Shimizu h

Shimada A., Nureki O., Domae N., Takio K., and Yokoyama S.: “Gene cloning, expression, crystallization and preliminary X-ray analysis of Thermus thermophilus arginyl-tRNA synthetase”, Acta Cryst. D57, 272-275 (2001).
Hori T., Kumasaka T., Yamamoto M., Nonaka T., Tanaka N., Hashimoto Y., Ueki T., and Takio K.: “Structure of a new 'aspzincin' metalloendopeptidase from Grifora frondosa: Implications for the catalytic mechanism and substrate specificity based on several different crystal forms”, Acta Cryst. D57, 361-368
Nonaka T., Fujihashi M., Kita A., Saeki K., Ito S., and Miki K.: “Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43”, Acta Cryst. D57, 717-718 (2001).
Krieger I., Kostyukova A., and Maeda Y.: “Crystallization and preliminary characterization of crystals of the C-terminal half fragment of tropomodulin”, Acta Cryst. D57, 743-744 (2001).
Tahirov T. H., Inoue-Bungo T., Sasaki M., Siina M., Kimura K., Sato K., Kumasaka T., Yamamoto M., Kamiya N., and Ogata K.: “Crystallization and preliminary X-ray analysis of quaternary, ternary and binary protein-DNA complexes with involbement of AML1/Runx-1/CBFα Runt domain, CBFβ and the C/EBPβ bZip region”, Acta Cryst. D57, 850-853 (2001).
Tahirov T. H, Inoue-Bungo T., Sasaki M., Fujikawa A., Kimura K., Sato K., Adachi S., Kamiya N., and Ogata K.: “Crystallization and preliminary X-ray analysis of the C/EBPβ C-terminal region in complex with DNA”, Acta Cryst. D57, 854-856 (2001).
Shimizu T., Nakatsu T., Miyairi K., Okuno T., and Kato H.: “Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum”, Acta Cryst. D57, 1171-1173
Toriumi Y., Park S.-Y., Hashimoto H., Shimizu H., Hirano M., and Kamiya N.: “Crystallization and preliminary X-ray diffraction analysis of light-harvesting protein phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus”, Acta Cryst. D57, 1326-1328 (2001).
Liu L., Iwata K., Kawarabayashi Y., Kikuchi H., Kita A., Yohda M., and Miki K.: “Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3”, Acta Cryst. D57,
Nakamura H., Saito K., and Shiro Y.: “Quantitative measurement of radioactive phosphorylated proteins in wet polyacrylamide gels”, Anal. Biochem. 294, 187-188 (2001).
Iizuka R., Yoshida T., Maruyama T., Shomura Y., Miki K., and Yohda M.: “Glycine at the 65th position plays an essential role in ATP-dependent protein folding by Archael group II chaperonin”, Biochem. Biophys. Res. Commun. 289, 1118-1124 (2001).
Noguchi T., and Sugiura M.: “Flash-induced fourier transform infrared detection of the structural changes during the S-state cycle of the oxygen-evolving complex in photosystem II”, Biochemistry 40, 1497-1502
Noguchi T., Tomo T., and Kato C.: “Triplet formation on a monomeric chlorophyll in the photosystem II reaction center as studied by time-resolved infrared spectroscopy”, Biochemistry 40, 2176-2185 (2001).
Lee D.-S., Park S.-Y., Yamane K., Obayashi E., Hori H., and Shiro Y.: “Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam”, Biochemistry 40, 2669-2677
Nakasako M., Fujisawa T., Adachi S., Kudo T., and Higuchi S.: “Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering”, Biochemistry 40, 3069-3079 (2001).
Shimizu H., Yamagata S., Masui R., Inoue Y., Shibata T., Yokoyama S., Kuramitsu S., and Iwama T.: “Cloning and overexpression of the oah1 gene encoding O-acetyl-L-homoserine sulfhydrylase of Thermus thermophilus HB8 and characterization of the gene product”, Biochim. Biophys. Acta 1549,
Lee D.-S., Kim N.-S., and Lee S.-H.: “2,2-diphenyl-1-picrylhydrazyl hydrate, a stable free radical, is an
α-glucosidase inhibitor”, Biol. Pharm. Bull. 24, 727-728 (2001).
Fujiwara T., Kimoto M., Sugiyama H., Hirao I., and Yokoyama S.: “Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides”, Bioorg. Med. Chem. Lett. 11, 2221-2223 (2001).
Oda T., Makino K., Yamashita I., Namba K., and Maéda Y.: “Distinct structural changes detected by X-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength”, Biophys. J. 80, 841-851 (2001).
