2014 : Protein Structure Hub

Publications

  1. Yamashita D., Sugawara T., Takeshita M., Kaneko J., Kamio Y., Tanaka I., Tanaka Y., Yao M.
    Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins
    Nature Commun. 5, 4897 (2014)
  2. Liu Y., Nakamura A., Nakazawa Y., Asano N., Ford K-A., Hohn M-J., Tanaka I., Yao M., Söll D.
    Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea
    Proc. Natl. Acad. Sci. USA. 111, 10520-10525 (2014)
  3. Zheng A., Yu J., Yamamoto R., Ose T., Tanaka I., Yao M.
    X-ray structures of eIF5B and the eIF5B-eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A
    Acta Cryst. D 70, 3090-3098 (2014)
  4. Shinoda A., Tanaka Y., Yao M., Tanaka I.
    Anchoring protein crystals to mounting loops with hydrogel using inkjet technology
    Acta Cryst. D 70, 2794-2799 (2014)
  5. Ito K., Honda T., Suzuki T., Miyoshi T., Murakami R., Yao M., Uchiumi T.
    Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1α
    Nucl. Acid Res. 42, 14042-14052 (2014)
  6. Ito S., Horikawa S., Suzuki T., Kawauchi H., Tanaka Y., Suzuki T., Suzuki T.
    Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible for N4-Acetylcytidine Formation in 18S RIbosomal RNA (rRNA)
    J. Biol. Chem. 289, 35724-35730 (2014)
  7. Hayashi T., Tanaka Y., Sakai N., Okada U., Yao M., Watanabe N., Tamura T., Tanaka I.
    Structural and genomic DNA analysis of the putative TetR transcriptional repressor SCO7518 from Streptomyces coelicolor A3(2)
    FEBS Lett. 588, 4311-4318 (2014)
  8. Srisucharitpanit K., Yao M., Promdonkoy B., Chimnaronk S., Tanaka I., Boonserm P.
    Crystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus
    Proteins 82, 2703-2712 (2014)
  9. Asano N., Nakamura A., Komoda K., Kato K., Tanaka I., Yao M.
    Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2-Rrs1 complex
    Acta Cryst. F 70, 1649-1652 (2014)
  10. Suzuki T., Yamashita K., Tanaka Y., Tanaka I., Yao M.
    Crystallization and preliminary X-ray crystallographic analysis of a bacterial Asn-transamidosome
    Acta Cryst. F 70, 790-793 (2014)
  11. Shen X., Saburi W., Gai Z-Q., Komoda K., Yu J., Ojima-Kato T., Kido Y., Matsui H., Mori H., Yao M.
    Crystallization and preliminary X-ray crystallographic analysis of alpha-glucosidase HaG from Halomonas sp. strain H11
    Acta Cryst. F 70, 464-466 (2014)
  12. Ushijima Y., Ohniwa R-L., Maruyama A., Saito S., Tanaka Y., Morikawa K.
    Nucleoid compaction by MrgAAsp56Ala/Glu60Ala does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophage
    FEMS Microbiol. Letters 360, 144-151 (2014)
  13. Suzuki T., Nakamura A., Kato K., Söll D., Tanaka I., Sheppard K., Yao M.
    Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
    Proc. Natl. Acad. Sci. USA. 112, 382-387 (2015)
  14. Tagami T., Yamashita K., Okuyama M., Mori H., Yao M., Kimura A.
    Structural Advantage of Sugar Beet α-Glucosidase to Stabilize the Michaelis Complex with Long-chain Substrate
    J. Biol. Chem. 290, 1796-1803 (2015)
  15. Kobayashi M., Saburi W., Nakatsuka D., Hondoh H., Kato K., Okuyama M., Mori H., Kimura A., Yao M.
    Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase
    FEBS Lett. 589, 484-489 (2015)
  16. Sone T., Haraguchi Y., Kuwahara A., Ose T., Takano M., Abe A., Tanaka M., Tanaka I., Asano K.
    Structural Characterization Reveals the Keratinolytic Activity of an Arthrobacter nicotinovorans Protease
    Protein Pept. Lett. 22, 63-72 (2015)
  17. Tomisawa S., Sato Y., Kamiya M., Kumaki Y., Kikukawa T., Kawano K., Demura M., Nakamura K., Ayabe T., Aizawa T.
    Efficient production of a correctly folded mouse a-defensin, cryptdin-4, by refolding during inclusion body solubilization
    Protein Expression and Purification, accepted (2014)
  18. Tamogami J., Iwano K., Matsuyama A., Kikukawa T., Demura M., Nara T., Kamo N.
    The effects of chloride ion binding on the photochemical properties of sensory rhodopsin II from Natronomonas pharaonis
    Journal of Photochemistry and Photobiology B: Biology, 141, 192-201 (2014)
  19. Tsukamoto T., Demura M., Sudo Y.
    Irreversible Trimer to Monomer Transition of Thermophilic Rhodopsin upon Thermal Stimulation
    Journal of Physical Chemistry B, 118, 12383-12394 (2014)
  20. Kushibiki T., Kamiya M., Aizawa T., Kumaki Y., Kikukawa T., Mizuguchi M., Demura M., Kawabata S.-I., Kawano K.
    Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide
    Biochim. Biophys. Acta – Proteins and Proteomics, 1844, 527-534 (2014)
  21. Fujioka Y., Suzuki SW., Yamamoto H., Kondo-Kakuta C., Kimura Y., Hirano H., Akada R., Inagaki F., ohsumi Y., Noda NN.
    Structural basis of starvation-induced assembly of the autophagy intiation complex.
    Nat Struct Mol Biol. 6, 513-521 (2014)
  22. Noda NN., Inagaki F.
    Mechanisms of Aautophagy.
    Annu Rev Biophys. [Epub ahead of print] (2015)

