Team Leader
Mikako Shirouzu
Ph.D.
Laboratory for Protein Functional and Structural Biology
LocationYokohama
E-mailmikako.shirouzu[at]riken.jp
Please replace [at] with @.
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.
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
Yamagata A, Ito K, Suzuki T, et al.
Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A.
Nature Communications
15(1), 3027 Thu Apr 18 00:00:00 JST 2024
doi: 10.1038/s41467-024-47322-4
Akiyama N, Ishiguro K, Yokoyama T, et al.
Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nature Structural & Molecular Biology
Wed Mar 27 00:00:00 JST 2024
doi: 10.1038/s41594-024-01238-1
Suzuki M, Uchibori K, Oh-Hara T, et al.
A macrocyclic kinase inhibitor overcomes triple resistant mutations in EGFR-positive lung cancer.
Npj Precision Oncology
8(1), 46 Fri Feb 23 00:00:00 JST 2024
doi: 10.1038/s41698-024-00542-9
Tanaka M, Yokoyama T, Saito H, et al.
Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nature Chemical Biology
Wed Jan 24 00:00:00 JST 2024
doi: 10.1038/s41589-023-01513-0
Furutani Y, Hirano Y, Toguchi M, et al.
A small molecule iCDM-34 identified by in silico screening suppresses HBV DNA through activation of aryl hydrocarbon receptor.
Cell Death Discovery
9(1), 467 Fri Dec 22 00:00:00 JST 2023
doi: 10.1038/s41420-023-01755-w
Zhao X, Ma D, Ishiguro K, et al.
Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
Cell
186(25), 5517-5535.e24 Thu Dec 07 00:00:00 JST 2023
doi: 10.1016/j.cell.2023.10.026
Kikuchi M, Morita S, Wakamori M, et al.
Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nature Communications
14(1), 4103 Mon Jul 17 00:00:00 JST 2023
doi: 10.1038/s41467-023-39735-4
Yamagata A, Murata Y, Namba K, et al.
Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter.
Nature Communications
13, 7180 Wed Nov 23 00:00:00 JST 2022
doi: 10.1038/s41467-022-34930-1
Ehara H, Kujirai T, Shirouzu M, et al.
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.
Science
377(6611), eabp9466 Fri Sep 09 00:00:00 JST 2022
doi: 10.1126/science.abp9466
Nakamura H, Hisano T, Rahman MM, et al.
Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria.
Proceedings of the National Academy of Sciences of the United States of America
119(27), e2123385119 Tue Jul 05 00:00:00 JST 2022
doi: 10.1073/pnas.2123385119
Park JH, Iwamoto M, Yun JH, et al.
Structural insights into the HBV receptor and bile acid transporter NTCP.
Nature
606(7916), 1027-1031 Wed Jun 01 00:00:00 JST 2022
doi: 10.1038/s41586-022-04857-0
Hosaka T, Nomura T, Kubo M, et al.
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.
Proceedings of the National Academy of Sciences of the United States of America
119(9), e2117433119 Tue Mar 01 00:00:00 JST 2022
doi: 10.1073/pnas.2117433119
Nakagawa Y, Shen HC, Komi Y, et al.
Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system.
Nature Chemical Biology
18(3), 321-331 Tue Mar 01 00:00:00 JST 2022
doi: 10.1038/s41589-021-00951-y
Kasahara K, Re S, Nawrocki G, et al.
Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.
Nature Communications
12, 4099 Wed Dec 01 00:00:00 JST 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 Thu Jul 01 00:00:00 JST 2021
doi: 10.1126/sciadv.abg3147
News
Mar. 16, 2023 Research
A nifty trick to help plants thrive in iron-poor soils
Jun. 9, 2022 Research
Imaging how a light-driven chloride pump works
Nov. 1, 2021 Research
Mapping the structural features that regulate a signaling protein’s specificity
Aug. 9, 2019 Research
How phosphorylation of eIF2 reduces protein synthesis
Dec. 7, 2018 Research
Cryo-electron microscopy shows how stabilizing proteins bind to microtubules