JAPANESE

MEXT Promotion of Development of a Joint Usage/ Research System Project:
Coalition of Universities for Research Excellence Program (CURE)
Multi-scale Quantum–Classical Life Interface Research Consortium

Papers

  1. Molecular Properties of a Novel Inward Proton Pump Rhodopsin, GhXeR

    Nanako Hattori, Yuma Ito, Yuji Furutani, Tatsuro Nishikino, and Hideki Kandori* . The Journal of Physical Chemistry B, published on the web,

    doi: 10.1021/acs.jpcb.6c01199

    • OBtRC

  2. Proton-Coupled Gate Closing Mechanism in Guillardia theta Anion Channelrhodopsin 1

    Miu Sudo†, Sayo Inoko†, Yuma Ito†, Takuma Watanabe†, Arisa Idenawa, Yuya Ohki, Keiko Ogawa, Makoto Demura, Hideki Kandori, Takashi Kikukawa, Yuji Furutani*, Takashi Tsukamoto* . Journal of Molecular Biology, published on the web,

    doi: 10.1016/j.jmb.2026.169856

    • OBtRC

  3. Site-resolved 13C/15N Solid-State Nuclear Magnetic Resonance Analysis of Schizorhodopsin 1 in Lipid Bilayers

    Akito Kitaguchi, Takumi Kanazawa, Toshio Nagashima, Toshio Yamazaki, Takashi Okitsu, Keiichi Inoue, Izuru Kawamura* . Biophysical Chemistry, 335, 1076356

    doi: 10.1016/j.bpc.2026.107635

    • ISSP

  4. Formation of a Proton-Conducting Hydrogen-Bond Network during the L/M Transition of NsXeR Uncovered by Light-Induced FTIR Spectroscopy

    Yuma Ito, Kirill Kovalev, Tatsuro Nishikino, Hideki Kandori, Yuji Furutani* . The Journal of Physical Chemistry Letters, published on the web,

    doi: 10.1021/acs.jpclett.6c00234

    • OBtRC

  5. Effects of Counter Ion Protonation on the Ultrafast Excited State Dynamics in Archaerhodopsin-3

    Krystyna Herasymenko, Danushka Walisinghe, Masae Konno, Vincent Ledentu, Miquel Huix-Rotllant, Xuchun Yang, Nicolas Ferré, Keiichi Inoue, Massimo Olivucci, Stefan Haacke* . Biophysical Journal, 125, 2416-2431

    doi: 10.1016/j.bpj.2026.02.034

    • ISSP

  6. Mechanistic insights into Na+ pumping by KR2: distinct roles of Asp102 and Asn112 coupled with retinal distortion in two O intermediates

    Sahoko Tomida, Rei Abe-Yoshizumi, Akimori Wada, Hideki Kandori, Yuji Furutani* . Journal of Biological Chemistry, published on the web,

    doi: 10.1016/j.jbc.2026.111313

    • OBtRC

  7. Surface Density-Dependent Interactions between Photoactivated Sensory Rhodopsin 2 and Its Transducer

    Tatsuya Sakamoto, Jingyi Tang, Soichiro Kato, Insyeerah Binti Muhammad Jauhari, Tatsuro Nishikino, Yuji Furutani* . ACS Omega, 11, 10478-10491 (2026)

    doi: 10.1021/acsomega.5c12030

    • OBtRC

  8. Novel light-driven schizorhodopsins from ANovel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria

    María del Carmen Marín*, Masae Konno, Andrey Rozenberg, Oded Béjà, Keiichi Inoue* . Biophysical Journal, 125, 2391-2404

    doi: 10.1016/j.bpj.2026.02.022

    • ISSP

  9. Spectral diversity of vertebrate retinal photoisomerase RGRs

    Takashi Nagata†,*, Chunyangguang Li†, Naoya Morimoto, Keiichi Inoue* . Biophysical Journal, 125, 2356-2362

    doi: 10.1016/j.bpj.2026.01.047

    • ISSP

  10. Light-harvesting by antenna-containing xanthorhodopsin from an antarctic cyanobacterium

    María del Carmen Marín*, Shunya Murakoshi, Andrey Rozenberg, Tatsuki Tanaka, Masae Konno, Wataru Shihoya*, Osamu Nureki*, Keiichi Inoue*, Oded Béjà* . Communications Biology, 9, 28 (2026)

    doi: 10.1038/s42003-025-09294-z

    • ISSP

  11. Protonation-enhanced energy transfer in xanthorhodopsin Kin4B8

    Kazuhiro J. Fujimoto*, Yuta A. Tsuzuki, Masae Konno, Takashi Nagata, Rintaro Murakami, Keiichi Inoue*, Takeshi Yanai* . The Journal of Physical Chemistry Letters, 16, 11884-11892 (2025)

