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RIKEN Center for Biosystems Dynamics Research Laboratory for Dynamic Structure of Biomolecules

Team Leader: Ichio Shimada (Ph.D.)

Research Summary

Ichio Shimada (Ph.D.)

Membrane proteins play fundamental roles in many biological processes, and are recognized as principal target proteins for drug development. Over the past decade, our structural understanding of the membrane proteins has dramatically progressed, owing to the growing numbers of their atomic resolution crystal and cryo-EM structures. However, these structures basically represent static snapshots and observed conformations may not be the same as those in in-situ environment. In this research team, by using NMR, which provides us information about dynamical protein structures in solution, we will investigate the relationships between the dynamical structures and the functions for biologically important membrane proteins.

Main Research Fields

  • Medicine, Dentistry & Pharmacy

Related Research Fields

  • Biological Sciences
  • Biology
  • Physical pharmacy
  • Structural biochemistry
  • Biophysics

Keywords

  • Nuclear Magnetic Resonance
  • Biomolecules
  • Membrane Proteins
  • Dynamical Structures
  • Structural Equilibrium

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1.* Mizumura T, Kondo K, Kurita M, Kofuku Y, Natsume M, Imai S, Shiraishi Y, Ueda T, and Shimada I*.:
    "Activation of adenosine A2A receptor by lipids from docosahexaenoic acid revealed by NMR"
    Sci. Adv. (2020) DOI: 10.1126/sciadv.eaay8544
  • 2.* Imai S, Yokomizo T, Kofuku Y, Shiraishi Y, Ueda T, and Shimada I*.:
    "Structural equilibrium underlying ligand -dependent activation of β2 -adreno receptor."
    Nat. Chem. Bio. (2020) DOI: 10.1038/s41589-019-0457-5.
  • 3.* Kano H, Toyama Y, Imai S, Iwahashi Y, Mase Y, Yokogawa M, Osawa M, and Shimada I*.:
    "Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel"
    Nat. Commun. 10(1),2008. (2019)
  • 4.* Shimada I*, Ueda T, Kofuku Y, Matthew T. Eddy, and Kurt Wuthrich*.:
    "GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures."
    Nat. Rev. Drug Discov. 18(1), 59-82 (2019)
  • 5.* Shiraishi Y, Natsume M, Kofuku Y, Imai S, Nakata K, Mizukoshi T, Ueda T, Iwai H, and Shimada I*.:
    "Phosphorylation-induced conformation of β2-adrenoceptor related to the arrestin recruitment revealed by NMR"
    Nat. Commun. 9(1):194 (2018). doi: 10.1038/s41467-017-02632-8
  • 6.* Toyama Y, Kano H, Mase Y, Yokogawa M, Osawa M, and Shimada I*.:
    "Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses"
    Nat. Commun. 8:14523 (2017), doi: 10.1038/ncomms14523
  • 7.* Tokunaga Y, Takeuchi K,Takahashi H, and Shimada I*.:
    "Allosteric enhancement of enzymatic activity and substrate selectivity of MAP kinase p38α by the docking interaction"
    Nat. Struct. Mol. Biol. 21, 704-11 (2014)
  • 8.* Kofuku Y, Ueda T, Okude J, Shiraishi Y, Kondo K, Maeda M, Tsujishita H, and Shimada I*.:
    "Efficacy of the β2-adrenergic receptor is determined by conformational equilibrium in the tansmembrane region"
    Nat. Commun. (2012) DOI: 10.1038/ncomms2046
  • 9.* Nishida N, Sumikawa H, Sakakura M, Shimba N, Takahashi H,Terasawa H, Suzuki E, Shimada I*.:
    "Novel Collagen-Binding Mode of the VWA Domain Determined by a Transferred Cross-Saturation Experiment"
    Nat. Struct. Biol. (2003) 10, 53-58.
  • 10.* Takahashi H, Nakanishi T, Kami K, Arata Y, and Shimada I*.:
    "A Novel NMR Method for the Determination of the Interface of Large Protein-protein Complexes"
    Nat. Struct. Biol. (2000) 7, 220-223

Lab Members

Principal investigator

Ichio Shimada
Team Leader

Contact Information

Central Research Building C520
1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa
230-0045, Japan
Email: ichio.shimada [at] riken.jp

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