2009 : Protein Structure Hub

Publications

  1. Fujii K., Nakamura S., Takahashi K., Inagaki F.
    Systematic characterization by mass spectrometric analysis of phosphorylation sites in IRF-3 regulatory domain activated by IKK-i.
    J Proteomics.,in press(2010)
  2. Kumeta H., Miwa N., Ogura K., Kai Y., Mizukoshi T., Shimba N., Suzuki E., Inagaki F.
    The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum.
    J Biomol NMR., 246, 251-5(2010)
  3. Noda NN., Ohsumi Y., Inagaki F.
    Atg8-family interacting motif crucial for selective autophagy.
    FEBS Lett., in press(2010).
  4. Fujioka Y., Noda NN., Nakatogawa H., Ohsumi Y., Inagaki F.
    imeric coiled-coil structure of Saccharomyces cerevisiae ATG16 and its functional significance in autophagy.
    J Biol Chem.,285,1508-15(2009).
  5. Kabeya Y., Noda NN., Fujioka Y., Suzuki K., Inagaki F., Ohsumi Y.
    Characterization of the Atg17-Atg29-Atg31 complex specifically required for starvation-induced autophagy in Saccharomyces cerevisiae.
    Biochem Biophys Res Commun.,389,612-5( 2009).
  6. Ogura K., Tandai T., Yoshinaga S., Kobashigawa Y., Kumeta H., Ito T., Sumimoto H., Inagaki F.
    NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae.
    J Biochem.,146,317-25(2009) .
  7. Saio T., Yokochi M., Inagaki F.
    The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-kappaB signaling pathway.
    J Biomol NMR.,45,335-41(2009) .
  8. Kawase H., Fujii K., Miyamoto M., Kubota KC., Hirano S., Kondo S., Inagaki F.
    Differential LC-MS-based Proteomics of Surgical Human Cholangiocarcinoma Tissues.
    J Proteome Res.,8,4092-103(2009).
  9. Takahasi K., Ochiai M., Horiuchi M., Kumeta H., Ogura K., Ashida M., Inagaki F.
    Solution structure of the silkworm {beta}GRP/GNBP3 N-terminal domain reveals the mechanism for　β-1,3-glucan-specific recognition.
    Proc Natl Acad Sci U S A.,106,11679-84(2009)
  10. Saio T., Ogura K., Yokochi M., Kobashigawa Y., Inagaki F.
    Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect.
    J Biomol NMR.,44,157-66(2009).
  11. Takahasi K., Kumeta H., Tsuduki N., Narita R., Shigemoto T., Hirai R., Yoneyama M., Horiuchi M., Ogura K., Fujita T., Inagaki F.
    Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-terminal domains: identification of the RNA recognition loop in RIG-I-like receptors.
    J Biol Chem.,284,17465-74(2009).
  12. Watanabe Y., Noda NN., Honbou K., Suzuki K., Sakai Y., Ohsumi Y., Inagaki F.
    Crystallization of Saccharomyces cerevisiae alpha-mannosidase, a cargo protein of the Cvt pathway.
    Acta Crystallogr Sect F Struct Biol Cryst Commun.,65,571-3(2009).
  13. Kobashigawa Y., Kumeta H., Kanoh D., Inagaki F.
    The NMR structure of the TC10- and Cdc42-interacting domain of CIP4.
    J Biomol NMR.,44,113-8(2009) .
  14. Birge RB., Kalodimos C., Inagaki F., Tanaka S.
    Crk and CrkL adaptor proteins: networks for physiological and pathological signaling.
    Cell Commun Signal.,7-13(2009).
  15. Yuzawa S., Miyano K., Honbou K., Inagaki F., Sumimoto H.
    The Domain Organization of　p67phox, a Protein Required for Activation of the Superoxide-Producing NADPH Oxidase in Phagocytes.
    J Innate Immun.,1,543-55(2009).
  16. Horiuchi M., Takeuchi K., Noda N., Muroya N., Suzuki T., Nakamura T.Kawamura-Tsuzuku J., Takahasi K., Yamamoto T., Inagaki F.
    Structural Basis for the Antiproliferative Activity of the Tob-hCaf1 Complex.
    J Biol Chem.,284,13244-55(2009).
  17. Satoo K., Noda NN., Kumeta H., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
    The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.
    EMBO J.,28,1341-50(2009).
  18. Noda NN., Ohsumi Y., Inagaki F.
    ATG systems from the protein structural point of view.
    Chem Rev.,109,1587-98(2009) .
  19. Nakamura A., Sheppard K., Yamane J., Yao M., Söll D., Tanaka I.
    Two distinct regions in Staphylococcus aureus GatCAB guaranteeaccurate tRNA recognition.
    Nucl. Acid Res., 38, 672-82 (2010).
  20. Naganuma T., Nomura N., Yao M., Mochizuki M., Uchiumi T., Tanaka I.
    Structural Basis for Translation Factor Recruitment to the Eukaryotic/Archaeal Ribosomes.
    J. Biol. Chem., 285, 4747-56 (2010).
  21. Yu J., Zhou Y., Tanaka I., Yao M.
    Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere.
    Bioinformatics, 26, 46-52 (2010).
  22. Tanaka H., Kato K., Yamashita E., Sumizawa T., Zhou Y., Yao M., Iwasaki K., Yoshimura M., Tsukihara T.
    The Structure of Rat Liver Vault at 3.5 Angstrom Resolution.
    Science., 323, 384-8 (2009).
  23. Sokabe M., Ose T., Nakamura A., Tokunaga K., Nureki O., Yao M., Tanaka I.
    The structure of alanyl-tRNA synthetase with editing domain.
    Proc. Natl. Acad. Sci. USA., 106, 11028-33 (2009).
  24. Tanaka Y., Yamagata S., Kitago Y., Yamada Y., Chimnaronk S., Yao M., Tanaka I.
    Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand.
    RNA., 15, 1498-506 (2009).
  25. Okuyama M., Kitamura M., Hondoh H., Kang M-S., Mori H., Kimura A., Tanaka I., Yao M.
    Catalytic Mechanism of Retaining α-Galactosidase Belonging to Glycoside Hydrolase Family 97.