    doi: 10.1021/acs.jpclett.5c02898

    • ISSP
    • ITbM

  12. Light-induced FTIR spectroscopy of visual rhodopsin microcrystals grown in lipidic cubic phase

    Yosuke Mizuno†, Valérie Panneels†, Yuji Furutani*, Gebhard F.X. Schertler, Hideki Kandori, Kota Katayama* . Journal of Molecular Biology, 437, 169487 (2025)

    doi: 10.1016/j.jmb.2025.169487

    • OBtRC

  13. Hydrated ionic liquids enhance stability and preserve functionality in transmembrane proteins

    Kyoko Fujita*, Kaho Ishii, Kazune Kobayashi, Yuji Furutani*, Yutaka Takebe, Eiichi Mizohata* . International Journal of Biological Macromolecules, 330, 148096 (2025)

    doi: 10.1016/j.ijbiomac.2025.148096

    • OBtRC

  14. Apusomonad rhodopsins: A new family of ultraviolet to blue light–absorbing rhodopsin channels

    Luis Javier Galindo*, Shunki Takaramoto, Takashi Nagata, Andrey Rozenberg, Hiroto Takahashi, Oded Béjà, Keiichi Inoue* . Proceedings of the National Academy of Sciences of the United States of America, 122, e2510619122 (2025)

    doi: 10.1073/pnas.2510619122

    • ISSP

  15. Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota

    Takayoshi Fujiwara, Toshiaki Hosaka, Masumi Hasegawa-Takano, Yosuke Nishimura, Kento Tominaga, Kaho Mori, Satoshi Nishino, Yuno Takahashi, Tomomi Uchikubo-Kamo, Kazuharu Hanada, Takashi Maoka, Shinichi Takaichi, Keiichi Inoue*, Mikako Shirouzu*, Susumu Yoshizawa* . Nature Microbiology, 10, 2603-2615 (2025)

    doi: 10.1038/s41564-025-02109-1

    • ISSP

  16. HulaChrimson: A Chrimson-like cation channelrhodopsin discovered using freshwater metatranscriptomics from Lake Hula

    Hiroto Takahashi, Shunki Takaramoto, Takashi Nagata, Shai Fainsod, Yoshitaka Kato, Oded Béjà, Keiichi Inoue . Biophysics and Physicobiology, 22, e220014 (2025)

    doi: 10.2142/biophysico.bppb-v22.0014

    • ISSP

  17. Significant effects of excitonic coupling and charge transfer on the circular dichroism spectrum of photosynthetic light-harvesting I complex

    Rio Tsuji, Kazuhiro J. Fujimoto*, Naho Hiwatashi, Zheng-Yu Wang-Otomo, Takeshi Yanai* . The Journal of Physical Chemistry B, 129, 6153–6162 (2025)

    doi: 10.1021/acs.jpcb.5c02145

    • ITbM

  18. In-insect synthesis of oxygen-doped molecular nanocarbons

    Atsushi Usami*, Hideya Kono, Vic Austen, Quan Manh Phung, Hiroki Shudo, Tomoki Kato, Hayato Yamada, Akiko Yagi, Kazuma Amaike, Kazuhiro J. Fujimoto*, Takeshi Yanai*, Kenichiro Itami* . Science, 388, 1055-1061 (2025)

    doi: 10.1126/science.adp9384

    • ITbM

  19. A constructive study based on Gloeobacter rhodopsin to explore the origin of extreme redshift and nontypical isomerization of bestrhodopsin

    Takashi Nagata, Yuma Kawasaki, Masae Konno, Keiichi Inoue* . The Journal of Physical Chemistry Letters, 16, 6622-6626

    doi: 10.1021/acs.jpclett.5c00869

    • ISSP

  20. Structural changes in the retinal chromophore and ion-conducting pathway of an anion channelrhodopsin GtACR1

    Keisei Shibata*, Yuma Kawasaki, Shunki Takaramoto, Masaya Watanabe, Masahiro Fukuda, Ryohei Ono, Hideaki E. Kato, Hidefumi Akiyama, Keiichi Inoue* . The Journal of Physical Chemistry Letters, 16, 6234-6241

    doi: 10.1021/acs.jpclett.5c01008

    • ISSP

  21. The role of retinal chromophore photoisomerization in enhanced inward proton-pumping activity of xenorhodopsin from Nanosalina

