多元物質科学研究所
米倉研究室
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論文（英語）

論文（英語）

2024年度

  1. Hasegawa T,Inoue S,Tsuzuki S,Horiuchi S,Matsui H,Okada T,Kumai R,Yonekura K,Maki-Yonekura S, “Exploration and development of Molecule-based Printed Electronics Materials: an integrated approach using experimental, computational, and data sciences”Science and Technology of Advanced Materials,2024年11月13日,doi:10.1080/14686996.2024.24
  2. Nikaido K,Inoue S,Tsuzuki S,Kumai R,Matsui H,Takaba K,Saori Maki-Yonekura S,Yonekura K,Hasegawa T,”Emergence of mixing-induced polymorphic phase with higher mobility in alkylated layered organic semiconductors”,Physical Review Materials,2024年11月1日,doi:https://doi.org/10.1103/physrevmaterials.8.115601
  3. Yonekura K “Artificial Intelligence-Driven Data Acquisition for Single-Particle Cryo-EM and Three-Dimensional Electron Diffraction” Cryo-Electron Microscopy in Structural Biology,2024年10月17日,doi:10.1201/9781003326106
  4. Tani K ,Maki-Yonekura S ,Kanno R, Negami T ,Hamaguchi T, Hall M, Mizoguchi A ,M. Humbel B, Terada T ,Yonekura K, Doi T,”Structure of endothelin ETB receptor–Gi complex in a conformation stabilized by unique NPxxL motif” Communications Biology, 2024年10月16日
  5. Toyonaga T,Kato T,Kawamoto A,Miyata T,Kawakami K,Fujita J,Hamaguchi T,Namba K,Miyata M,”Dimeric assembly of F1-like ATPase for the gliding motility of Mycoplasma”,bioRxiv,2024年6月11日,doi:10.1101/2024.06.11.597861

2023年度

  1. Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima S, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen J, Nagao R 　“The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs”　Proceedings of the National Academy of Sciences of the United States of America, 2024年3月 ,  doi: 10.1073/pnas.2319658121
  2. Takaba K,Maki-Yonekura S,Inoue I,Tono K,Fukuda Y,Shiratori Y,Peng Y,Morimoto J,Inoue S,Higashino T,Sando S,Hasegawa T,Yabashi M,Yonekura K, “Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds ”  Journal of the American Chemical Society, 2024年2月28日,doi : 10.1021/jacs.3c11523
  3. Higashino T, Inoue S, Arai S, Tsuzuki S, Matsui H, Kumai R, Takaba K, Maki-Yonekura S, Kurokawa H, Inoue I, Tono K,Yonekura K,Hasegawa T  “Effects of Thiophene-Fused Isomer on High-Layered Crystallinity in π-Extended and Alkylated Organic Semiconductors” Chemistry of Materials 36(2) 848-859.2024年1月5日,doi : 10.1021/acs.chemmater.3c02500
  4. Yonekura K, Maki-Yonekura S, Kiyofumi Takaba “Applications and limitations of electron 3D crystallography” Structure 31(11) 1328-1334 2023年11月2日,doi : 10.1016/j.str.2023.09.007
  5. Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima S, Suzuki T, Kawakami K,Dohmae N,Yonekura K,Jian-Ren S,Nagao R  “Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs” BioRxiv 2023年10月27日, doi:10.1101/2023.10.25.563911
  6. Takaba K, Maki-Yonekura S, Inoue I,  Tono K, Fukuda Y, Shiratori Y, Peng Y, Morimoto J, Inoue S, Higashino T,Sando S,Hasegawa T,Yabashi M,Yonekura K  “Comprehensive application of XFEL micro crystallography for novel organic compounds” ChemRxiv 2023年10月5日,doi: 10.26434/chemrxiv-2023-69p99
  7. Ono-Ogasawara C, Yamamoto S, Ogura Y, Okamura H, Takaba K, Yoshida S, Sato S, Yonekura K, Takikawa H, “Synthesis of (±)-zeapyranolactone, a noncanonical strigolactone isolated from maize, and determination of its overall relative configuration” Tetrahedron Letters 127(1) 1-4.2023年9月, doi:10.1016/j.tetlet.2023.154695
  8. Aizawa H, Sato T, Maki-Yonekura S, Yonekura K, Takaba K, Hamaguchi T, Minato T, M. Yamamoto H, “Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect” Nature Communications 14(1).2023年7月28日,doi : 10.1038/s41467-023-40133-z
  9. Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K, “Measurement of charges and chemical bonding in a cryo-EM structure” Communications Chemistry 6(1) 2023年5月31日 （プレスリリース）,doi : 10.1038/s42004-023-00900-x
  10. Morimoto J, Shiratori Y, Yokomine M, Ueda T, Nakamuro T, Takaba K, Maki-Yonekura S, Umezawa K, Miyanishi K, Fukuda Y , Watanabe T, Mizukami W,Takeuchi K, Yonekura K, Nakamura E, Sando  S  “Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine” ChemRxiv , doi:10.26434/chemrxiv-2023-c4mw6.2023年5月16日, doi : 10.26434/chemrxiv-2023-c4mw6

