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

  1. Quasi-degenerate extension of local N-electron valence state perturbation theory with pair-natural orbital method based on localized virtual molecular orbitals

    M. Hayashi, M. Saitow, K. Uemura, T. Yanai* . The Journal of Chemical Physics, 160, 194105 (2024)

    doi: 10.1063/5.0204419

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  2. Osimertinib’s Proton-Catalyzed, Pseudoconcerted EGFR Inhibition Guides Next-Generation Inhibitor Design

    Akihiro Kondo, Kazuhiro J. Fujimoto*, Shin-ichi Koda, Shinji Saito, and Takeshi Yanai* . Journal of Chemical Information and Modeling, 66, 1203–1213 (2026)

    doi: 10.1021/acs.jcim.5c02787

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  3. Ca2+-Driven Protein Compaction Tunes NIR Absorption in the Thermophilic Purple Bacterial LH1

    Kazuhiro J. Fujimoto*, Rio Tsuji, Zheng-Yu Wang-Otomo, and Takeshi Yanai* . The Journal of Physical Chemistry Letters, 17, 4173–4180 (2026)

    doi: 10.1021/acs.jpclett.6c00317

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  4. A copper-dependent redox-based hydrogen peroxide perception in plants

    Nobuaki Ishihama, Yohta Fukuda, Yumiko Shirano, Kazuhiro J. Fujimoto, Kaori Takizawa, Ryoko Hiroyama, Hiroki Ito, Mayumi Nishimura, Takeshi Yanai, Tsuyoshi Inoue, Ken Shirasu & Anuphon Laohavisit* . Nature Communications, 17, 4236 (2026)

    doi: 10.1038/s41467-026-72573-8

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  5. Data-driven approach to visualize the correlation between photocatalytic activity and rate constants from excited states

    R. Kunisada, M. Hayashi, T. Rohlfs, T. Nagano, K. Sano, N. Inai, N. Noto*, T. Ogaki, Y. Matusi, H. Ikeda, O. G. Mancheño, T. Yanai*, S. Saito* . Chemical Science, 17, 176–186 (2026)

    doi: 10.1039/D5SC06465A

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  6. Concerted Proton-Electron Transfer via Vibration Correlation Function Approach with Effective Anharmonicity: Beyond Classical Approximation with Duschinsky Effects

    T. Iino, S. Sendo, T. Yanai* . The Journal of Chemical Physics, 164, 084112 (2026)

    doi: 10.1063/5.0305257

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  7. Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning

    Katsuki Sato, Yui Kanaoka, Tomoya Tsukazaki, Takayuki Uchihashi, Takaharu Mori* . Journal of Chemical Information and Modeling, 66, 4484–4498 (2026)

    doi: 10.1021/acs.jcim.6c00142

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  8. Key Role of Pro230 in the Hinge Region on the Architecture and Function of IgG1

    Yuuki Koseki, Yuki Yamaguchi, Michihiko Aoyama, Kentaro Hiraka, Minoru Tada, Atsuji Kodama, Akinobu Senoo, Akiko Ishii-Watabe, Takayuki Uchihashi, Kazuyoshi Murata, Susumu Uchiyama, Koichi Kato, Saeko Yanaka*, Jose M.M. Caaveiro* . Journal of Medicinal Chemistry, 69, 3902–3914 (2026)

    doi: 10.1021/acs.jmedchem.5c02419

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  9. Visualizing the Functional Dynamics of P-Glycoprotein and Its Modulation by Elacridar via High-Speed Atomic Force Microscopy

    Yui Kanaoka, Norie Hamaguchi-Suzuki, Takeshi Murata*, Takayuki Uchihashi* . International Journal of Molecular Sciences, 27, 356 (2026)

    doi: 10.3390/ijms27010356

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  10. Assessment of the time correlation function-based approach for absorption spectrum calculations using time-dependent density functional theory and molecular dynamics simulations

