H., Dohmae, N., Takio, K., Sakamoto, H., and Shimura, Y., J. Biomol. NMR 17, 153-165 (2000) 
  • NMR analysis on intra- and inter-molecular stems in the dimerization initiation site of the HIV-1 genome, Takahashi, K., Baba, S., Hayashi, S., Koyanagi, Y., Yamamoto, N., Takaku, H., and Kawai, G., J. Biochem. 127, 681-686 (2000) 
  • Structural Requirement for the Two-Step Dimerization of Human Immunodeficiency Virus Type-1 Genome, Takahashi, K., Baba, S., Chattopadhyay, P., Koyanagi, Y., Yamamoto, N., Takaku, H., and Kawai, G., RNA 6, 96-102 (2000) .
  • An NMR and mutational analysis of an RNA pseudoknot of E. coli tmRNA involved in transtranslation, Nameki, N., Chattopadhyay, P., Himeno, H., Muto, A., and Kawai, G., Nucleic Acids Res. 27, 3667-3675 (1999) 
  • Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein (OppA): Involvement of a structural change of the Shine-Dalgarno sequence and the initiation codon AUG in OppA mRNA, Yoshida, M., Meksuriyen, D., Kashiwagi, K., Kawai, G., and Igarashi, K., J. Biol. Chem. 274, 22723-22728 (1999) 
  • The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity, Hosono, K., Hosaka, H., Kawai, G., Takai, K., and Takaku, H., Biochem. Biophys. Acta 1489, 374-382 (1999) 
  • Formation of a Complex Containing ATP, Mg2+, and Spermine: Structural Evidence and Biological Significance, Meksuriyen, D., Fukuchi-Shimogori, T., Tomitori, H., Kashiwagi, K., Toida, T., Imanari, T., Kawai, G., and Igarashi, K. J. Biol. Chem. 273, 30939-30944 (1998) 
  • Stable Isotopic-Edited NMR Analysis of Ascaris suum Mitochondrial tRNAMet Having a TV-Replacement Loop, Ohtsuki, T., Kawai, G., and Watanabe, K. J. Biochem. 124, 28-34 (1998) 
  • Structural and functional effect of Trp-62-->Gly and Asp-101-->Gly substitutions on substrate-binding modes of mutant hen egg-white lysozymes. Maenaka K, Matsushima M, Kawai G, Kidera A, Watanabe K, Kuroki R, Kumagai I Biochem J. 333,71-76 (1998) 
  • Structural analysis of mutant hen egg-white lysozyme preferring a minor binding mode, Maenaka K, Matsushima M, Kawai G, Watanabe K, Kuroki R, Kumagai I, Biochim Biophys Acta 1384, 23-31 (1998) 
  • Paramagnetic Inversion of the Sign of the Interference Contribution to the Transverse Relaxation of the Imido Protons of the Coordinated Imidazoles in the Uniformly 15N-Labeled Cytochrome c3, Ohmura, T., Harada, E., Fujiwara, T., Kawai, G., Watanabe, K. and Akutsu, H., J. Magn. Reson. 131, 367-372 (1998) 
  • Hairpin Structure of an RNA 28-mer, Which Contains a Sequence of the Enzyme Component of a Hammerhead Ribozyme System: Evidence for Tandem G:A Pairs That Are Not of Side-by-Side Type, Sakamoto, T., Kawai, G., Katahira, M., Kim, M. H., Tanaka, Y., Kurihara, Y., Kohno, T., Watanabe, S., Yokoyama, S., Watanabe, K., and Uesugi, S., J. Biochem. 122, 556-562 (1997) 
  • Regional Polysterism in the GTP-Bound Form of the Human c-Ha-Ras Protein, Ito, Y., Yamasaki, K., Iwahara, J., Terada, T., Kamiya, A., Shirouzu, M., Muto, Y., Kawai, G., Yokoyama, S., Laue, E. D., Waelchli, M., Shibata T., Nishimura, S. and Miyazawa, T., Biochemistry 36, 9109-9119 (1997) 
  • GNA Trinucleotide Loop Sequences Producing Extraordinary Stable DNA Minihairpins, Yoshizawa, S., Kawai, G., Watanabe, K., Miura, K., and Hirao, I., Biochemistry 36, 4761-4767 (1997) 
  • Molecular Design for a Pinpoint RNA Scission. Interposition of Oligoamines between Two DNA Oligomers, Endo, M., Azuma, Y., Saga, Y., Kuzuya, A., Kawai, G. and Komiyama, M., J. Org. Chem. 62, 846-852 (1997)