    J. Mol. Biol., 392, 1232-41 (2009).
  26. Chimnaronk S., Forouhar F., Sakai J., Yao M., Tron C-M., Atta M., Fontecave M., Hunt J-F., Tanaka I.
    Snapshots of Dynamics in Synthesizing N6-Isopentenyladenosine at the tRNA Anticodon.
    Biochemistry., 48, 5057-65 (2009).
  27. Watanabe N., Takasaki Y., Sato C., Ando S., Tanaka I.
    Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
    Acta Cryst., D65, 1326-33 (2009).
  28. Sasaki T., Aizawa T., Kamiya M., Kikukawa T., Kawano K., Kamo N., Demura M.
    Effect of chloride binding on the thermal trimer-monomer conversion of halorhodopsin in the solubilized system
    Biochem., 48, 12089-95(2009).
  29. Sonoyama M., Kikukwa T., Yokoyama Y., Demura M., Kamo N., Mitaku S.
    Effect of Molecular Assembly on Photocycle of Reconstituted Bacteriorhodopsin: Significant Blue Shift of the Late M Photointermediate in the Liquid Crystalline Phase
    Chem. Lett., 38, 1134-5 (2009).
  30. Umetsu Y., Aizawa T., Muto K., Yamamoto H., Kamiya M., Kumaki Y., Mizuguchi M., Demura M., Hayakawa Y., Kawano K.
    C-terminal elongation of growth-blocking peptide enhances its biological activity and micelle binding affinity
    J Biol Chem., 284, 29625-34(2009).
  31. Ishihara H., Matsuo G., Sasaki T., Saito Y., Demura M., Tsujii K.
    Electrophoresis of Dyes and Proteins in Poly(Acrylamide) Gel Containing Immobilized Bilayer Membranes
    Progress in Colloid and Polymer Science., 136, 143-8(2009)
  32. Kouno T., Mizuguchi M., Aizawa T., Shinoda H., Demura M., Kawabata S.-i., Kawano K.
    A novel -defensin structure: big defensin changes its N-terminal structure to associate with the target membrane
    Biochemistry., 48, 7629-35(2009).
  33. Nakashima K., Nakamura T., Takeuchi S., Shibata M., Demura M., Tahara T., Kandori H.
    Property of Anion Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump-Probe Spectroscopy and Low-Temperature FTIR Spectroscopy
    Journal of Physical Chemistry., 113, 8429-34(2009).
  34. Nakatogawa S., Oda Y., Kamiya M., Kamijima T., Aizawa T., K.D.Clark, Demura M., Kawano K., M.R.Strand, Hayakawa Y.
    A Novel Peptide Mediates Aggregation and Migration of Hemocytes From an Insect
    Current Biology., 19, 779-85(2009).
  35. Takiya S., Saito S., Yokoyama T., Matsumoto D., Aizawa T., Kamiya M., Demura M., Kawano K.
    DNA-Binding Property of the Novel DNA-Binding Domain STPR in FMBP-1 of the Silkworm Bombyx mori
    J. Biochem., 146, 103-11(2009).
  36. Takahashi M.,Mizuguchi M.,Shinoda H.,Aizawa T.,Demura M.,Okazawa H.,Kawano K.
    Polyglutamine tract binding protein-1 is an intrinsically unstructured protein
    Biochimica et Biophysica Acta – Proteins and Proteomics., 1794, 936-43(2009).
  37. Nonaka Y., Akieda D., Aizawa T., Watanabe N., Kamiya M., Kumaki Y., Mizuguchi M., Kikukawa T., Demura M., Kawano K.
    X-ray crystallography and structural stability of digestive lysozyme from cow stomach
    FEBS J., 276, 2192-00(2009).
  38. Inoue K., Kubo M., Demura M., Kamo N., Terazima M.
    Reaction dynamics of halorhodopsin studied by time-resolved diffusion method
    Biophys. J., 96, 3724-34(2009).
  39. Kubo M., Kikukawa T., Miyauchi S., Seki A., Kamiya M., Aizawa T., Kawano K., Kamo N., Demura M.
    Role of Arg123 in light-driven anion pump mechanisms of pharaonis halorhodopsin
    Photochem. Photobiol., 85, 547-55(2009).
  40. Kobashigawa Y, Kumeta H, Ogura K, Inagaki F.
    Attachment of an NMR-invisible solubility enhancement tag using a sortase-mediated protein ligation method.
    Journal of Biomolecular NMR., 43, 145-50 (2009).
  41. Matsushita T., Sadamoto R., Ohyabu N., Nakata H., Fumoto M., Fujitani N., Takegawa Y., Sakamoto T., Kurogochi M., Hinou H., Shimizu H., Ito T., Naruchi K., Togame H., Takemoto H., Kondo H., and Nishimura S.-I.,
    “Functional Neoglycopeptides: Synthesis and Characterization of New Class MUC1 Glycoprotein Models Having Core 2-based O-Glycan and Complex-type N-Glycan Chains”
    Biochemistry., 48, 11117-33(2009).
  42. Yanaka S., Kudou M., Tanaka Y., Sasaki T., Takemoto S., Sakata A., Hattori Y., Koshi T., Futaki S., Tsumoto K., Nakashima T.
    Contribution of the flexible loop region to the function of Staphylococcal enterotoxin B (SEB)
    Protein Eng. Des. Select., 23, 415-21 (2010).
  43. Sakamoto S., Caaveiro J.M., Sano E., Tanaka Y., Kudou M., Tsumoto K.
    Contributions of interfacial residues of human Interleukin15 to the specificity and affinity for its private alpha-receptor
    J. Mol. Biol., 389, 880-94 (2009).
  44. Nagatoishi S., Tanaka Y., Kudou M., Tsumoto K.
    The interaction of hyperthermophilic TATA-box binding protein with single-stranded DNA is entropically favorable and exhibits a large negative heat capacity change at high salt concentration
    Mol. BioSyst., 5, 957-61 (2009).
  45. Abe R., Kudou M., Tanaka Y., Arakawa T., Tsumoto K.
    Immobilized metal affinity chromatography in the presence of arginine
    Biochem. Biophys. Res. Commun., 381, 306-10 (2009).

