2008 : Protein Structure Hub


  1. Satoo K., Noda N., 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(9),1341-50(2009)
  2. 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(19),13244-55(2009)
  3. Noda N., Ohsumi Y., Inagaki F.
    ATG systems from the protein structural point of view
    Chem Rev., 109(4),1587-98(2009)
  4. Noda N., Kumeta H., Nakatogawa H., Satoo K., Adachi W., Ishii J., Fujioka Y.,
    Ohsumi Y., Inagaki F.
    Structural basis of target recognition by Atg8/LC3 during selective autophagy
    Genes Cell., 13,1211-8(2008)
  5. Fujioka Y., Noda N., Matsushita M., Ohsumi Y., Inagaki F.
    Crystallization of the coiled-coil domain of Atg16 essential for autophagy
    Acta Crystallograph. Sect. F Struct. Biol. Cryst. Commun., 64(pt11),1046-8(2008)
  6. Ogura K., Shiga T., Yokochi M., Yuzawa S., Burke TR Jr., Inagaki F.
    Solution structure of the Grb2 SH2 domain complexed with a high-affinity inhibitor
    J Biomol .NMR., 42(3),197-207(2008)
  7. Kobashigawa Y., Kumeta H., Ogura K., Inagaki F.
    Attachment of an NMR-invisible solubility enhancement tag using a sortase-mediated protein ligation method
    J Biomol NMR. ,43(3),145-50(2009)
  8. Noda N.N., Fujioka Y., Ohsumi Y., Inagaki F.
    Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free interface diffusion method
    J. Synchrotron Radiat.,15,(Pt 3)266-8(2008)
  9. Chimnaronk S., Suzuki T., Manita T., Ikeuchi Y., Yao M., Suzuki T., Tanaka I.
    RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon
    The EMBO J.,28, 1362-73 (2009).
  10. Gao Y-G., Suzuki H., Itou H., Zhou Y., Tanaka Y., Wachi M., Watanabe N., Tanaka I., Yao M.
    Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in L-lactate and sugar utilization
    Nucl. Acid Res.,36, 7110-23 (2008).
  11. Kitamura M., Okuyama M., Tanzawa F., Mori H., Kitago Y., Watanabe N., Kimura A., Tanaka I., Yao M.
    Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron
    J. Biol. Chem.,283, 36328-37 (2008).
  12. Watanabe M., Tanaka Y., Suenaga A., Kuroda M., Yao M., Watanabe N., Arisaka F., Ohta T., Tanaka I., Tsumoto K.
    Structural Basis for Multimeric Heme Complexation through a Specific Protein-Heme Interaction: the case of the third NEAT domain of IsdH from Staphylococcus aureus
    J. Biol. Chem.,283, 28649-59 (2008).
  13. Nonaka Y., Aizawa T., Akieda D., Yasui M., Watanabe M., Watanabe N., Tanaka I., Kamiya M., Mizuguchi M., Demura M., Kawano K.
    Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions
    Proteins.,72, 313-22 (2008).
  14. Gao Y-G., Yao M., Tanaka I.
    Structure of protein PH0536 from Pyrococcus horikoshii at 1.7 A resolution reveals a novel assembly of an oligonucleotide/oligosaccharide-binding fold and an α-helical bundle
    Proteins.,71, 503-8 (2008).
  15. Kuroda M., Ito R., Tanaka Y., Yao M., Matoba K., Saito S., Tanaka I., Ohta T.
    Staphylococcus aureus Surface Protein SasG Contributes to Intercellular Autoaggregation of Staphylococcus aureus
    Biochem. Biophys. Res. Commun.,377, 1102-6 (2008).
  16. Sakamoto S., Tanaka Y., Tanaka I., Takei T., Yu J., Kuroda M., Yao M., Ohta T., Tsumoto K.
    Electron Microscopy and Computational Studies of Ebh, a Giant Cell-wall-associated Protein from Staphylococcus aureus
    Biochem. Biophys. Res. Commun.,376, 261-6 (2008).
  17. Kawamura T., Watanabe N., Tanaka I.
    Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii
    Acta Cryst.,D64, 1267-76 (2008).
  18. Begum P., Sakai N., Hayashi T., Gao Y-G., Tamura T., Watanabe N., Yao M., Tanaka I.
    Crystal Structure of SCO6571 from Streptomyces coelicolor A3(2)
    Protein & Peptide Letters.,15, 709-12 (2008).
  19. 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)
  20. 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).
  21. Kamijima T.,Ohmura A.,Sato T., Akimoto K., Itabashi M.,Mizuguchi M.,Kamiya M. ,Kikukawa T.,Aizawa T.,Takahashi M.,Kawano K.,Demura M.
