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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

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About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Ichio Shimada

Team Leader
Ichio Shimada Ph.D.

Laboratory for Dynamic Structure of Biomolecules

LocationYokohama

E-mailichio.shimada[at]riken.jp

Please replace [at] with @.

Understanding structural basis for the function of biomolecules from dynamic structures

Membrane proteins play fundamental roles in many biological processes, and are recognized as principal target proteins for drug development. RNAs have become recognized asa novel remedy to solve the depletion of targets in drug development.Over the past decade, our structural understanding of biomolecules such as the membrane proteins and RNAshas 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 structures of biomolecules in solution, we will investigate the relationships between the dynamical structures and the functions for biologically important biomolecules.

Research Theme

  • Elucidation of functional mechanism of biomolecules from dynamic structures
  • Elucidation of signal transduction mechanism of GPCRs from dynamic structures
  • Development of methods for dynamic structures of membrane proteins in lipid bilayers
  • Development of NMR methods applicable to high-molecular-weight biomolecules

Selected Publications

Kaneko S, Imai S, Asao N, et al.
Activation mechanism of the μ-opioid receptor by an allosteric modulator.
Proceedings of the National Academy of Sciences 119(16), e2121918119 (2022) doi: 10.1073/pnas.2121918119

Shiraishi Y, Kofuku Y, Ueda T, et al.
Biphasic activation of β-arrestin 1 upon interaction with a GPCR revealed by methyl-TROSY NMR
Nature Communications 12, 7158 (2021) doi: 10.1038/s41467-021-27482-3

Iwahashi Y, Toyama Y, Imai S, et al.
Conformational equilibrium shift underlies altered K+ channel gating as revealed by NMR.
Nature Communications 11, 5168 (2020) doi: 10.1038/s41467-020-19005-3

Mizukoshi Y, Takeuchi K, Tokunaga Y, et al.
Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium.
Science Advances 6(40), eabd0480 (2020) doi: 10.1126/sciadv.abd0480

Zhao Q, Fujimiya R, Kubo S, et al.
Real-Time In-Cell NMR Reveals the Intracellular Modulation of GTP-Bound Levels of RAS.
Cell Reports 32(8), 108074 (2020) doi: 10.1016/j.celrep.2020.108074

Mizumura T, Kondo K, Kurita M, et al.
Activation of adenosine A2A receptor by lipids from docosahexaenoic acid revealed by NMR.
Science Advances 6(12), eaay8544 (2020) doi: 10.1126/sciadv.aay8544

Imai S, Yokomizo T, Kofuku Y, et al.
Structural equilibrium underlying ligand -dependent activation of β2 -adreno receptor.
Nature Chemical Biology 16, 430-439 (2020) doi: 10.1038/s41589-019-0457-5

Kano H, Toyama Y, Imai S, et al.
Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel.
Nature Communications 10(1), 2008 (2019) doi: 10.1038/s41467-019-10038-x

Shimada I, Ueda T, Kofuku Y, et al.
GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures.
Nature Reviews Drug Discovery 18(1), 59-82 (2019) doi: 10.1038/nrd.2018.180

Shiraishi Y, Natsume M, Kofuku Y, et al.
Phosphorylation-induced conformation of β2-adrenoceptor related to the arrestin recruitment revealed by NMR.
Nature Communications 9(1), 194 (2018) doi: 10.1038/s41467-017-02632-8

Members

Ichio Shimada

Team Leader

Shunsuke Imai

Senior Scientist

Yutaro Shiraishi

Research Scientist

Yuki Toyama

Research Scientist

Satoko Tamura

Technical Staff I

Shun Kaneko

Junior Research Associate

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