2012 : Protein Structure Hub

Publications

  1. Noda NN., Fujioka Y., Hanada T., Ohsumi Y., Inagaki F.
    Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation.
    EMBO Rep.,14, 206-211 (2012)
  2. Nyirenda J., Matsumoto S., Saitoh T., Maita N., Noda NN., Inagaki F., Kohda D.
    Crystallographic and NMR Evidence for Flexibility in Oligosaccharyltransferases and Its Catalytic Significance.
    Structure., 21, 32-41 (2012)
  3. Yamaguchi M., Matoba K., Sawada R., Fujioka Y., Nakatogawa H., Yamamoto H., Kobashigawa Y., Hoshida H.,
    Akada R., Ohsumi Y., Noda NN., Inagaki F.
    Non-canonical recognition and ambiguous Ubl-loading to two distinct E2s by autophagy-essential E1, Atg7.
    Nat. Struct. Mol. Biol., 19, 1250-1256 (2012)
  4. Yokogawa M., Kobashigawa Y., Yoshida N, Ogura K., Harada K., Inagaki F.
    NMR analyses of the interaction between the FYVE domain of early endosome antigen 1 (EEA1) and phosphoinositide embedded in a lipid bilayer.
    J Biol Chem., 287, 34936-34945 (2012)
  5. Watanabe Y., Kobayashi T., Yamamoto H., Hoshida H., Akada R., Inagaki F., Ohsumi Y., Noda NN.
    Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18.
    J Biol Chem., 287, 31681-31690 (2012)
  6. Hayashi T., Senda M, Morohashi H., Higashi H., Horio M., Kashiba Y., Nagase L., Sasaya D., Shimizu T., Venugopalan N., Kumeta H., Noda NN., Inagaki F., Senda T., Hatakeyama M.
    Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA.
    Cell Host Microbe., 12, 20-33 (2012)
  7. Ogura K., Okamura H., Katahira M, Katoh E., Inagaki F.
    Conformational dynamics of yeast calmodulin in the Ca(2+)-bound state probed using NMR relaxation dispersion.
    FEBS Lett., 586, 2548-2554 (2012)
  8. Horiuchi M., Takahasi K., Kobashigawa Y., Ochiai M., Inagaki F.
    A low-cost affinity purification system using β-1,3-glucan recognition protein and curdlan beads.
    Protein Eng Des Sel., 25, 405-413 (2012)
  9. Kobashigawa Y., Inagaki F.
    Structural biology: CrkL is not Crk-like.
    Nat Chem Biol., 8, 504-505 (2012)
  10. Yamaguchi M., Noda NN., Yamamoto H., Shima T., Kumeta H., Kobashigawa Y., Akada R., Ohsumi Y., Inagaki F.
    Structural insights into Atg10-mediated　formation　of the autophagy-essential Atg12-Atg5 conjugate.
    Structure., 20, 1244-1254 (2012)
  11. Kobashigawa Y., Saio T., Ushio M., Sekiguchi M., Yokochi M., Ogura K., Inagaki F.
    Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination.
    J Biomol NMR., 53, 53-63 (2012)
  12. Noda NN., Kobayashi T., Adachi W., Fujioka Y., Ohsumi Y., Inagaki F.
    Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 16 and its specific role in autophagy.
    J Biol Chem., 287, 16256-16266 (2012)
  13. Englert M., Xia S., Okada C., Nakamura A., Tanavde V., Yao M., Eom S-H., Konigsberg W-H., Soll D., and Wang J.
    Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3′-terminal phosphate and 5′-OH.
    Proc. Natl. Acad. Sci. USA, 109, 15235-15240 (2012)
  14. Ariyawutthiphan O., Ose T., Minami A., Sinde S., Tsuda M., Gao Y-G., Yao M., Oikawa H., and Tanaka I.
    Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation.
    Acta Cryst., D68, 1558-1569 (2012)
  15. Matsui T., Yamane J., Mogi N., Yamaguchi H., Takemoto H., Yao M., and Tanaka I.
    Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus.
    Acta Cryst., D68, 1175-1188 (2012)
  16. Fujihashi M., Hiraki M., Ueno G., Baba S., Murakami H., Suzuki M., Watanabe N., Tanaka I., Nakagawa A., Wakatsuki S., Yamamoto M., and Miki K.
    Crystal sample pins and a storage cassette system compatible with the protein crystallography beamlines at both the Photon Factory and SPring-8.
    J. Appl. Cryst., 45, 1156-1161 (2012)
  17. Sunagawa N., Tajima K., Hosoda M., Kawano S., Kose R., Satoh Y., Yao M., Dairi T.
    Cellulose production by Enterobacter sp. CJF-002 and identification of genes for cellulose biosynthesis.
    Cellulose, 19, 1989-2001 (2012)
  18. Gai, Z. Kitagawa, Y., Tanaka, Y., Shimizu, N., Komoda, K., Tanaka, I., and Yao, M.
    The binding mechanism of eIF2{beta} with its partner proteins, eIF5 and eIF2Be
    Biochem. Biophys. Res. Commun. 423, 515-519 (2012)
  19. Fujiwara T., Komoda K., Sakurai N., Tajima K., Tanaka I., and Yao M.
    The c-di-GMP recognition mechanism of the PilZ domain of bacterial cellulose synthase subunit A.
    Biochem. Biophys. Res. Commun., 431, 802-807 (2013)
  20. Tsukamoto T., Sasaki T., Fujimoto K J., Kikukawa T., Kamiya M., Aizawa T., Kawano K., Kamo N., Demura M.
    Homo-trimer Formation and Dissociation of pharaonis Halorhodopsin in Detergent System
    Biophys. J., 102, 2906-2915 (2012).
  21. Muroda K., Nakashima K., Shibata M., Demura M., Kandori H.
    Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps.
    Biochemistry, 51, 4677-4684 (2012).
  22. Mizuguchi M., Takeuchi M., Ohki S., Nabeshima Y., Kouno T., Aizawa T., Demura M., Kawano K., Yutani K.
    Structural characterization of a trapped folding intermediate of pyrrolidone carboxyl peptidase from a hyperthermophile.
    Biochemistry, 51, 6089-6096 (2012).
  23. Furutani Y., Fujiwara K., Kimura T., Kikukawa T., Kandori H.
    Dynamics of Dangling Bonds of Water Molecules in pharaonis Halorhodopsin during Chloride Ion Transportation
    J.Phys.Chem.Lett., 3, 2964-2969 (2012).
  24. Reissig L., Iwata T., Kikukawa T., Demura M., Kamo N., Kandori H., Sudo Y.
    Influence of halide binding on the hydrogen bonding network in the active site of Salinibacter sensory rhodopsin I.
    Biochemistry, 51, 8802-8813 (2012).
  25. Tamogami J., Kikukawa T., Nara T., Shimono K., Demura M., Kamo N.
    Photoinduced proton release in proteorhodopsin at low pH: the possibility of a decrease in the pK(a) of Asp227.
    Biochemistry, 51, 9290-9301 (2012).
  26. Tsukamoto T., Kikukawa T., Kurata T., Jung KH., Kamo N., Demura M.
    Salt bridge in the conserved His-Asp cluster in Gloeobacter rhodopsin contributes to trimer formation.
    FEBS Lett., 587, 322-327 (2013).
  27. Hayashi S., Tamogami J., Kikukawa T., Okamoto H., Shimono K., Miyauchi S., Demura M., Nara T., Kamo N.
    Thermodynamic parameters of anion binding to halorhodopsin from Natronomonas pharaonis by isothermal titration calorimetry
    Biophysical Chemistry, 172, 61-67 (2013).
  28. Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K.
    Crystal Structure of Enzyme CapF of Staphylococcus aureus Reveals a Unique Architecture Composed of Two Functional Domains.
    Biochem J. 443, 671-680 (2012)
  29. Ui, M., Tanaka, Y., Araki, Y., Wada, T., Takei, T., Tsumoto, K., Endo, S., and Kinbara, K.
    Application of photoactive yellow protein as a photoresponsive module for controlling hemolytic activity of staphylococcal α-hemolysin
    Chem. Commun. 48, 4737-4739 (2012)
  30. Tsukamoto, K., Arimitsu, H., Ochi, S., Nakamura, K., Tanaka, Y., Nuemket, N., Taniguchi, K., Kozaki, S., and Tsuji, T.
    P19 embryonal carcinoma cells exhibit high sensitivity to botulinum type C and D/C mosaic neurotoxins.
    Microbiol. and Immunol.56, 664-672 (2012)
  31. Kita, S., Tanaka, Y., Hirano, N., Kimura, S., Suzuki, T., Suzuki, T., Yao, M., and Tanaka. I.
    Crystal structure of a putative methyltransferase SAV1081 from Staphylococcus aureus.
    Protein & Pept. Lett. 20, 530-537(2013)
  32. Kumeta H., Ogura K., Nishimiya Y., Miura A., Inagaki F., Tsuda S.
    NMR structure note: a defective isoform and its activity-improved variant of a type III antifreeze protein from Zoarces elongates Kner.
    Journal of Biomolecular NMR 55, 225-230 (2013)

