Original Papers (only) <Year 2001>

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 (2001). BL45XU

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/CBF? Runt domain, CBF? and the C/EBP??bZip region”, Acta Cryst. D57, 850-853 (2001). BL45XU

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/EBP? C-terminal region in complex with DNA”, Acta Cryst. D57, 854-856 (2001). BL44B2/BL45XU

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 (2001).

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, 1674-1676 (2001). BL44B2

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 (2001).

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 (2000).

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). BL44B2/BL45XU/BL45SAXS

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, 61-72 (2001).

Lee D.-S., Kim N.-S., and Lee S.-H.: “2,2-diphenyl-1-picrylhydrazyl hydrate, a stable free radical, is an ?-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 Maeda 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 Maeda 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 CBF?”, Cell 104, 755-767 (2001). BL45XU

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., Menetrey 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., Muller 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). BL44B2

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 Maeda Y.: “The shapes and sizes of two domains of tropomodulin, the P-end capping protein of actin-tropomyosin”, FEBS Lett. 498, 67-71 (2001). BL45SAXS

Lee D.-S., and Lee S.-H.: “Genistein, a soy isoflavone, is a potent ?-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, 231-234 (2001).

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 S?-C? 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, 319-329 (2001).

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, 727-730 (2001).

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, 3723-3726 (2001).

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 (2001). BL45SAXS

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). BL44B2

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). BL44B2

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). BL45XU

Hara T., Tanaka T., Seike T., Bizen T., Marechal 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). BL44B2

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). BL45SAXS

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). BL44B2

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). BL45SAXS

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, 225-228 (2001).

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, 4337-4342 (2001).

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 ? 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). BL41

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). BL44B2

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). BL44B2

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 Maeda 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 (2001).

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).BL45XU