Kostyukova A., Tiktopulo E., and Maéda Y.: “Folding properties of functional domains of tropomodulin”, Biophys. J. 81, 345-351 (2001).
Tahirov T. H., Inoue-Bungo T., Morii H., Fujikawa A., Sasaki M., Kimura K., Shiina M., Sato K., Kumasaka T., Yamamoto M., Ishii S., and Ogata K.: “Structural analyses of DNA recognition by the AML1/Runx-1 runt domain and its allosteric control by CBFβ”, Cell 104, 755-767 (2001).
Hirao I., Nojima T., Mitsui T., and Yokoyama S.: “Synthesis of DNA templates containing the fifth base, 2-amino-6-(dimethylamino)purine, for specific transcription involving unnatural base pairs”, Chem. Lett. 2001, 914-915 (2001).
Renault L., Kerjan P., Pasqualato S., Ménétrey J., Robinson J., Kawaguchi S., Vassylyev D., Yokoyama S., Mirada M., and Cherfils J.: “Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry”, EMBO J. 20, 570-578 (2001).
Kawaguchi S., Müller J., Linde D., Kuramitsu S., Shibata T., Inoue Y., Vassylyev D.G., and Yokoyama S.: “The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus”, EMBO J. 20, 562-569 (2001).
Fathir I., Mori T., Nogi T., Kobayashi M., Miki K., and Nozawa T.: “Structure of the H subunit of the photosynthetic reaction center from the thermophilic purple sulfur bacterium, Thermochromatium tepidum: Implications for the specific binding of the lipid molecule to the membrane protein complex”, Eur. J. Biochem. 268, 2652-2657 (2001).
Kiga D., Sakamoto K., Sato S., Hirao I., and Yokoyama S.: “Shifted positioning of the anticodon
nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase”, Eur. J. Biochem. 268, 6207-6213 (2001).
Sogabe S., and Miki K.: “Crystal structure of the oxidized cytochrome c2 from Blastochloris viridis”,
FEBS Lett. 491, 174-179 (2001).
Fujisawa T., Kostyukova A., and Maéda Y.: “The shapes and sizes of two domains of tropomodulin, the P-end capping protein of actin-tropomyosin”, FEBS Lett. 498, 67-71 (2001).
Lee D.-S., and Lee S.-H.: “Genistein, a soy isoflavone, is a potent α-glucosidase inhibitor”, FEBS Lett. 501, 84-86 (2001).
Hashimoto Y., Yano T., Kuramitsu S., and Kagamiyama H.: “Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker”, FEBS Lett. 506,
Matsumoto S., Yoshiga T., Yokoyama N., Iwanaga M., Koshiba S., Kigawa T., Hirota H., Yokoyama S., Okano K., Mita K., Shimada T., and Tatsuki S.: “Characterization of acyl-CoA-binding protein (ACBP) in the pheromone gland of the silkworm, Bombyx mori”, Insect Biochem. Mol. Biol. 31, 603-609 (2001).
Odoko M., Yao M., Yamashita E., Nakashima R., Hirata K., Aoyama H., Muramoto K., Shinzawa-Itoh K., Yoshikawa S., and Tsukihara T.: “Optimization of the energy constant of the methionine Sδ-Cε bond for
X-PLOR refinement of protein structure”, J. Appl. Crystallogr. 34, 80-81 (2001).
Ura H., Harata K., Matsui I., and Kuramitsu S.: “Temperature dependence of the enzyme-substrate recognition mechanism”, J. Biochem. 129, 173-178 (2001).
Ura H., Nakai T., Kawaguchi S., Miyahara I., Hirotsu K., and Kuramitsu S.: “Substrate recognition mechanism of thermophilic dual-substrate enzyme”, J. Biochem. 130, 89-98 (2001).
Nogi T., and Miki K.: “Structural basis of bacterial photosynthetic reaction centers”, J. Biochem. 130,
Ito N., Nureki O., Shirouzu M., Yokoyama S., and Hanaoka F.: “Crystallization and preliminary X-ray analysis of a DNA primase from hyperthermophilic archaeon Pyrococcus horikoshii”, J. Biochem. 130,
Sekine S., Shimada A., Nureki O., Jean C. J., Moras D., Vassylyev D., and Yokoyama S.: “Crucial role of the HIGH-loop lysine for the catalytic activity of arginyl-tRNA synthetase”, J. Biol. Chem. 276,
Nakajima H., Honma Y., Tawara T., Kato T., Park S.-Y., Miyatake H., Shiro Y., and Aono S.: “Redox properties and coordination structure of the heme in the CO-sensing transcriptional activator CooA”, J. Biol. Chem. 276, 7055-7061 (2001).
