Centers & Labs

RIKEN Center for Sustainable Resource Science

Biomolecular Characterization Unit

Unit Leader: Naoshi Dohmae (Ph.D.)
Naoshi  Dohmae(Ph.D.)

Our unit provides high quality structural characterization methods to the field of biological science, aiming to further understand the mechanism and action of biological molecules. We manage specialized and technical instruments including protein chemical analyses, mass spectrometry. Our challenge to research, develop and fine-tune novel characterization methods for biological molecules, is an endless yet rewarding process.

Main Research Field

Biology

Related Research Fields

Environmental science / Chemistry / Biological Sciences / Agricultural sciences / Medicine, dentistry, and pharmacy

Research Subjects

  • Development and application of analytical methods for structural details on biological molecules
  • Development of quantitative analysis of biomolecules
  • Identification and characterization of RNA by mass spectrometry

Selected Publications

  1. Yanagisawa T, Takahashi H, Suzuki T, Masuda A, Dohmae N, Yokoyama S.:
    "Neisseria meningitidis Translation Elongation Factor P and Its Active-Site Arginine Residue Are Essential for Cell Viability."
    PLoS ONE11, e0147907 (2015)
  2. Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M.:
    "Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile."
    Angew Chem Int Ed Engl54,10763-10767 (2015)
  3. Huang C, Harada Y, Hosomi A, Masahara-Negishi Y, Seino J, Fujihira H, Funakoshi Y, Suzuki T, Dohmae N, Suzuki T.:
    "Endo-beta-N-acetylglucosaminidase forms N-GlcNAc protein aggregates during ER-associated degradation in Ngly1-defective cells."
    Proc Natl Acad Sci U S A112,1398-1403 (2015)
  4. Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, Tsukazaki T, Nureki O.:
    "Structural basis of Sec-independent membrane protein insertion by YidC."
    Nature509,516-520 (2014)
  5. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O.:
    "Crystal structure of cas9 in complex with guide RNA and target DNA."
    Cell156,935-949 (2014)
  6. Yamagata K, Goto Y, Nishimasu H, Morimoto J, Ishitani R, Dohmae N, Takeda N, Nagai R, Komuro I, Suga H, Nureki O.:
    "Structural Basis for Potent Inhibition of SIRT2 Deacetylase by a Macrocyclic Peptide Inducing Dynamic Structural Change."
    Structure22,345-352 (2014)
  7. Staals RH, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJ, Yonekura K, van der Oost J, Shinkai A.:
    "Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus."
    Mol Cell52,135-145 (2013)
  8. Unoki M, Masuda A, Dohmae N, Arita K, Yoshimatsu M, Iwai Y, Fukui Y, Ueda K, Hamamoto R, Shirakawa M, Sasaki H, Nakamura Y.:
    "Lysyl 5-hydroxylation, a novel histone modification, by Jumonji domain containing 6 (JMJD6)."
    J Biol Chem288,6053-6062 (2013)
  9. Nishizawa T, Kita S, Maturana AD, Furuya N, Hirata K, Kasuya G, Ogasawara S, Dohmae N, Iwamoto T, Ishitani R, Nureki O.:
    "Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger."
    Science341,168-172 (2013)
  10. Masuda A, Dohmae N.:
    "Examination of an absolute quantity of less than a hundred nanograms of proteins by amino acid analysis."
    Anal Bioanal Chem405,8073-8081 (2013)

Lab Members

Principal Investigator

Naoshi Dohmae
Unit Leader

Core Members

Hiroshi Nakayama
Senior Research Scientist
Kowashi Watanabe
Senior Technical Scientist
Takehiro Suzuki
Senior Technical Scientist
Hogeun Kwak
Postdoctoral Researcher
Masami Koike
Technical Staff I

Contact information

Bioscience Building,
2-1 Hirosawa,
Wako, Saitama
351-0198, Japan

Email: dohmae [at] riken.jp

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