Books etc

  1. Noda NN., Ohsumi Y., Inagaki F.
    Atg8-family interacting motif crucial for selective autophagy.
    FEBS Lett., in press（ 2010）.
  2. Noda NN., Ohsumi Y., Inagaki F.
    ATG systems from the protein structural point of view.
    Chem Rev., 109, 1587-98（ 2009）.
  3. 北郷悠、渡邉信久、田中　勲
    ターゲットタンパク研究プログラムの紹介　2.解析部門 高難度蛋白質をターゲットとした放射光X線結晶構造解析技術の開発　非標識蛋白質構造解析のための結晶マウント法の開発
    蛋白質 核酸 酵素., 54（ 12）, 1490-2（ 2009）
  4. 田中勲
    ノーベル化学賞－翻訳装置・リボソームの解析
    パリティ., 24(12), 28-31 (2009).
  5. Mizuguchi M.,Aizawa T.,Kawano K.,Demura M.
    NMR studies of protein folding: Folding studies of calcium-binding lysozyme and alpha-lactalbumin
    Annual Reports on NMR Spectroscopy., 65, 53-76(2009).
  6. Noda N.N., Ohsumi Y., Inagaki F.
    Atg8-family interacting motif crucial for selective autophagy.
    FEBS Lett., 584, 1379-85 (2010).
  7. Noda N.N., Ohsumi Y., Inagaki F.
    ATG systems from the protein structural point of view.
    Chem. Rev., 109, 1587-98 (2009).
  8. 田中良和
    タンパク質の結晶構造解析を通して得られる予期せぬ発見
    生物工学会誌　第87巻10号（2009）.

