Centers & Labs

Global Research Cluster

Structural Glycobiology Team

Team Leader: Yoshiki Yamaguchi (Ph.D)
Yoshiki  Yamaguchi(Ph.D)

In order to elucidate the functions of the glycans attached to proteins, it is important to analyze the glycans from the structural point of view. Our team aims to reveal the functions of glycans through the three-dimensional structures of glycoproteins and oligosaccharide-related proteins, in collaboration with Max Planck Institute. We prepare the glycoconjugates samples with the techniques of organic synthesis and cell-engineering, and determine the three-dimensional structures using biophysical methods such as NMR or X-ray crystallography. Furthermore, we construct databases of oligosaccharide structures using bioinformatics-based approaches and decode the 'glycosignals' from the structural information. We particularly focus on disease-related glycoproteins, and develop diagnostic and therapeutic agents.

Main Research Field

Biological Sciences

Related Research Fields

Interdisciplinary science and engineering / Chemistry / Engineering / Biology / Medicine, dentistry, and pharmacy

Keywords

  • NMR
  • Glycan
  • 3D structure
  • Glycoprotein
  • Lectin

Selected Publications

  1. Nagae, M., Mishra, S.K., Neyazaki, M., Oi, R., Ikeda, A., Matsugaki, N., Akashi, S., Manya, H., Mizuno, M., Yagi, H., Kato, K., Senda, T., Endo, T., Nogi, T., and Yamaguchi, Y.
    "3D structural analysis of protein O-Mannosyl Kinase, POMK, a causative gene product of dystroglycanopat"
    Genes to Cells, 22(4), 348-59 (2017)
  2. Nagae, M., Hirata, T., Morita-Matsumoto, K., Theiler, R., Fujita, M., Kinoshita, T., and Yamaguchi, Y.
    "3D structure and interaction of p24β and p24δ Golgi dynamics domains: implication for p24 complex formation and cargo transport"
    J Mol Biol., 428(20):4087-99 (2016)
  3. Dulal, H.P., Nagae, M., Ikeda, A., Morita-Matsumoto, K., Adachi, Y., Ohno, N., and Yamaguchi, Y.
    "Enhancement of solubility and yield of a β-glucan receptor Dectin-1 C-type lectin-like domain in Escherichia coli with a solubility-enhancement tag"
    Protein Expr Purif., 123, 97-104 (2016)
  4. Nagae, M., Ikeda, A., Hanashima, S., Kojima, T., Matsumoto, N., Yamamoto, K. and Yamaguchi, Y.
    "Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain reveals the binding mode with N-glycan"
    FEBS Lett., 590(8), 1280-8 (2016)
  5. Nagae, M., Kanagawa, M., Morita-Matsumoto, K., Hanashima, S., Kizuka, Y., Taniguchi, N., and Yamaguchi, Y.
    "Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins"
    Sci Rep., 6:22973 (2016)
  6. Hanashima, S., Gotze, S., Liu, Y., Ikeda, A., Kojima-Aikawa, K., Taniguchi, N., Silva, DV, Feizi, T., Seeberger, PH., and Yamaguchi, Y.:
    "Defining the interaction of human soluble lectin ZG16p and mycobacterial phosphatidylinositol mannosides"
    Chembiochem., 16(10), 1502-11 (2015)
  7. Nagae, M., Morita-Matsumoto, K., Kato, M., Kaneko, MK., Kato, Y., and Yamaguchi Y.:
    "A platform of C-type lectin-like receptor CLEC-2 for binding O-glycosylated podoplanin and nonglycosylated rhodocytin"
    Structure, 22(12), 1711-21 (2014)
  8. Kanagawa, M., Liu, Y., Hanashima, S., Ikeda, A., Chai, W., Nakano, Y., Kojima-Aikawa, K., Feizi, T., and Yamaguchi, Y.:
    "Structural basis for multiple sugar recognition of Jacalin-related human ZG16p lectin"
    J Biol Chem., 289(24), 16954-65 (2014)
  9. Nagae, M., Ikeda, A., Kitago, Y., Matsumoto, N., Yamamoto, K. and Yamaguchi, Y.:
    "Crystal structures of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) reveal a common domain-swapped dimer"
    Proteins, 82(7), 1512-8 (2014)
  10. Hanashima, S., Ikeda, A., Tanaka, H., Adachi, Y., Ohno, N., Takahashi, T., and Yamaguchi Y.:
    "NMR study of short β(1,3)-glucans provides insights into the structure and interaction with Dectin-1"
    Glycoconj J., 31(3), 199-207 (2014)

Lab Members

Principal Investigator

Yoshiki Yamaguchi
Team Leader

Core Members

Masamichi Nagae
Research Scientist
Sushil Mishra
Visiting Researcher
Hari Dulal
International Program Associate
Akemi Ikeda
Technical Staff I
Yutaro Hayashi
Research Consultant
Jun Uzawa
Part-timer1
Noriko Tanaka
Part-timer2
Kana Morita
Temporary Staffing
Yoko Yamaguchi
Visiting Scientist
Shinya Hanashima
Visiting Scientist