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Research

Research

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

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BDR hosts annual symposium and regular seminars inviting international scientists in life science.

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About Us

About Us

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

Photo of Team leder, Mikako Shirouzu

Team Leader
Mikako Shirouzu Ph.D.

Laboratory for Protein Functional and Structural Biology

LocationYokohama

E-mailmikako.shirouzu[at]riken.jp

Please replace [at] with @.

Establishment of a structural analysis technology platform that contributes to "life innovation" such as drug development and medical treatment.

The high-resolution structural information of proteins related to diseases shall increasingly become important for drug development leading to future individualized medicine. We plan to establish a structural analysis technology platform to contribute to "Life innovation" such as drug discovery as well as development of methods for the sample preparation of challenging proteins including membrane proteins/biomolecular complexes and for the structural analysis by cryo-electron microscopy (cryo-EM). The 3D-structural information will be used for in-silico screening/design of chemical compounds and for dynamic structural analysis toward simulation research of cell function.

cryo-EM (FEI Tecnai Arctica)

Research Theme

  • Analysis of developmental process using theoretical cell models
  • Study of evolutionary dynamics of microorganisms by comprehensive phenotypic/genetic analysis
  • Development of algorithm for high-resolution comprehensive phenotypic/genetic analysis

Selected Publications

Kasahara K, Re S, Nawrocki G, et al.
Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.
Nature Communications 12, 4099 (2021) doi: 10.1038/s41467-021-24349-5

Kukimoto-Niino M, Katsura K, Kaushik R, et al.
Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex.
Science Advances 7(30), eabg3147 (2021) doi: 10.1126/sciadv.abg3147

Bracun L, Yamagata A, Christianson BM, et al.
Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution.
Science Advances 7(25), eabf8864 (2021) doi: 10.1126/sciadv.abf8864

Sugizaki A, Sato K, Chiba K, et al.
POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos.
Proceedings of the National Academy of Sciences of the United States of America 118(11), e2019071118 (2021) doi: 10.1073/pnas.2019071118

Kobayashi H, Hatakeyama H, Nishimura H, et al.
Chemical reversal of abnormalities in cells carrying mitochondrial DNA mutations.
Nature Chemical Biology 17, 335-343 (2020) doi: 10.1038/s41589-020-00676-4

Ihara K, Hato M, Nakane T, et al.
Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Scientific Reports 10(1), 19305 (2020) doi: 10.1038/s41598-020-76277-x

Yokoyama T, Machida K, Iwasaki W, et al.
HCV IRES Captures an Actively Translating 80S Ribosome.
Molecular Cell 74(6), 1205-1214 e1208 (2019) doi: 10.1016/j.molcel.2019.04.022

Kashiwagi K, Yokoyama T, Nishimoto M, et al.
Structural basis for eIF2B inhibition in integrated stress response.
Science 364(6439), 495-499 (2019) doi: 10.1126/science.aaw4104

Ehara H, Kujirai T, Fujino Y, et al.
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science 363(6428), 744-747 (2019) doi: 10.1126/science.aav8912

Matsuda T, Ito T, Takemoto C, et al.
Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction.
PloS one 13(2), e0193158 (2018) doi: 10.1371/journal.pone.0193158

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