2011 : Protein Structure Hub

Publications

  1. Kondo-Okamoto N., Noda NN, Suzuki SW., Nakatogawa H., Takahashi I., Matsunami M., Hashimoto A., Inagaki F., Ohsumi Y., Okamoto K.
    Autophagy-related protein 32 acts as an autophagic degron and directly initiates mitophagy.
    J Biol Chem., [Epub ahead of print] (2011)
  2. Ogura K., Kumeta H., Takahasi K., Kobashigawa Y., Yoshida R, Itoh H., Yazawa M, Inagaki F.
    Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin.
    Genes Cells.,17, 159-172 (2011)
  3. Kobashigawa Y., Tomitaka A., Kumeta H., Noda NN., Yamaguchi M., Inagaki F.
    Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b.
    Proc Natl Acad Sci U S A., 108 , 20579-20584 (2011)
  4. Noda NN., Satoo K., Fujioka Y., Kumeta H., Ogura K., Nakatogawa H., Ohsumi Y., Inagaki F.
    Structural basis of atg8 activation by a homodimeric e1, atg7.
    Mol Cell., 44, 462-475 (2011)
  5. Saio T., Ogura K, Shimizu K., Yokochi M., Burke TR Jr., Inagaki F.
    An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe.
    J Biomol NMR., 51, 395-408 (2011)
  6. Sekiguchi M., Kobashigawa Y., Kawasaki M., Yokochi M., Kiso T., Suzumura KI., Mori K., Teramura T., Inagaki F.
    An evaluation tool for FKBP12-dependent and -independent mTOR inhibitors using a combination of FKBP-mTOR fusion protein, DSC and NMR.
    Protein Eng Des Sel., 24, 811-817(2011)
  7. Yamashita K., Kawai Y., Tanaka Y., Hirano N., Kaneko J., Tomita N., Ohta M., Kamio Y., Yao M., Tanaka I.
    Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components.
    Proc. Natl. Acad. Sci. USA, 108, 17314-17319 (2011)
  8. Yu F., Tanaka Y., Yamashita K., Suzuki T., Nakamura A., Hirano N., Suzuki T., Yao M., Tanaka I.
    Molecular basis of dihydrouridine formation on tRNA.
    Proc. Natl. Acad. Sci. USA, 108, 19593-19598 (2011)
  9. Yamane J., Yao M., Zhou Y., Hiramatsu Y., Fujiwara K., Yamaguchi T., Yamaguchi H., Togame H., Tsujishita H., Takemoto H., Tanaka I.
    In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities.
    J. Appl. Cryst., 44, 798-804 (2011)
  10. Nuemket N., Tanaka Y., Tsukamoto K., Tsuji T., Nakamura K., Kozaki S., Yao M., Tanaka I.
    Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: Insight into the ganglioside binding mechanism.
    Biochem. Biophys. Res. Commun., 411, 433-439(2011)
  11. Ariyawutthiphan O., Ose T., Tsuda M., Gao Y-G., Yao M., Minami A., Oikawa H., Tanaka I.
    Crystallization and preliminary X-ray crystallographic study of a methyltransferase involved in 2-methylisoborneol biosynthesis in Streptomyces lasaliensis.
    Acta Cryst., F67, 417-420 (2011)
  12. Yu F., Tanaka Y., Yamamoto S., Nakamura A., Kita S., Hirano N., Tanaka I., Yao M.