Kharel Y., Zhang Y., Fujihashi M., Miki K., and Koyama T.: “Identification of significant residues for homoallylic substrate binding of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase”, J. Biol. Chem. 276, 28459-28464 (2001).
Kagawa W., Kurumizaka H., Ikawa S., Yokoyama S., and Shibata T.: “Homologous pairing promoted by the human Rad52 protein”, J. Biol. Chem. 276, 35201-35208 (2001).
Nakama T., Nureki O., and Yokoyama S.: “Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase”, J. Biol. Chem. 276, 47387-47393 (2001).
Denisov I. G., Hung S.-C., Weiss K. E., McLean M. A., Shiro Y., Park S.-Y., Champion P. M., and Sligar S. G.: “Characterization of the oxygenated intermediate of the thermophilic cytochrome P450 CYP119”, J. Inorg. Biochem. 87, 215-226 (2001).
Iwamoto H., Oiwa K., Suzuki T., and Fujisawa T.: “X-ray diffraction evidence for the lack of stereospecific protein interactions in highly activated actomyosin complex”, J. Mol. Biol. 305, 863-874
Terada T., Shirouzu M., Fukumori Y., Fujimori F., Ito Y., Kigawa T., Yokoyama S., and Uchida T.: “Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, h Par14”, J. Mol. Biol. 305, 917-926 (2001).
Naoi Y., Chong K. T., Yoshimatsu K., Miyazaki G., Tame J. R. H., Park S.-Y., Adachi S., and Morimoto H.: “The functional similarity and structural diversit of human and cartilaginous fish hemoglobins”, J. Mol. Biol. 307, 259-270 (2001).
Fukami T. A., Yohda M., Taguchi H., Yoshida M., and Miki K.: “Crystal structure of chaperonin-60 from Paracoccus denitrificans”, J. Mol. Biol. 312, 501-509 (2001).
Koshiba S., Kigawa T., Kikuchi A., and Yokoyama S.: “Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin”, J. Struct. Funct. Genom. 2, 1-8 (2001).
Kigawa T., Yamaguchi-Nunokawa E, Kodama K., Matsuda T., Yabuki T., Matsuda N., Ishitani R., Nureki O., and Yokoyama S.: “Selenomethionine incorporation into a protein by cell-free synthesis”, J. Struct. Funct. Genom. 2, L87-L104 (2001).
Kikuchi A., Park S.-Y., Miyatake H., Sun D., Sato M., Yoshida T., and Shiro Y.: “Crystal structure of rat biliverdin reductase”, Nature Struct. Biol. 8, 221-225 (2001).
Sekine S., Nureki O., Shimada A., Vassylyev D, G., and Yokoyama S.: “Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase”, Nature Struct. Biol. 8, 203-206 (2001).
Samatey F. A., Imada K., Nagashima S., Vonderviszt F., Kumasaka T., Yamamoto M., and Namba K.: “Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling”, Nature 410, 331-337 (2001).
Hara T., Tanaka T., Seike T., Bizen T., Maréchal X., Kouda T., Inoue K., Oka T., Suzuki T., Nagi N., and Kitamura H.: “In-vacuum X-ray helical undulator for high flux beamline at SPring-8”, Nucl. Instrum. Methods Phys. Res. A 467/468, 165-168 (2001).
Inoue K., Oka T., Suzuki T., Yagi N.,Takeshita K., Goto S., and Ishikawa T.: “Present status of high flux beamline (BL40XU) at SPring-8”, Nucl. Instrum. Methods Phys. Res. A 467/468, 674-677 (2001).
Adachi S., Oguchi T., Tanida H., Park S.-Y., Shimizu H., Miyatake H., Kamiya N., Shiro Y., Inoue Y., Ueki T., and Iizuka T.: “The RIKEN structural biology beamline II(BL44B2) at the SPring-8”, Nucl. Instrum. Methods Phys. Res. A 467/468, 711-714 (2001).
Toyokawa H., Fujisawa T., Inoko Y., Nagayoshi T., Nishii Y., Nishikawa Y., Ochi A., Suzuki M., and Tanimori T.: “Performance of a micro-strip gas chamber in solution X-ray scattering”, Nucl. Instrum. Methods Phys. Res. A 467/468, 1144-1147 (2001).