    Heat-treatment method for producing fatty acid-bound alpha-lactalbumin that induces tumor cell death
    Biochem.Biophys.Res.Commun., 376, 211-4 (2008).
  22. Kouno T.,Fujitani N.,Mizuguchi M.,Osaki T.,Nishimura S.,Kawabata S.,Aizawa T.,Demura M.,Nitta K., Kawano K.
    A Novel beta-defensin Structure: a Strategy of Big Defensin for a Resistance by Gram-positive Bacteria
    Biochemistry., 47, 10611-9 (2008).
  23. Mizuguchi M.,Hayashi A.,Takeuchi M.,Dobashi M.,Mori Y.,Shinoda H.,Aizawa T.,Demura M.,Kawano K.
    Unfolding and aggregation of transthyretin by the truncation of 50 N-terminal amino acids.
    Proteins., 72, 261-9 (2008).
  24. Wang W.,Itoh S.,Matsuda A.,Aizawa T.,Demura M.,Ichinose S.,Shinomiya K.,Tanaka J.
    Enhanced nerve regeneration through a bilayered chitosan tube: The effect of introduction ofglycine spacer into the CYIGSR sequence
    J Biomed Mater Res A., 85A, 919-28 (2008)
  25. T. Nakamura, S. Takeuchi, M. Shibata, M. Demura, H. Kandori, T. Tahara
    Ultrafast Pump-Probe Study of the Primary Photoreaction Process in pharaonis Halorhodopsin:
    Halide-Ion Dependence and Isomerization Dynamics
    Journal of Physical Chemistry B., 112, 12795-800 (2008).
  26. T. Sasaki, M. Kubo, T. Kikukawa, M. Kamiya, T. Aizawa, K. Kawano, N. Kamo and M. Demura
    Halorhodopsin from Natronomonas pharaonis forms a trimer even in the presence of a detergent,
    Photochem. Photobiol., 85, 130-6 (2009).
  27. Saito S.,Yokoyama T.,Aizawa T.,Kawaguchi K.,Yamaki T.,Matsumoto D.,Kamijima T., Kamiya M.,Kumaki Y.,Mizuguchi M.,Takiya S.,Demura M.,Kawano K.
    Structural Properties of the DNA-Bound Form of a Novel Tandem Repeat DNA-Binding Domain, STPR
    Proteins., 72, 414-26 (2008)
  28. Nonaka Y.,Aizawa T.,Akieda D.,Yasui M.,Watanabe M.,Watanabe N.,Tanaka I.,Kamiya M., Mizuguchi M.,Demura M.,Kawano K.
    Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions
    Proteins., 72, 313-22 (2008)
  29. Sakai N. and Ayabe T.
    Antimicrobial peptides in the gut innate immunity
    International Journal of Probiotics and prebiotics., 3, 123-6 (2008).
  30. Nakakido M., Tanaka Y., Mitsuhori M., Kudou M., Ejima D., Arakawa T., Tsumoto K.
    Structure-based analysis reveals hydration changes induced by arginine hydrochloride
    Biophys. Chem., 137, 105-9 (2008)
  31. Kuroda M., Tanaka Y., Aoki R., Shu D., Tsumoto K., Ohta T.
    Staphylococcus aureus Giant Protein Ebh is Involved in Tolerance to Transient Hyperosmotic Pressure
    Biochem. Biophys. Res. Comm., 374, 237-41 (2008)
  32. Ui M., Tanaka Y., Tsumuraya T., Fujii I., Inoue M., Hirama M., Tsumoto K.
    How Protein Recognizes Ladder-Like Polycyclic Ethers: Interactions Between Ciguatoxin (CTX3C) Fragments and Its Specific Antibody 10C9
    J. Biol. Chem., 283, 19440-7 (2008)
  33. Nakakido M., Tanaka Y., Sokabe M., Tsumoto K.
    Thermodynamic Analysis Reveals that GTP Binding Affects the Interaction between the alpha- and gamma-subunits of Translation Initiation Factor 2
    Biochem. Biophys. Res. Comm., 371, 596-9 (2008)
  34. Miyafusa T., Tanaka Y., Kuroda M., Ohta T., Tsumoto K.
    Expression, Purification, Crystallization, and Primary Diffraction Analysis of CapF, a Capsular Polysaccharide Synthesis Enzyme from Staphylococcus aureus
    Acta Cryst. , F64, 512-5 (2008)
  35. Tsumoto K., Yokota A., Tanaka Y., Ui M., Tsumuraya T., Fujii I., Kumagai I., Nagumo Y., Oguri H., Inoue M., Hirama M.
    Critical contribution of aromatic rings to specific recognition of polyether rings: the case of ciguatoxin CTX3C and its specific antibody 1C49
    J. Biol. Chem., 283, 512259-66 (2008)
  36. TanakaY., Sakamoto S., Kuroda M., Goda S., Gao Y., Tsumoto K., Hiragi Y., Yao M., Watanabe N., Ohta T., Tanaka I.
    A helical string of alternately connected two three-helix bundles for the 1.1-Megadalton cell wall-associated adhesion protein Ebh from Staphylococcus aureus
    Structure., 16, 488-96, (2008)

