2013 : Protein Structure Hub

Publications

  1. Nakamura A., Nemoto T., Heinemann I.-U., Yamashita K., Sonoda T., Komoda K., Tanaka I., Soll D., Yao M.
    Structural basis of reverse nucleotide polymerization.
    Proc. Natl. Acad. Sci. USA, 110, 20970-20975 (2013)
  2. Yamashita K., Zhou Y., Tanaka I., Yao M.
    New model-fitting and model-completion programs for automated iterative nucleic acid refinement.
    Acta Cryst., D69, 1171-1179 (2013)
  3. Baba K., Tumuraya K., Tanaka I., Yao M., Uchiumi T.
    Molecular dissection of the silkworm ribosomal stalk complex: the role of multiple copies of the stalk proteins.
    Nucl. Acid Res., 41, 3635-3643 (2013)
  4. Tagami T., Yamashita K., Okuyama M., Mori H., Yao M., Kimura A.
    Molecular Basis for the Recognition of Long-chain Substrates by Plant α-Glucosidase.
    J. Biol. Chem., 288, 19296-19303 (2013)
  5. Hayashi T., Tanaka Y., Sakai N., Okada U., Yao M., Watanabe N., Tamura T., Tanaka I.
    SCO4008, a Putative TetR Transcriptional Repressor from Streptomyces coelicolor A3(2), Regulates Transcription of sco4007 by Multidrug Recognition.
    J. Mol. Biol., 425, 3289-3300 (2013)
  6. Matsumoto K., Tanaka Y., Watanabe T., Motohashi R., Ikeda K., Tobitani K., Yao M., Tanaka I., Taguchi S.
    Directed Evolution and Structural Analysis of NADPH-Dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) Reductase from Ralstonia eutropha Reveals Two Mutations Responsible for Enhanced Kinetics.
    Appl. Environ. Microbiol., 79, 6134-6139 (2013)
  7. Fujiwara T., Saburi W., Inoue S., Mori H., Matsui H., Tanaka I., Yao M.
    Crystal structure of Ruminococcus albus cellobiose 2-epimerase: Structural insights into epimerization of unmodified sugar.
    FEBS Lett., 587, 840-846 (2013)
  8. Hayashi T., Tanaka Y., Sakai N., Watanabe N., Tamura T., Tanaka I., Yao M.
    Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): Regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape.
    Biochem. Biophys. Res. Commun., 435, 28-33 (2013)
  9. Gai Z., Nakamura A., Tanaka Y., Hirano N., Tanaka I., Yao M.
    Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation.
    J. Synchrotron Rad., 20, 854-858 (2013)
  10. Shao X., Li C., Chen S., Yao K., Yao M.
    Functional two-dimensional organic-inorganic hybrid materials with regular peptides.
    Colloids and Surfaces A: Physicochem. Eng. Aspects, 424, 66-73 (2013)
  11. Sunagawa N., Fujiwara T., Yoda T., Kawano S., Satoh Y., Yao M., Tajima K., Dairi T.
    Cellulose complementing factor (Ccp) is a new member of the cellulose synthase complex (terminal complex) in Acetobacter xylinum.
    J. Biosci. Bioeng., 115, 607-612 (2013)
  12. Sugawara T., Yamashita D., Tanaka Y., Kaneko J., Kamio Y., Tanaka I., Yao M.
    Preliminary X-ray crystallographic study of staphylococcal α-haemolysin monomer.
    Acta Cryst., F69, 868-870 (2013)
  13. Chen M., Yu J., Tanaka Y., Tanaka M., Tanaka I., Yao M.
    Structure of dihydrouridine synthase C (DusC) from Escherichia coli.
    Acta Cryst., F69, 834-838 (2013)
  14. Komoda K., Narita M., Tanaka I., Yao M.
    Expression, purification, crystallization and preliminary X-ray crystallographic study of the nucleocapsid protein of Tomato spotted wilt virus.
    Acta Cryst., F69, 700-703 (2013)
  15. Srisucharitpanit K., Yao M., Chimnaronk S., Promdonkoy B., Tanaka I., Boonserm P.
    Crystallization and preliminary X-ray crystallographic analysis of the functional form of BinB binary toxin from Bacillus sphaericus.
    Acta Cryst., F69, 170-173 (2013)
  16. Yu J., Ogata D., Gai Z., Taguchi S., Tanaka I., Ooi T., Yao M.
    Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism.
    Acta Cryst., D70, 553-564 (2014)
  17. Matsui T., Han X., Yu J., Yao M., Tanaka I.
    Structural Change in FtsZ Induced by Intermolecular Interactions between Bound GTP and the T7 Loop.
    J. Biol. Chem., 289, 3501-3509 (2014)
  18. Fujiwara T., Saburi W., Matsui H., Mori H., Yao M.
    Structural Insights into the Epimerization of beta-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars.
    J. Biol. Chem., 289, 3405-3415 (2014)
  19. Asano N., Atsuumi H., Nakamura A., Tanaka Y., Tanaka I., Yao M.
    Direct interaction between EFL1 and SBDS is mediated by an intrinsically disordered insertion domain.
    Biochem. Biophys. Res. Commun., 443, 1251-1256 (2014)
  20. Miyafusa T., Caaveiro J.M., Tanaka Y., Tsumoto K.
    Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.