Conference Activities & Talks

(Invited talk)

  1. Septemer 2009
    Ohtsu,Japan
    The 5th International　Symposium on autophagy
    Structural basis of cargo recognition during selective autopyagy
    Noda NN., Ohsumi Y., Inagaki F.
  2. October 2009
    Sapporo, JAPAN
    The 7th Symposium for Future Drug Discovery and Medical Care
    Structural Biology of autophagy
    Inagaki F.
  3. October 2009
    Jeju Island, Korea
    The 3rd Asia-Pacific NMR symposium
    NMR methods useful for structural analyses of proteinligand and protein-protein coplexes
    Inagaki F.
  4. December 2009
    Suita, Japan
    Taiwan-Japan Joint Seminar on Crystallography and IPR Seminar
    Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes
    Yao M.
  5. December 2009
    Sapporo, Japan
    The 1st Hokkaido University – Academia Sinica Joint Symposium and The 7th Symposium for Future Drug Discovery and Medical Care
    Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes
    Yao M.
  6. August 2009
    Regensburg, Germany
    Ribosome Synthesis Meeting, Kolpinghaus Regensburg
    The structure of the archaeal ribosomal stalk complex: insights into the function of translation factor recruitment in eukarya/archaea mode
    Yao M.
  7. April 2009
    Zhengzhou, China
    International Society of Biochemistry Molecular Pharmacology
    Protein crystallography and structure-based drug design
    Yao M.
  8. September 2009
    OTSU, JAPAN
    5th International Symposium on Autophagy
    Structural basis of target recognition during selective autophagy
    Noda N.N., Ohsumi Y., Inagaki F.
  9. May 2009
    Sapporo, Japan
    Hokkaido University Mahidol University Joint Symposium
    Regulated roles of Paneth cell a-defensin in mouse small intestine and its molecular mechanism of bactericidal activity
    Rie Fukaya, Koji Masuda, Naoki Sakai and Tokiyoshi Ayabe.
  10. May 2009
    SAPPORO, JAPAN
    Hokkaido University – Mahidol University Joint Symposium
    RNA binding mechanism of ThiI
    Yoshikazu TANAKA.
  11. May 2009
    Sapporo, Japan
    北海道大学-Mahidol大学若手合同シンポジウム
    Structure of alanyl-tRNA synthetase shows two distinct tRNA binding sites for aminoacylation and editing
    Toyoyuki Ose, Masaaki Sokabe, Akiyoshi Nakamura, Keita Tokunaga, Osamu Nureki, Min Yao, Isao Tanaka.

Invited talk (in Japan)

  1. 2009年11月
    福岡市
    第48回NMR討論会
    From Structural Chemistry to Structural Biology
    稲垣冬彦
  2. 2009年12月
    札幌市
    第7回北海道大学脳科学研究教育センター・シンポジウム
    脳科学と構造生物学
    稲垣冬彦
  3. 2009年12月
    西宮市
    日本結晶学会2009年度年会
    タンパク質結晶場に捕捉された分子の振るまい－精密結晶構造解析の新利用
    田中　勲
  4. 2009年12月
    豊中市
    特定領域研究「生体超分子の構造形成と機能制御の原子機構」第6回公開シンポジウム
    タンパク質結晶場における化学反応の追尾
    田中　勲
  5. 2010年3月
    岡崎市
    分子研研究会「拡がるロドプシンの仲間から“何がわかるか”“何をもたらすか”」
    ハロロドプシン３量体形成の理解から何がわかるか
    出村　誠
  6. 2009年10月
    神戸市
    第82会日本生化学会　シンポジウム講演
    真正細菌におけるセレノシステイン特異的翻訳伸長因子SelB とSECIS mRNA の相互作用基盤
    尾瀬農之、Linda Rasubala、神田大輔、Nicolas Soler、吉澤聡子、Dominique Fourmy、前仲勝実

Patent

  1. 2010/3/4（特願2010-048003）
    アルツハイマー病の検査方法、アルツハイマー病に対して治療効果を有する物質のスクリーニング方法およびアルツハイマー病の検査キット
    出願人：国立大学法人北海道大学
    　　　　国立大学法人弘前大学
    　　　　三菱化学メディエンス株式会社
  2. 2010/3/4（特願2010-048004）
    多発性硬化症の検査方法、多発性硬化症に対して治療効果を有する物質のスクリーニング方法および多発性硬化症の検査キット
    出願人：国立大学法人北海道大学
    　　　　国立大学法人弘前大学
    　　　　三菱化学メディエンス株式会社
  3. 2009/12/4（国際特許出願番号：PCT/JP2009/006641）
    糖ペプチドの製造方法
    発明者：西村紳一郎、藤谷直樹