2022年度

  1. Takaba K, Maki-Yonekura S, Inoue I, Tono K, Hamaguchi T, Kawakami K, Naitow H, Ishikawa T, Yabashi M, Yonekura K*, “Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography” Nature Chemistry, 15, 491-497. 2023年3月20日　(プレスリリース) ,doi : 10.1038/s41557-023-01162-9
  2. Himiyama T*, Hamaguchi T, Yonekura K, Nakamura T  “Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins” Bioconjugate Chemistry 34(4) 764-771 .2023年3月8日,doi : 10.1021/acs.bioconjchem.3c00057
  3. Matsuike D, Tahara Y.-O., Nonaka T, Wu H.N, Hamaguchi T, Kudo H, Hayashi Y, Arai M, Miyata M, “Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding”  Journal of Bacteriology, Journal of BacteriologyVol. 205, No. 3. 2023年2月7日
  4. Kosumi D, Bandou-Uotani M, Kato S, Kawakami K, Yonekura K, Kamiya N, “Ultrafast energy transfer and charge separation dynamics in PSII-dimer from Thermosynechococcus vulcanus” Research Square .2023年2月27日,doi : 10.21203/rs.3.rs-2613905/v1
  5. Nagao R*, Kato K, Hamaguchi T(equally contribution), Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K*, Shen J.R* “Structure of a monomeric photosystem I core associated with iron-stressed-induced-A proteins from Anabaena sp. PCC 7120” Nature Communications. 14, 920.2023年2月17日 　(プレスリリース), doi : 10.1038/s41467-023-36504-1
  6. Sekiyama N, Takaba K, Maki-Yonekura S, Akagi K., Ohtani Y, Imamura K, Terakawa T, Yamashita K, Yonekura K, Kodama T.S, Tochio H “ALS mutations in the TIA-1 prion-like domain induce pathological structures”  Proc. Natl. Acad. Sci. USA 119, e2122523119 (2022).2022年9月20日,doi : 10.1073/pnas.2122523119
  7. Kato K , Hamaguchi T (equally contribution), Nagao R, Kawakami K, Ueno Y, Suzuki T, Uchida H, Murakami A, Nakajima Y, Yokono M, Akimoto S, Dohmae N, Yonekura K, and Shen J.R. 2022. “Structural Basis for the Absence of Low-Energy Chlorophylls in a Photosystem I Trimer from Gloeobacter violaceus. ” ELife 11:73990. doi: 10.7554/ELIFE.73990.　(プレスリリース)
  8. Kawakami K,  Hamaguchi T (equally contribution), Hirose Y, Kosumi D, Miyata M, Kamiya N, and Yonekura K 2022. “Core and Rod Structures of a Thermophilic Cyanobacterial Light-Harvesting Phycobilisome.”  Nature Communications 2022 13:1 13(1):1–13. doi: 10.1038/s41467-022-30962-9.2022年6月(プレスリリース)
  9. Kimura A,  Kitoh-Nishioka H, Aota T, Hamaguchi T, Yonekura K, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Ifuku K, Yamashita E, Kashino Y, and Itoh S. 2022.  “Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange.”  The Journal of Physical Chemistry B 126(22):4009–21. doi: 10.1021/ACS.JPCB.2C00869.2022年5月26日
  10. Inoue S, Nikaido K, Higashino T, Arai S, Tanaka M, Kumai R, Tsuzuki S, Horiuchi S, Sugiyama H, Segawa Y, Takaba K, Maki-Yonekura S, Yonekura K, and Hasegawa T. 2022.  “Emerging Disordered Layered-Herringbone Phase in Organic Semiconductors Unveiled by Electron Crystallography.”  Chemistry of Materials 34(1). doi: 10.1021/acs.chemmater.1c02793.
  11. Kato K, Hamaguchi T (equally contribution), Nagao R, Kawakami K, Ueno Y, Suzuki T, Uchida H, Murakami A, Nakajima Y, Yokono M,  “Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus” eLife 11. 2022年4月11日,doi : 10.7554/elife.73990