    Crystallization and preliminary X-ray crystallographic analysis of dihydrouridine synthase from Thermus thermophilus and its complex with tRNA.
    Acta Cryst., F67, 685-688 (2011)
  13. Zheng A., Yamamoto R., Sokabe M., Tanaka I., Yao M.
    Crystallization and preliminary X-ray crystallographic analysis of eIF5BΔN and the eIF5BΔN-eIF1AΔN complex.
    Acta Cryst., F67, 730-733 (2011)
  14. Kawaguchi A., Ose T., Yao M., Tanaka I.
    Crystallization and preliminary X-ray structure analysis of human ribosomal protein L30e.
    Acta Cryst., F67, 1516-1518 (2011)
  15. Nomura N., Honda T., Baba K., Naganuma T., Tanzawa T., Arisaka F., Noda M., Uchiyama S., Tanaka I., Yao M., Uchiumi T.
    Archaeal ribosomal stalk protein interacts with translation factors in a nucleotide-independent manner via its conserved C terminus.
    Proc. Natl. Acad. Sci. USA, 109, 3748-3753 (2012)
  16. Dai G., Zhang Y., Tamogami J., Demura M., Kamo N, Kandori H., Iwasa T.
    An amino acid residue (S201) in the retinal binding pocket regulates the photoreaction pathway of phoborhodopsin
    Biochemistry., 50, 7177-7183 (2011)
  17. Yamashita Y., Kikukawa T., Tsukamoto T., Kamiya M., Aizawa T., Kawano K., Miyauchi S., Kamo N., Demura M.
    Expression of salinarum halorhodopsin in Escherichia coli cells: solubilization in the presence of retinal yields the natural state
    Biochim. Biophys. Acta., 1808, 2905-2912, (2011)
  18. Asakura T., Nishi H., Nagano A., Yoshida A., Nakazawa Y., Kamiya M., Demura M.
    NMR analysis of the fibronectin cell-adhesive sequence, Arg-Gly-Asp, in a recombinant silk-like protein and a model peptide
    Biomacromolecules., 12, 3910-3916 (2011)
  19. Tamogami J., Kikukawa T., Ikeda Y., Demura M., Nara T., Kamo N.
    Photo-induced Bleaching of Sensory Rhodopsin II (Phoborhodopsin) from Halobacterium salinarum by Hydroxylamine: Identification of the Responsible Intermediates
    Journal of Photochemistry and Photobiology B: Biology., 106, 87-94 (2012)
  20. Ooi T., Ogata D., Matsumoto K., Nakamura G., Yu J., Yao M., Kitamura M., Taguchi S.
    Flavin-binding of azoreductase: Direct evidences for dual-binding property of apo-azoreductase with FMN and FAD.
    J. Mol. Catal. B: Enzymatic, 74, 204-208 (2012)
  21. Moriwaki, Y., Caaveiro, JM., Tanaka, Y., Tsutsumi, H., Hamachi, I., Tsumoto K.
    Molecular Basis of Recognition of Antibacterial Porphyrins by Heme-Transporter IsdH-NEAT3 of Staphylococcus aureus.
    Biochemistry. 50, 7311-7320 (2011)
  22. Murota K., Hagiwara-Komoda Y., Komoda K., Onouchi H., Ishikawa M., Naito S.
    Arabidopsis cell-free extract, ACE, a new in vitro translation system derived from Arabidopsis callus cultures.
    Plant Cell Physiol., 52, 1443-1453(2011)