    FEBS Lett., 587, 3824-3830 (2013)
  21. Miyafusa T., Caaveiro J.M., Tanaka Y., Tanner M.E., Tsumoto K.
    Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
    Biosci. Rep., 33, 463-474 (2013)
  22. Kubo M., Nakashima S., Yamaguchi S., Ogura T., Mochizuki M., Kang J., Tateno M., Shinzawa-Itoh K., Kato K., Yoshikawa S.
    Effective pumping-proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system.
    J. Bio. Chem., 288, 30259-30269 (2013)
  23. Hirata K., Shinzawa-Itoh K., Yano N., Takemura S., Kato K., Hatanaka M., Muramoto K., Kawahara T., Tsukihara T., Yamashita E., Tono K., Ueno G., Hikima T., Murakami H., Inubushi Y., Yabashi M., Ishikawa T., Yamamoto M., Ogura T., Sugimoto H., Shen J-R., Yoshikawa S., Ago H.
    Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
    Nature Methods, 11, 734-736 (2014)
  24. Kushibiki T., Kamiya M., Aizawa T., Y. Kumaki, 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)
  25. Shibasaki K., Shigemura H. , Kikukawa T., Kamiya M., Aizawa T., Kawano K., Kamo N., Demura M.
    Role of Thr218 in the Light-Driven Anion Pump Halorhodopsin from Natronomonas pharaonis.
    Biochemistry, 52, 9257-9268 (2013)
  26. Asakura T., Suzuki Y., Nagano A., Knight D., Kamiya M., Demura M.
    Synthesis and Characterization of Water-soluble Silk Peptides and Recombinant Silk Protein containing Polyalanine, the Integrin Binding Site and Two Glutamic Acids at Each Terminal Site as a Possible Candidate for Use in Bone Repair Materials
    Biomacromolecules, 14, 3731-3741 (2013)
  27. Tsukamoto T., Li X., Morita H., Minowa T., Aizawa T., Hanagata N., Demura M.
    Role of S-palmitoylation on IFITM5 for the interaction with FKBP11 in osteoblast cells
    PLoS One, 8, e75831(2013)
  28. Tomisawa S., Hojo E., Umetsu Y., Ohki S., Kato Y., Miyazawa M., Mizuguchi M., Kamiya M., Kumaki Y., Kikukawa T., Kawano K., Demura M., Aizawa T.
    Overexpression of an antimicrobial peptide derived from C. elegans using an aggregation-prone protein coexpression system
    AMB Express, 3, 45 (2013).
  29. Tomisawa S., Abe C., Kamiya M., Kikukawa T., Demura M., Kawano K., Aizawa T.
    A new approach to detect small peptides clearly and sensitively by Western blotting using a vacuum-assisted detection method
    Biophysics, 9, 79-83 (2013).
  30. Nakamura T., Aizawa T., Kariya R., Okada S., Demura M., Kawano K., Makabe K., Kuwajima K.
    Molecular mechanisms of the cytotoxicity of human alpha-lactalbumin made lethal to tumor cells (HAMLET) and other protein-oleic acid complexes
    J. Biol. Chem., 288, 14408-14416 (2013).
  31. 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).
  32. Tsukamoto T., Kikukawa T., Kurata T., Jung K.H., 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).
  33. Kumeta H, Sakakibara H, Enokizono Y, Ogura K, Horiuchi M, Matsumoto M, Seya T, Inagaki F.
    The N-terminal domain of TIR domain-containing adaptor molecule-1, TICAM-1.　
    J Biomol NMR. 58, 227-230 (2014)
  34. Enokizono Y, Kumeta H, Funami K, Horiuchi M, Sarmiento J, Yamashita K, Standley DM, Matsumoto M, Seya T, Inagaki F
    Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling.
    Proc Natl Acad Sci U S A., 110, 19908-19913 (2013)
  35. Tamura N., Oku M., Ito M., Noda NN., Inagaki F., Sakai Y.: Atg18
    phosphoregulation controls organellar dynamics by modulating its phosphoinositide-binding activity.
    J Cell Biol., 202, 685-698 (2013)
  36. Sekiguchi M., Kobashigawa Y., Moriguchi H., Kawasaki M., Yuda M, Teramura T., Inagaki F.
    High-Throughput Evaluation Method for Drug Association with Pregnane X Receptor (PXR) Using Differential Scanning Fluorometry.
    J Biomol Screen., 18 ,1084-1091 (2013)
  37. Tsuganezawa K., Shinohara Y., Ogawa N., Tsuboi S., Okada N., Mori M., Yokoyama S., Noda NN., Inagaki F., Ohsumi Y., Tanaka A
    Two-Colored Fluorescence Correlation Spectroscopy Screening for LC3-P62 Interaction Inhibitors.
    J Biomol Screen., 18, 1103-1109 (2013)
  38. Ogura K., Kobashigawa Y., Saio T., Kumeta H., Torikai S., Inagaki F.
    Practical applications of hydrostatic pressure to refold proteins from inclusion bodies for NMR structural studies.
    Protein Eng Des Sel., 26, 409-416 (2013)
  39. Sakoh-Nakatogawa M., Matoba K., Asai E., Kirisako H., Ishii J., Noda NN., Inagaki F., Nakatogawa H., Ohsumi Y.
    Atg12-Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site.
    Nat Struct Mol Biol., 20 ,433-439 (2013)