2021年度以前（2019以降論文のみ）

  1. Hamaguchi T, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Itoh S, Ifuku K, Yamashita E, Maeda K, Yonekura K, and Kashino Y. 2021. “Structure of the Far-Red Light Utilizing Photosystem I of Acaryochloris marina.”  Nature Communications 12(1):2333. doi: 10.1038/s41467-021-22502-8.
  2. Hiragi K, Nishio K, Moriyama S, Hamaguchi T, Mizoguchi A, Yonekura K, Tani K, and Mizushima T. 2021. “Structural Insights into the Targeting Specificity of Ubiquitin Ligase for S. cerevisiae Isocitrate Lyase but Not C. Albicans Isocitrate Lyase.” Journal of Structural Biology 213(3):107748. doi: 10.1016/j.jsb.2021.107748.
  3. Kato K, Miyazaki N, Hamaguchi T (equally contribution), Nakajima Y, Akita F, Yonekura K, and Shen J.R. 2021. “High-Resolution Cryo-EM Structure of Photosystem II Reveals Damage from High-Dose Electron Beams.” Communications Biology 4(1):382. doi: 10.1038/s42003-021-01919-3.
  4. Kawakami K, Nagao R, Tahara Y-O., Hamaguchi T, Suzuki T, Dohmae N, Kosumi D, Shen J.R, Miyata M, Yonekura K, and Kamiya N. 2021. “Structural Implications for a Phycobilisome Complex from the Thermophilic Cyanobacterium Thermosynechococcus vulcanus.”  Biochimica et Biophysica Acta (BBA) – Bioenergetics 1862(9):148458. doi: 10.1016/J.BBABIO.2021.148458.
  5. Yonekura K, Maki-Yonekura S, Hamaguchi T, Naitow H, Takaba K, and Kawakami K. 2021. “Cryo-EM and ED with a Cold-Field Emission Beam and Energy Filtration.” 233–41. doi: 10.1007/978-981-16-2982-2_23.
  6. Yonekura K, Maki-Yonekura S, Naitow H, Hamaguchi T, and Takaba K. 2021. “Machine Learning-Based Real-Time Object Locator/Evaluator for Cryo-EM Data Collection.” Communications Biology 2021 4:1 4(1):1–8. doi: 10.1038/s42003-021-02577-1.　(プレスリリース)
  7.  Yu H, Hamaguchi T (equally contribution), Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, and Shen J.R. 2021. “Cryo-EM Structure of Monomeric Photosystem II at 2.78 Å Resolution Reveals Factors Important for the Formation of Dimer.”  Biochimica et Biophysica Acta (BBA) – Bioenergetics 1862(10):148471. doi: 10.1016/J.BBABIO.2021.148471.
  8. Yonekura K, Maki-Yonekura S, Takaba K, Hamaguchi T, Naitow H, and Kawakami K. 2021. “Complementary Use of High-Resolution and High-Precision Cryo-ED and EM.” Microscopy and Microanalysis 27(S1). doi: 10.1017/s143192762100132x.
  9. Kato K, Takaba K, Maki-Yonekura S, Mitoma N, Nakanishi Y, Nishihara T, Hatakeyama T, Kawada T, Hijikata Y, Pirillo J, Scott L.T, Yonekura K, Segawa Y, and Itami K. 2021. “Double-Helix Supramolecular Nanofibers Assembled from Negatively Curved Nanographenes.” Journal of the American Chemical Society 143(14). doi: 10.1021/jacs.1c00863.
  10. Maki-Yonekura S,  Hamaguchi T, Naitow H, Takaba K, and Yonekura K. 2020. “Advances in Cryo-EM and ED with a Cold-Field Emission Beam and Energy Filtration —Refinements of the CRYO ARM 300 System in RIKEN SPring-8 Center—.” Microscopy 2020:1–9. doi: 10.1093/jmicro/dfaa052.