Yamamoto M., Kumasaka T., Yamazaki H., Sasaki K., Yokozawa Y., and Ishikawa T.: “Development of high-speed imaging plate detector”, Nucl. Instrum. Methods Phys. Res. A 467/468, 1160-1162 (2001).
Kawamoto M., Kawano Y., and Kamiya N.: “The biocrystallography beamline (BL41XU) at SPring8”, Nucl. Instrum. Methods Phys. Res. A 467/468, 1375-1379 (2001).
Nishikawa Y., Fujisawa T., Inoko Y., and Moritoki M.: “Improvement of a high pressure cell with diamond windows for solution X-ray scattering of proteins”, Nucl. Instrum. Methods Phys. Res. A 467/468, 1384-1387 (2001).
Yamagata A., Masui R., Kakuta Y., Kuramitsu S., and Fukuyama K.: “Overexpression, purification, and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain”, Nucleic Acids Res. 29, 4617-4624 (2001).
Miyano M.: “How the G protein-coupled receptor activates GTP-binding protein”, Pharmacogenet. J. 1,
Sasaki Y. C., Okumura Y., Adachi S., Suda H., Taniguchi Y., and Yagi N.: “Picometer-scale dynamical X-ray imaging of single DNA molecules”, Phys. Rev. Lett. 87, 248102-1-248102-4 (2001).
Fujihashi M., Zhang Y.-W., Higuchi Y., Li X.-Y., Koyama T., and Miki K.: “Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase”, Proc. Natl. Acad. Sci. USA 98,
Kurumizaka H., Ikawa S., Nakada M., Eda K., Kagawa W., Takata M., Takeda S., Yokoyama S., and Shibata T.: “Homologous-pairing activity of the human DNA-repair proteins X·Rad51C”, Proc. Natl. Acad. Sci. USA 98, 5538-5543 (2001).
Konishi H., Yamauchi E., Taniguchi H., Yamamoto T., Matsuzaki H., Takemura Y., Ohmae K., Kikkawa U., and Nishizuka Y.: “Phosphorylation sites of protein kinase C δ in H2O2-treated cells and its activity
by tyrosine kinase in vitro”, Proc. Natl. Acad. Sci. USA 98, 6587-6592 (2001).
Shibata T., Nishinaka T., Mikawa T., Aihara H., Kurumizaka H., Yokoyama S., and Ito Y.: “Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material”, Proc. Natl. Acad. Sci. USA 98, 8425-8432 (2001).
Shimada A., Nureki O., Goto M., Takahashi S., and Yokoyama S.: “Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase”, Proc. Natl. Acad. Sci. USA 98, 13537-13542 (2001).
Komori H., Masui R., Kuramitsu S., Yokoyama S., Shibata T., Inoue Y., and Miki K.: “Crystal structure of thermostable DNA photolyase: Pyrimidine-dimer recognition mechanism”, Proc. Natl. Acad. Sci. USA 98, 13560-13565 (2001).
Komori H., Tsujiuchi H., Masui R., Kuramitsu S., Yokoyama S., Shibata T., Inoue Y., and Miki K.: “Crystallization and preliminary X-ray studies of a thermostable DNA photolyase from Thermus thermophilus HB8”, Protein and Peptide Letters 8, 495-498 (2001).
Ota M., Isogai Y., and Nishikawa K.: “Knowledge-based potential defined for a rotamer library to design protein sequences”, Protein Eng. 14, 557-564 (2001).
Inaka K., Kanaya E., Kikuchi M., and Miki K.: “Crystal structure of a mutant human lysozyme with a substituted disulfide bond”, Proteins: Struct., Funct., Genet. 43, 413-419 (2001).
Oda T., Makino K., Yamashita I., Namba K., and Maéda Y.: “The helical parameters of F-actin precisely determined from X-ray fiber diffraction of well-oriented sols”, Results and Problems in Cell Differentiation 32, 43-58 (2001).
Nakashima T., Yao M., Kawamura S., Iwasaki K., Kimura M., and Tanaka I.: "Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding", RNA 7, 692-701
Itoh T., Koshiba S., Kigawa T., Kikuchi A., Yokoyama S., and Takenawa T.: “Role of the ENTH domain in phosphatidylinositol-4,5-bisphosphate binding and endocytosis”, Science 291, 1047-1051 (2001).
Kitano K,. Maeda N., Fukui T., Atomi H., Imanaka T., and Miki K.: “Crystal structure of a novel-type archaeal Rubisco with pentagonal symmetry”, Structure 9, 473-481 (2001).

Source: http://rsc.riken.jp/biology/pdf/research2001.pdf