Laboratories
Biomolecular Characterization Team
Naoshi DOHMAE
Team Leader
Naoshi DOHMAE (Ph.D.)
mail Click

Research Areas

This team is engaged in structural characterization of biological molecules and in development of methodology for analysis of them to elucidate biological phenomena. Proteins in particular cause the biological phenomena and have various biological activities. Investigation of protein structures helps us to elucidate a mechanism of the biological activities, regulation of the activities, or gene functions. We support biological researchers by developing equipment and analytical methods and managing them, or giving advice on methodologies. A qualitative identification of small amount of proteins becomes easy with the development of the mass spectrometry, the excellent database, and the search program of it. The structural analysis and quantitative analysis of proteins with unknown modification or sequence is, however, still difficult. We are wrestling with development of new characterization methods for such proteins by combining sophisticated mass spectrometry with chemical methods. Our activities include mass spectrometry, protein chemical analyses, ultracentrifugal analysis, and x-ray analysis. We also established mail-in system with RIKEN SPring-8 center to deliver protein crystals prepared in Wako campus.

Research Subject

  1. Development and application of analytical methods for structural details on biological molecules
  2. Development of quantitative analysis of biomolecules
  3. Studies on structural biology and its related technologies
  4. RNA mass spectrometry

Related links

  1. RIKEN Advanced Science Institute Website_Laboratories PageNew Window
  2. Individual Website Laboratory PageNew Window

Press release

Octorber 06,2010
First-ever system for automatic protein hydrolysis developed using solid acid catalyst
April 16, 2007
Bioarchitect Research Group and Biomolecular Characterization Team in DRI produced contractile myofiber cells from myofibroblast by making use of intracellular stress.

RIKEN RESEARCH

April 10, 2009
Finding an opening
A detailed structural analysis reveals new insights into the operating mechanism of a protein pore New Window
August 10, 2007
A better way to make a muscle?
New revelations about how muscle tissue forms could help scientists develop more effective strategies for therapeutic tissue replacement New Window

List of Selected Publications

  1. Nishimasu H, Okudaira S, Hama K, Mihara E, Dohmae N, Inoue A, Ishitani R, Takagi J, Aoki J, Nureki O.:
    "Crystal structure of autotaxin and insight into GPCR activation by lipid mediators."
    Nat Struct Mol Biol., 18(2):205-12 (2011)
  2. Hamamoto R, Cho HS, Suzuki T, Dohmae N, Hayami S, Unoki M, Yoshimatsu M, Toyokowa G, Takawa M, Chen T, Kurash JK, Field H, Ponder BA, Nakamura Y.:
    "Demethylation of RB regulator MYPT1 by histone demethylase LSD1 promotes cell cycle progression in cancer cells."
    Cancer Res., 71(3):655-60 (2011)
  3. Masuda A, Dohmae N.:
    "Automated Protein Hydrolysis Delivering Sample to a Solid Acid Catalyst for Amino Acid Analysis."
    Anal Chem. , 82(21), 8939-45(2010)
  4. Kuraishi T, Nakagawa Y, Nagaosa K, Hashimoto Y, Ishimoto T, Moki T, Fujita Y, Nakayama H, Dohmae N, Shiratsuchi A, Yamamoto N, Ueda K, Yamaguchi M, Awasaki T, Nakanishi Y.:
    "Pretaporter, a Drosophila protein serving as a ligand for Draper in the phagocytosis of apoptotic cells."
    EMBO J., 28(24):3868-78 (2009)
  5. Arakawa T, Kawano Y, Katayama Y, Nakayama H, Dohmae N, Yohda M, Odaka M.:
    "Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification."
    J Am Chem Soc., 131(41):14838-43 (2009)
  6. Nishimura K, Okudaira H, Ochiai E, Higashi K, Kaneko M, Ishii I, Nishimura T, Dohmae N, Kashiwagi K, Igarashi K.:
    "Identification of proteins whose synthesis is preferentially enhanced by polyamines at the level of translation in mammalian cells."
    Int J Biochem Cell Biol., 41(11):2251-61 (2009)
  7. Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T.:
    "Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data."
    Nucleic Acids Res., 37(6):e47 (2009)
  8. Kurokawa K, Lee H, Roh KB, Asanuma M, Kim YS, Nakayama H, Shiratsuchi A, Choi Y, Takeuchi O, Kang HJ, Dohmae N, Nakanishi Y, Akira S, Sekimizu K, Lee BL.:
    "The Triacylated ATP Binding Cluster Transporter Substrate-binding Lipoprotein of Staphylococcus aureus Functions as a Native Ligand for Toll-like Receptor 2."
    J Biol Chem., 284(13):8406-11 (2009)
  9. Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K, Nureki O.:
    "Conformational transition of Sec machinery inferred from bacterial SecYE structures."
    Nature, 455(7215):988-91 (2008)
  10. Kawatani M, Okumura H, Honda K, Kanoh N, Muroi M, Dohmae N, Takami M, Kitagawa M, Futamura Y, Imoto M, Osada H.:
    "The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I."
    Proc. Natl. Acad. Sci. U. S. A., 105(33):11691-6 (2008)

Members

Principal Investigator

Naoshi DOHMAE
Team Head

Staff Scientist

Nobuhiro MORISHIMA
Senior Research Scientist
Hideyuki MIYATAKE
Senior Research Scientist
Hiroshi NAKAYAMA
Senior Research Scientist
Kowashi WATANABE
Senior Technical Scientist
Takehiro SUZUKI
Technical Scientist

Postdoctoral Fellow

Akiko MASUDA
ASI Technical Scientist