    Shion Sendo, Kazuhiro J. Fujimoto*, Tomoya Miyashita, Shinji Saito*, Takeshi Yanai* . The Journal of Chemical Physics, 163, 134116 (2025)

    doi: 10.1063/5.0281605

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  11. PyGraSO: Analytical Nuclear Derivatives of Spin–Orbit Coupling for Intersystem Crossing Dynamics Simulations

    Masaya Hagai*, Kazuhiro J. Fujimoto*, and Takeshi Yanai* . Journal of Chemical Theory and Computation, 21, 11604–11619 (2025)

    doi: 10.1021/acs.jctc.5c01442

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  12. Analytical nuclear gradients for second-order Møller-Plesset perturbation theory using pair-natural orbitals based on localized virtual molecular orbitals

    M. Hayashi, M. Saitow, T. Yanai* . The Journal of Chemical Physics, 163, 234114 (2025)

    doi: 10.1063/5.0302950

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  13. Large-Scale Modeling of Proton-Coupled Electron Transfer Based on Absolutely Localized Molecular Orbitals

    L. Lampe, T. Yanai*, J. Neugebauer* . Journal of Chemical Theory and Computation, 21, 12545–12556 (2025)

    doi: 10.1021/acs.jctc.5c01287

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  14. Microgravity-Assisted Exploration of the Conformational Space of Amyloid β Affected by Tottori-Type Familial Mutation D7N

    Maho Yagi-Utsumi, Saeko Yanaka, Raymond N. Burton-Smith, Takayuki Uchihashi, Kazuyoshi Murata, Koichi Kato* . ACS Chemical Neuroscience, 16, 2682 (2025)

    doi: 10.1021/acschemneuro.5c00217

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  15. Structural basis for the interaction between the bacterial cell division proteins FtsZ and ZapA

    Junso Fujita, Kazuki Kasai, Kota Hibino, Takayuki Uchihashi*, Hiroyoshi Matsumura* . Nature Communications, 16, 5985 (2025)

    doi: 10.1038/s41467-025-60940-w

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  16. A look beyond topography: Transient phenomena of Escherichia coli cell division

    Christian Ganser*, Shigetaka Nishiguchi, Feng-Yueh Chan, Takayuki Uchihashi* . Science Advances, 11, eads3010 (2025)

    doi: 10.1126/sciadv.ads3010

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  17. AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex

    Yui Kanaoka, Takaharu Mori, Takayuki Uchihashi*, Tomoya Tsukazaki* . Nature Communications, 16, 225(2025)

    doi: 10.1038/s41467-024-54875-x

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  18. Nanoscale visualization of Drosophila E-cadherin ectodomain fragments and their interactions

    Hiroki Oda*, Shigetaka Nishiguchi, Chihong Song, Kazuyoshi Murata, Takayuki Uchihashi, Yuki Suzuki . Journal of Molecular Biology, 437, 168875 (2025)

    doi: 10.1016/j.jmb.2024.168875

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  19. 第1章「物質・生体間の相互作用の基礎」 第5節「高速AFMによるソフトマテリアルの動態イメージング技術」

    内橋貴之 . 「界面制御による革新的生体適合性材料開発」(高井まどか、三浦佳子 監修) , (株)エヌ・ティー・エス, 2025年12月, ISBN:978-4-86043-782-4 C3047

    doi:

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  20. 2.3.1「走査システムの高速化」

    内橋貴之 . 表面分析技術選書「走査プローブ顕微鏡/分光法 第2版」(公益社団法人 日本表面真空学会 編), 丸善出版, 2025年10月31日, ISBN:9784621312018

    doi:

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  21. 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
  22. 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

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  23. 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

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  24. 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
  25. 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

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  26. 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
  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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  37. 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

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  38. 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

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  39. 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

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  40. 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

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  41. 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

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  42. 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

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  43. 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

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  44. 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

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  45. 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

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  46. 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

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  47. 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

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  48. 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

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  49. 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

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  50. 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

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  51. 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

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  52. 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

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  53. 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

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  54. 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

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  55. 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

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  56. 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, 300, 107797

    doi: 10.1016/j.jbc.2024.107797

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  57. 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

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  58. 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

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  59. 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

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  60. 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

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  61. 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

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  62. 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

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