Books etc

  1. 田中良和、陳明皓、姚閔
    tRNAジヒドロウリジン合成酵素の分子機構
    生化学 86, 395-399 (2014)
  2. 坂井直樹、田中勲
    タンパク質結晶学と創薬
    現代化学 522, 54-55 (2014)
  3. 田中良和
    黄色ブドウ球菌の2成分性膜孔形成毒素γヘモリジンの膜孔形成メカニズム 失敗から明らかになった毒素の戦略
    化学と生物 53, 136-137 (2015)
  4. Kikukawa T., Kamo N., Demura M.
    Photochemistry of Halorhodopsin in Optogenetics (Eds. Hideki Kandori, Hiromu Yawo, Amane Koizumi)
    Springer., in press (2015)
  5. 出村誠
    光のエネルギー利用・ハロロドプシン『光と生命の事典』(真嶋哲朗、飯野盛利、七田好則、藤堂剛 編)
    朝倉書店、印刷中 (2014)

Conference Activities & Talks

(Invited talk)

  1. October 2014
    Shiga, Japan
    16th International Conference on Retinal Protein (ICRP2014)
    Analyses of Cl–pumping photocycle of halorhodopsin
    Demura M.
  2. August 2014
    Hyatt Regency Dalla
    ICMRBS 2014
    Paramagnetic lanthanide probe visualizes change of domain orientation induced by substrate and inhibitor binding and is a useful tool for drug screening.
    Inagaki F.

Invited talk (in Japan)

  1. 2014年9月
    札幌市
    第52回日本生物物理学会年会
    対称性を持つタグを利用したタンパク質結晶化確率の向上
    (Use of symmetric tag to increase the probability of protein crystallization)
    姚 閔
  2. 2014年11月
    東京都文京区
    平成26年度日本結晶学会
    タンパク質結晶学方法論の開発とその応用
    田中 勲
    (平成26年度日本結晶学会西川賞受賞講演)
  3. 2015年2月
    東京都千代田区
    PDIS最先端セミナー「創薬につなぐ日本の創薬基盤技術 構造生物学とゲノム科学の最前線はここまで来た」
    (非標識タンパク質構造解析法のための)結晶マウント技術の開発と薬剤探索自動化への応用
    田中 勲
  4. 2015年3月
    つくば市
    第3回物構研サイエンスフェスタ・第6回MLFシンポジウム・第32回PFシンポジウム
    RNAを鋳型依存的に3’→5’方向へ伸長させる酵素の分子機構
    (Molecular base of 3’→5’ nucleotide addition enzyme)
    姚 閔
  5. 2015年1月
    東京都
    東海大学 テニュアトラック制度シンポジウム
    他大学の優れた取組1
    出村 誠
  6. 2014年3月
    札幌市
    2013年度 遠友学舎・炉辺談話
    『サイエンスビジョン:生命融合科学のアプローチ』
    出村 誠
  7. 2014年9月
    東京都
    ISN Special Conference 2014
    Activation mechanism of FGFRI receptor by phosphorylation.
    稲垣 冬彦

Patent

  1. 特許出願(PCT/JP2015/059332)
    「生物学的試料をハイドロゲルで高速固定する方法およびそのための装置」
    発明者:田中勲、篠田晃、姚閔、田中良和
  2. 特許出願(PCT/JP2014/062215)
    「結晶化促進ポリペプチド」
    発明者:姚閔、薦田圭介、于健、田中良和