Books etc

  1. 出村誠、菊川峰志、加茂直樹
    ハロロドプシンの構造と分子機能解析
    『オプトジェネティクス（光遺伝学）-光工学と遺伝子による行動制御技術の最前線-』 , エヌ・ティー・エス, 24-33(2013)
  2. 小橋川敬博、稲垣冬彦
    構造が解き明かすがんおよび自己免疫疾患に関わるユビキチリンリガーゼCblのリン酸化による活性化機構
    生化学　85（9）, 794-798

Conference Activities & Talks

(Invited talk)

  1. November 2013
    Okinawa, Japan
    The 2nd OIST CCP4 Workshop on Structure Solution
    LAFIRE: Automated refinement program for protein crystallography
    Yao M.
  2. March 2014
    Sapporo, Japan
    International Life-Science Symposium
    Macromolecular crystallography on life science
    Yao M.
  3. Octover 2013
    Brisbane, Australia
    Brisbane Convention and Exhibition Centre
    Ligand-driven conformational changes of MurD characterized by paramagnetic NMR, APNMR5（5th Asia-Pacific NMR Symposium in　conjunction with ANZMAG　2013）
    Inagaki F.

Invited talk (in Japan)

  1. 2013年5月
    つくば市
    第1回タンパク質X線溶液散乱講習会
    結晶解析と溶液散乱による相関解析1
    姚　閔
  2. 2013年10月
    京都市
    第51回日本生物物理学会年会
    結晶構造解析と小角散乱の併用
    Applications of SAXS in structural analysis with macromolecular crystallography
    姚　閔
  3. 2013年12月
    東京都千代田区
    先端計測分析技術・機器開発プログラム 新技術説明会
    ペプチド性タグを利用したタンパク質結晶化の技術
    姚　閔
  4. 2013年12月
    神戸市
    創薬等支援技術基盤プラットフォーム 平成25年度例会
    創薬等支援のためのタンパク質立体構造解析総合技術基盤プラットフォームによる支援と高度化
    田中　勲
  5. 2013年12月
    吹田市
    大阪大学蛋白質研究所セミナー －量子ビームの連携利用に向けた新しいタンパク質結晶学－
    X線・中性子の融合利用によるアミド基転移酵素のアンモニア輸送制御機構の解明
    姚　閔
  6. 2013年8月
    豊中市
    大阪大学蛋白質研究所セミナー 　世界をリードするNMRとその科学技術・社会へのインパクト
    北海道先端 NMR ファシリティの共用促進
    出村 誠
  7. 2014年3月
    札幌市
    第1回　北海道大学 オープンファシリティシンポジウム ～最先端共用機器による社会貢献とイノベーション創出～
    北海道先端 NMR ファシリティの共用促進
    出村 誠
  8. 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
  9. 2013年12月
    神戸市
    第36回日本分子生物学会年会
    金属イオンを利用した古くて新しい常磁性 NMR 解析
    稲垣　冬彦
  10. 2013年11月
    札幌市
    2013年度合同シンポジウム（生命現象の分子レベルでの解明）
    スルメイカ由来巨大ヘモシアニンの構造生物学
    加藤公児

Patent

なし