    Yuma Ito, Tatsuro Nishikino, Hideki Kandori, Yuji Furutani . Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1866, 149556 (2025)

    doi: 10.1016/j.bbabio.2025.149556

    • OBtRC

  22. Light-harvesting by antenna-containing rhodopsins in pelagic Asgard archaea

    Gali Tzlil, María del Carmen Marín, Yuma Matsuzaki, Probal Nag†, Shota Itakura, Yosuke Mizuno, Shunya Murakoshi, Tatsuki Tanaka, Shirley Larom, Masae Konno, Rei Abe-Yoshizumi, Ana Molina-Márquez, Daniela Bárcenas-Pérez, José Cheel, Michal Koblížek, Rosa León, Kota Katayama, Hideki Kandori, Igor Schapiro, Wataru Shihoya*, Osamu Nureki*, Keiichi Inoue*, Andrey Rozenberg*, Ariel Chazan*, Oded Béjà* . Nature Microbiology, 10, 1484-1500 (2025)

    doi: 10.1038/s41564-025-02016-5

    • ISSP
    • OBtRC

  23. Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters

    Krystyna Herasymenko, Danushka Walisinghe, Masae Konno, Leonardo Barneschi, Isabelle de Waele, Michel Sliwa, Keiichi Inoue*, Massimo Olivucci*, Stefan Haacke* . Chemical Science, 16, 761-774 (2025)

    doi: 10.1039/D4SC05120C

    • ISSP

  24. Weak organic acid effect of bacterial light-driven proton-pumping rhodopsin

    Zikun Lyu, Shunki Takaramoto, Keiichi Inoue* . The Journal of Physical Chemistry B, 129, 3198-3206 (2025)

    doi: 10.1021/acs.jpcb.4c06891

    • ISSP

  25. HulaCCR1, a Pump-like Cation Channelrhodopsin Discovered in a Lake Microbiome

    Shunki Takaramoto, Shai Fainsod, Takashi Nagata, Andrey Rozenberg, Oded Béjà, Keiichi Inoue* . Journal of Molecular Biology, 436, 168844 (2024)

    doi: 10.1016/j.jmb.2024.168844

    • ISSP

  26. Single-Molecule Kinetic Observation of Antibody Interactions with Growing Amyloid β Fibrils

    Maho Yagi-Utsumi, Yui Kanaoka, Shogo Miyajima, Satoru G. Itoh, Katsuhiko Yanagisawa, Hisashi Okumura, Takayuki Uchihashi*, Koichi Kato* . Journal of the American Chemical Society, 146, 31518–31528

    doi: 10.1021/jacs.4c08841

    • ExCELLS

  27. Quantitative Analysis of Therapeutic Antibody Interactions with Fcγ Receptors Using High-Speed Atomic Force Microscopy

    Saeko Yanaka, Hiroki watanabe, Rina Yogo, Mesayamas Kongsema, Sachiko Kondo, Hirokazu Yagi, Takayuki Uchihashi, and Koichi Kato . Biological and Pharmaceutical Bulletin, 4, 1334-338

    doi: 10.1248/bpb.b23-00751

    • ExCELLS

  28. Prominent Role of Charge Transfer in the Spectral Tuning of Photosynthetic Light-Harvesting I Complex

    Kazuhiro J. Fujimoto*, Rio Tsuji, Zheng-Yu Wang-Otomo, Takeshi Yanai* . ACS Physical Chemistry Au, 4, 499-509

    doi: 10.1021/acsphyschemau.4c00022

    • ITbM

  29. Glu1022.53-mediated early conformational changes in the process of light-induced green cone pigment activation

    Takuma Sasaki, Kota Katayama*, Hiroo Imai, Hideki Kandori* . Biochemistry, 63, 843-854

    doi: 10.1021/acs.biochem.3c00594

    • OBtRC

  30. Photoisomerization pathway of the microbial rhodopsin chromophore in solution

    Masahiro Sugiura, Hideki Kandori* . Photochemical & Photobiological Sciences, 23, 1435-1443

    doi: 10.1007/s43630-024-00602-w

    • OBtRC

  31. Unique hydrogen-bonding network in a viral channelrhodopsin rhodopsin

    Mako Aoyama, Kota Katayama, Hideki Kandori* . Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1865, 149148

    doi: 10.1016/j.bbabio.2024.149148

    • OBtRC

  32. FTIR study of light-induced proton transfer and Ca2+ binding in T82D mutant of TAT rhodopsin

    Teppei Sugimoto, Kota Katayama, Hideki Kandori* . Biophysical Journal, 123, published on the web

    doi: 10.1016/j.bpj.2024.08.005

    • OBtRC

  33. SNap bond, a crucial hydrogen bond between Ser in helix 3 and Asn in helix 4, regulates the structural dynamics of heliorhodopsin

