Biomolecular Characterization Team

Team Head

Naoshi Dohmae

  • Ph.D.
  • Naoshi Dohmae
  • Brief resume
    1993
    Ph.D., Saitama University
    1993
    Technical Scientist, Division of Biomolecular Characterization, RIKEN
    2003
    Team Leader, Biomolecular Characterization Team, RIKEN
    2006
    Visiting Associate Professor, Saitama University (-current)
    2007
    Sub-team Leader, Sub-team for Nano Protein Science, RIKEN
    2008
    Team Head, Biomolecular Characterization Team, RIKEN (-current)

Outline

Biomolecular Characterization Team

Protein is one of the most important molecules of life and our purpose is to clarify the correlation of a gene and its functions by examining its protein structure. To that end, we have been developing characterization methods of protein post-translational modifications (PTMs) in the latest proteomics technology. In the general LC-MS/MS based proteomics, there are many cases overlooking PTMs due to a low sequence cover rate. We have established less-oversight analysis methods for PTMs by combining mass spectrometry of whole proteins, the LC-MS/MS analysis that improved cover rate and amino acid composition analysis. Furthermore, we support protein X-ray crystallographic analysis using SPring-8, Harima. In addition, we developed the RNA MS search engine Ariadne.

Recent Research Topic

Ariadne: Database search for RNA identification using tandem mass spectrometry data
Fig. 1: Ariadne: Database search for RNA identification using tandem mass spectrometry data

Selected Publications

  1. H. Nakayama, N. Takahashi, T. Isobe, Informatics for mass spectrometry-based RNA analysis, Mass Spectrom Rev. 2011, 30, 1000.
  2. H. Nishimasu, S. Okudaira, K. Hama, E. Mihara, N. Dohmae, A. Inoue, R. Ishitani, J. Takagi, J. Aoki,O. Nureki, Crystal structure of autotaxin and insight into GPCR activation by lipid mediators, Nat Struct Mol Biol. 2011, 18, 205.
  3. A. Masuda, N. Dohmae, Automated Protein Hydrolysis Delivering Sample to a Solid Acid Catalyst for Amino Acid Analysis, Anal Chem. 2010, 82, 8939.
  4. T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, DG. Vassylyev, K. Ito, O. Nureki, Conformational transition of Sec machinery inferred from bacterial SecYE structures, Nature 2008, 455, 988.
  5. M. Kawatani, H. Okumura, K. Honda, N. Kanoh, M. Muroi, N. Dohmae, M. Takami, M. Kitagawa, Y. Futamura, M. Imoto, H. Osada, The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I, Proc Natl Acad Sci USA. 2008, 105, 11691.
  6. Y. Ito, I. Nakanomyo, H. Motose, K. Iwamoto, S. Sawa, N. Dohmae, H. Fukuda, Dodeca-CLE peptides as suppressors of plant stem cell differentiation, Science 2006, 313, 842.
  7. H. Kaku, Y. Nishizawa, N. Ishii-Minami, C. Akimoto-Tomiyama, N. Dohmae, K. Takio, E. Minami, N. Shibuya, Plant cells recognize chitin fragments for defense signaling through a novel plasma membrane receptor, Proc Natl Acad Sci USA. 2006, 103, 11086.
  8. M. Umezu-Goto, Y. Kishi, A. Taira, K. Hama, N. Dohmae, K. Takio, T. Yamori, GB. Mills, K. Inoue, J. Aoki, H. Arai, Autotaxin has lysophospholipase D activity leading to tumor cell growth and motility by lysophosphatidic acid production, J Cell Biol. 2002, 158, 227.
  9. H. Fujiwara, M. Hasegawa, N. Dohmae, A. Kawashima, EM. asliah, MS. Goldberg, J. Shen, K. Takio, T. Iwatsubo, alpha-Synuclein is phosphorylated in synucleinopathy lesions, Nat Cell Biol. 2002, 4 160.
  10. C. Masutani, R. Kusumoto, A. Yamada, N. Dohmae, M. Yokoi, M. Yuasa, M. Araki, S. Iwai, K. Takio, F. Hanaoka, The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta, Nature 1999, 399, 700.

Core Members

Principal Investigator add delete
Naoshi Dohmae Team Head    
Staff Scientist add delete
Nobuhiro Morishima Senior Research Scientist (Senior Research Scientist, Molecular Membrane Biology Laboratory)    
Hideyuki Miyatake Senior Research Scientist 　  
Hiroshi Nakayama Senior Research Scientist 　  
Kowashi Watanabe Senior Technical Scientist 　  
Takehiro Suzuki Technical Scientist 　  
Postdoctoral Fellow add delete
Akiko Masuda Contract Researcher    
Student Trainee add delete
Technical Assistant add delete
Misaki Akiyama Technical Staff I    
Masami Koike Technical Staff II    
Administrative Assistant add delete
Visiting Research Staff add delete
Other Staff add delete

( ) indicates primary affiliation in RIKEN.

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