Laboratory for Protein Functional and Structural Biology | RIKEN BDR

Laboratory for Protein Functional and Structural Biology

Team Leader

Mikako ShirouzuPh.D.

Photo of principal investigator

  • Location:Yokohama
  • E-mail:mikako.shirouzu[at]riken.jpPlease replace [at] with @.

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

Research Summary

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

  • Three-dimensional structure determination for drug development
  • Development of methods for preparing difficult proteins including membrane proteins
  • Structural analysis for huge complex of biomolecules by cryo-EM

Main Publications List

  • Kukimoto-Niino M, Katsura K, Kaushik R, et al.
    Cryo-EM structure of the human ELMO1-DOCK5 complex.
    Science Advances 7(30). eabg3147 (2021) doi: 10.1126/sciadv.abg3147
  • 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
  • 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.
  • Zyryanova AF, Kashiwagi K, Rato C, et al.
    ISRIB blunts the integrated stress response by allosterically antagonising the inhibitory effect of phosphorylated eIF2 on eIF2B.
    Molecular Cell 81(1). 88-103.e6 (2021) doi: 10.1016/j.molcel.2020.10.031
  • Kobayashi H, Hatakeyama H, Nishimura H, et al.
    Chemical reversal of abnormalities in cells carrying mitochondrial DNA mutations.
    Nature Chemical Biology 17(3). 335-343 (2021) 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.
  • Murayama K, Kato-Murayama M, Itoh Y, et al.
    Structural basis for inhibitory effects of Smad7 on TGF-beta family signaling.
    Journal of Structural Biology 212(3). 107661 (2020) doi: 10.1016/j.jsb.2020.107661.
  • 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.
  • Kukimoto-Niino M, Tsuda K, Ihara K, et al.
    Structural basis for the dual substrate specificity of DOCK7 guanine nucleotide exchange factor.
    Structure 27(5). 741-748.e3 (2019) doi: 10.1016/j.str.2019.02.001.
  • 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

All Publications