    Toshiki Nakamura, Manish Singh, Masahiro Sugiura, Soichiro Kato, Ryo Yamamoto, Hideki Kandori, Yuji Furutani* . Journal of Molecular Biology, 436, 168666

    doi: 10.1016/j.jmb.2024.168666

    • OBtRC

  34. Low-temperature FTIR spectroscopy of the L/Q switch of proteorhodopsin

    Tatsuro Nishikino, Teppei Sugimoto, Hideki Kandori* . Physical Chemistry Chemical Physics, 26, 22959-22967

    doi: 10.1039/d4cp02248c

    • OBtRC

  35. Negative interference with antibody-dependent cellular cytotoxicity mediated by rituximab from its interactions with human serum proteins

    Saeko Yanaka, Rina Yogo, Hirokazu Yagi, Masayoshi Onitsuka, Natsumi Wakaizumi, Yuki Yamaguchi, Susumu Uchiyama, and Koichi Kato . Frontiers in Immunology, 14, 1090898

    doi: 10.3389/fimmu.2023.1090898

    • ExCELLS

  36. Light-driven Anion-Pumping Rhodopsin with Unique Cytoplasmic Anion-release Mechanism

    Tomohiro Ishizuka, Kano Suzuki, Masae Konno, Keisei Shibata, Yuma Kawasaki, Hidefumi Akiyama, Takeshi Murata*, Keiichi Inoue* . Journal of Biological Chemistry, , in press

    doi: 10.1016/j.jbc.2024.107797

    • ISSP

  37. The high-light-sensitivity Mechanism and Optogenetic Properties of the Bacteriorhodopsin-like Channelrhodopsin GtCCR4

    Tatsuki Tanaka†, Shoko Hososhima†, Yo Yamashita, Teppei Sugimoto, Toshiki Nakamura, Shunta Shigemura, Wataru Iida, Fumiya K. Sano, Kazumasa Oda, Takayuki Uchihashi, Kota Katayama, Yuji Furutani, Satoshi P. Tsunoda, Wataru Shihoya,* Hideki Kandori*, Osamu Nureki* . Molecular Cell, 84, 3530-3544.e6

    doi: 10.1016/j.molcel.2024.08.016

    • OBtRC
    • ExCELLS

  38. Magnetic Damping of NiFe Thin Films Grown on Two-Dimensional Chiral Hybrid Lead-iodide Perovskites

    Tempei Hatajiri, Shoya Sakamoto*, Hidetoshi Kosaki, Zikang Tian, Miuko Tanaka, Toshiya Ideue, Keiichi Inoue, Daigo Miyajima, Shinji Miwa* . Physical Review B, 10, 054435

    doi: 10.1103/PhysRevB.110.054435

    • ISSP

  39. Hydrogen-Bonding and Hydrophobic Interaction Networks as Structural Determinants of Microbial Rhodopsin Function

    Éva Bertalan†, Masae Konno†, María del Carmen Marín, Reza Bagherzadeh, Takashi Nagata, Leonid Brown, Keiichi Inoue*, Ana-Nicoleta Bondar* . The Journal of Physical Chemistry B, 128, 7407–7426

    doi: https://doi.org/10.1021/acs.jpcb.4c02946

    • ISSP

  40. Molecular Mechanisms behind Circular Dichroism Spectral Variations between Channelrhodopsin and Heliorhodopsin Dimers

    Kazuhiro J. Fujimoto*, Yuta A. Tsuzuki, Keiichi Inoue, Takeshi Yanai* . The Journal of Physical Chemistry Letters, 15, 2389-2397 (2024)

    doi: 10.1021/acs.jpclett.4c00879

    • ISSP
    • ITbM

  41. Extended Theoretical Modeling of Reverse Intersystem Crossing for Thermally Activated Delayed Fluorescence Materials

    Masaya Hagai*, Naoto Inai, Takuma Yasuda*, Kazuhiro J. Fujimoto*, Takeshi Yanai* . Science Advances, 10, eadk3219 (2024)

    doi: 10.1126/sciadv.adk3219

    • ITbM

  42. Spectral Tuning and Excitation-Energy Transfer by Unique Carotenoids in Diatom Light-Harvesting Antenna

    Kazuhiro J. Fujimoto*, Takuya Seki, Takumi Minoda, Takeshi Yanai* . Journal of the American Chemical Society, 146, 3984-3991 (2024)

    doi: 10.1021/jacs.3c12045

    • ITbM