Books etc

  1. 稲垣冬彦
    蛋白質核酸酵素,53(5),600-3 (2008).
  2. 田中勲、 渡邉信久、 姚閔、 坂井直樹
    特集 タンパク3000プロジェクトの産んだもの 第I部 成果とインパクト:個別的解析拠点の研究成果転写・翻訳 翻訳系蛋白質を中心に ‘Team transcription & translation’ aiming at 100 structures
    蛋白質 核酸 酵素, 53, 608-11 (2008).
  3. 姚閔
    日本結晶学会 ,50, 218-23 (2008).

Conference Activities & Talks

  1. January 2009
    Oosaka, Japan
    International Symposium on Molecular Soft Interactions in Biological Systems
    Soft interaction phagocyte oxidation system
    Inagaki F.
  2. September 2008
    International Conference On Structural Genomics Organization
    Structural Biology of Autophagy
    Inagaki F.
  3. August 2008
    San Diego,America
    International Conference on Magnetic Resonance in Biological Systems
    Structural basis for the transforming activity of human-cancer related signaling adaptor protein CRK
    Inagaki F.
  4. June 2008
    13th Int.Conf.Retinal Protein
    Megumi Kubo1, Takashi Kikukawa2, Seiji Miyauchi3, Masakatsu Kamiya1, Tomoyasu Aizawa1, Keiichi Kawano4, Naoki Kamo1,3, and Makoto Demura1
  5. August 2008
    Kyoto, Japan
    IUCr Commission on Crystallographic Computing School Kyoto 2008
    Automated refinement for protein crystallography:LAFIRE
    Min Yao
  6. Octover 2008
    Regulation in Innate Immunity
    “Mechanistic analysis of the 21st amino acid incorporaton”
    Toyoyuki Ose, Nicolas Soler, Linda Rasubala, Kimiko Kuroki, Daisuke Kohda, Dominique Fourmy, Satoko Yoshizawa, Katsumi Maenaka

Invited talk (in Japan)

  1. 2008年12月
  2. 2008年12月
    「Solution structure of RIG-like receptor C-terminal domains」
  3. 2008年9月
  4. 2008年6月
  5. 2009年3月
    田中 勲、長沼孝雄、野村直子、望月正弘、姚 閔、内海利男
  6. 2008年12月
    BMB2008(第31回日本分子生物学会年会・第81回日本生化学会大会 合同大会)
    中村彰良、山根潤二、姚 閔、田中 勲
  7. 2008年12月
    BMB2008(第31回日本分子生物学会年会・第81回日本生化学会大会 合同大会)
    内海利男、長沼孝雄、野村直子、三好智博、姚 閔、田中 勲
  8. 2008年4月
    出村 誠
  9. 2008年7月
    出村 誠
  10. 2009年3月
    出村 誠
  11. 2008年9月
    第3回IPABセミナー アクセラレータWG
    姚 閔
  12. 2008年10月29日
    Regulation in Innate Immunity, from Recognition Molecules to Antimicrobial Peptides
    「Regulated roles of Paneth cell α-defensin in mouse small intestine and its molecular mechanism of bactericidal activity」
  13. 2008年8月
  14. 2008年8月
  15. 2008年7月
    JCS2008 – Joint Conference in Sapporo 2008 - 自然免疫の最前線
    尾瀬農之、Linda Rasubala、神田大輔、Nicolas Soler、吉澤聡子、Dominique Fourmy、前仲勝実1