Books etc

  1. 出村　誠
    広がるNMRの世界―40人の研究者からの熱いメッセージ―
    コロナ社, 42-45（2011）
  2. Kikukawa T., Tamogami J., Shimono J., Demura M., Nara T., Kamo N.
    Photo-induced Proton Transfers of Microbial Rhodopsins in Photochemistry
    InTech, (2011)

Conference Activities & Talks

(Invited talk)

  1. September 2011
    Himeji, Japan
    プロテイン・アイランド・松山 国際シンポジウム2011
    Structural and Functional Studies of Proteins by NMR
    Fuyuhiko Inagaki
  2. October 2011
    Beijing, China
    17th International Biophysics Congress（IUPAB）
    Structural biology of autophagy
    Fuyuhiko Inagaki
  3. March 2012
    Sapporo, Japan
    Sapporo Symposium on Advanced Protein Crystallography
    LAFIRE: Automated refinement software for biomacromolecular crystallography
    Yamashita K., Zhou Y., Yao M., Tanaka I.
  4. January 2012
    Sapporo, Japan
    Japan-Australia Symposium on Plant Sciences for Agriculture (JAS2012)
    Crystal structure of pore-forming toxin from Staphylococcus aureus – An example of the utility of crystal structure analysis –
    Tanaka Y., Yamashita K., Kawai Y., Kaneko J., Tomita N., Ohta M., Kamio Y., Yao M., and Tanaka I.
  5. November 2011
    Sendai, Japan
    The Eighth International Conference on Flow Dynamics (ICFD2011)
    Crystal Structure of the Octameric Pore of Staphylococcal gamma-hemolysin
    Tanaka Y., Yamashita K., Kawai Y., Hirano N., Kaneko J., Tomita N., Ohta M., Kamio Y., Yao M., and Tanaka I.

(Oral presentation)

  1. May 2011
    Toront,Canada
    International Conference on Structural Genomics
    Structural biology of Selective Autophagy
    Fuyuhiko Inagaki
  2. June 2011
    Kyoto, Japan
    The 16th Annual Meeting of the RNA Society and The 13th Annual Meeting of the RNA Society of Japan (RNA2011)
    Crystal structure of dihydrouridine synthase in complex with RNA reveals its tRNA recognition and reaction mechanisms
    Tanaka Y., Yu F., Yamashita K., Nakamura A., Suzuki T., Hirano N., Suzuki T., Yao M., Tanaka I.
  3. August 2011
    Madrid, Spain
    XXII Congress and General Assembly of the International Union of Crystallography (IUCr2011)
    LAFIRE: Automated refinement software for biomacromolecular crystallography
    Yamashita K., Zhou Y., Yao M., Tanaka I.
  4. March 2012
    Sapporo, Japan
    IGP International Symposium 2012 for Young Researchers in Life-Sciences
    Structural Determination of the Mosquite-Larvicidal Binary Toxin from Bacillus sphaericus
    Srisucharitpanit K., Yao M., Tanaka I., Boonserm P.
  5. March, 2012
    Sapporo, Japan
    9th Japan-Korea Bilateral Symposium on Biological NMR
    Solid-State NMR Study of Seven-Transmembrane Microbial Rhodopsin
    Tamaki H, Kido H, Higuchi M, Egawa A, Kamiya M, Kikukawa T, Aizawa T, Kawano K, Fujiwara T, Demura M.

Invited talk (in Japan)

  1. 2011年6月
    吹田市
    第11回日本蛋白質科学会年会
    構造細胞生物学研究を行う上で有用なNMR ツールの開発と応用
    稲垣 冬彦
  2. 2011年9月
    姫路市
    第49回日本生物物理学会年会
    リン酸化により誘起されるタンパク質の構造変化と生物学的意義
    稲垣 冬彦
  3. 2011年11月
    横浜市
    平成23年度日本分光学会年次講演会
    Lanthanide probe method and its application to ligand screening
    稲垣 冬彦
  4. 2011年7月
    東京都文京区
    第58回毒素シンポジウム
    黄色ブドウ球菌由来2成分性毒素の膜孔構造
    田中良和，山下恵太郎，河合優香，平野なぎ沙，金子淳，神尾好是，姚閔，田中勲
  5. 2012年3月
    吹田市
    大阪大学蛋白質研究所セミナー
    化学反応の足場としての蛋白質結晶の利用
    田中勲
  6. 2011年9月
    宮崎市
    宮崎大学自然共生技術センター講演会・セルロース学会西部支部共催講演会
    X線結晶構造解析によるバクテリアセルロース合成機構の研究
    姚閔
  7. 2012年3月
    つくば市
    北海道大学・高エネルギー加速器研究機構 連携シンポジウム
    北大構造生物学研究室の放射光利用
    姚閔
  8. 2011年9月
    仙台市
    日本化学会東北支部　化学系学協会東北大会
    黄色ブドウ球菌由来巨大蛋白質 Ebh の全体構造に関する研究
    田中良和

Patent

なし