Books etc

  1. Liljas A., Liljas L., Piskur J., Lindblom G., Nissen P., Kjeldgaard M. 著
    田中勲、三木邦夫 訳
    『構造生物学』
    Textbook of Structural Biology
    化学同人（2012年9月20日）

Conference Activities & Talks

(Invited talk)

  1. August 2012
    Lyon, France
    XXVth International Conference on　Magnetic Resonance in Biological Systems
    NMR-based drug discovery utilizing paramagnetic lanthanide probe.
    T Saio., K Ogura., K Shimizu., M Yokochi., Fuyuhiko Inagaki.
  2. October, 2012
    Sapporo, Japan
    The 10th International Symposium for Future Drug Discovery and Medical Care -Frontiers of Interdisciplinary Research in Medicine-
    Structure-based drug discovery in Hokkaido University
    Tanaka I.

(Oral presentation)

  1. October, 2012
    Osaka, Japan
    Towards Comprehensive Understanding of Immune Dynamism 2012
    Structural Biology of Innate Immunity.
    Fuyuhiko INAGAKI., Daron STANDLEY.

Invited talk (in Japan)

  1. 2012年10月
    仙台市
    平成24年度日本結晶学会年会
    結晶場を利用した阻害剤設計
    田中勲
  2. 2012年9月
    名古屋市
    第50回日本生物物理学会年会
    Structure and Molecular Function of Halorhodopsin
    出村　誠
  3. 2012年10月
    東京都
    日本分光学会NMR分光部会集中講義
    Pseudo Contact Shiftが生み出す構造情報とその取り扱い
    小椋賢治
  4. 2013年1月
    札幌市
    第19回未来創薬・医療イノベーションセミナー
    常磁性NMR法の創薬への応用
    小椋賢治
  5. 2013年3月
    高知市
    高知大学DCセミナー
    タンパク質NMRの新展開〜ダイナミクスと創薬〜
    小椋賢治

Patent

なし