  11. Takaba K, Maki-Yonekura S, Inoue S, Hasegawa T, and Yonekura K. 2021. “Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector.” Frontiers in Molecular Biosciences 7. doi: 10.3389/fmolb.2020.612226.
  12. Yonekura K, Maki-Yonekura S, Hamaguchi T, Naitow H, Takaba K, and Kawakami K. 2021. “Cryo-EM and ED with a Cold-Field Emission Beam and Energy Filtration.” 233–41. doi: 10.1007/978-981-16-2982-2_23.
  13. Naitow H, Hamaguchi T(equally contribution), Maki-Yonekura S, Isogai M, Yoshikawa N, and Yonekura K. n.d. “Apple Latent Spherical Virus Structure with Stable Capsid Frame Supports Quasi-Stable Protrusions Expediting Genome Release.” doi: 10.1038/s42003-020-01217-4.
  14. Takaba K, Maki-Yonekura S, and Yonekura K. 2020. “Collecting Large Datasets of Rotational Electron Diffraction with ParallEM and SerialEM.” Journal of Structural Biology 211(2):107549. doi: 10.1016/j.jsb.2020.107549.
  15. Kurokawa H, Ambo T, Takahashi S, and Koyama T. 2020. “Crystal Structure of Thermobifida fusca Cis-Prenyltransferase Reveals the Dynamic Nature of Its RXG Motif-Mediated Inter-Subunit Interactions Critical for Its Catalytic Activity.” Biochemical and Biophysical Research Communications 532(3). doi: 10.1016/j.bbrc.2020.08.062.
  16. Hamaguchi T, and Yonekura K. 2020.  “Tidy up Cryo-EM Sample Grids with 3D Printed Tools.” Journal of Structural Biology 209(1):107414. doi: 10.1016/j.jsb.2019.107414.
  17. Guzmán-Afonso C, Hong Y.L, Colaux H, Iijima H, Saitow A, Fukumura T, Aoyama Y, Motoki S, Oikawa T, Yamazaki T, Yonekura K, and Nishiyama Y. 2019. “Understanding Hydrogen-Bonding Structures of Molecular Crystals via Electron and NMR Nanocrystallography.” Nature Communications 10(1). doi: 10.1038/s41467-019-11469-2.
  18. Kato T, Makino F, Nakane T, Terahara N, Kaneko T, Shimizu Y, Motoki S, Ishikawa I, Yonekura K, and Namba K. 2019. “CryoTEM with a Cold Field Emission Gun That Moves Structural Biology into a New Stage.” Microscopy and Microanalysis 25(S2). doi: 10.1017/s1431927619005725.
  19. Kubota M,Matsuoka R, Suzuki T, Yonekura K, Yanagi Y, and Hashiguchi T. 2019. “Molecular Mechanism of the Flexible Glycan Receptor Recognition by Mumps Virus.” Journal of Virology 93(15). doi: 10.1128/jvi.00344-19.
  20. Hamaguchi T,  Maki-Yonekura S, Naitow H, Matsuura Y, Ishikawa T, and Yonekura K. 2019. “A New Cryo-EM System for Single Particle Analysis.” Journal of Structural Biology 207(1):40–48. doi: 10.1016/j.jsb.2019.04.011.
  21. Yonekura K,  Ishikawa T, and Maki-Yonekura S. 2019. “A New Cryo-EM System for Electron 3D Crystallography by EEFD.” Journal of Structural Biology 206(2). doi: 10.1016/j.jsb.2019.03.009.
  22. Hamaguchi T, , Kawakami M, Furukawa H, and Miyata M. 2019. “Identification of Novel Protein Domain for Sialyloligosaccharide Binding Essential to Mycoplasma mobile Gliding.” FEMS Microbiology Letters 366(3). doi: 10.1093/femsle/fnz016.