Publications

2025

  1. Neval Yilmaz*, Hiroki Tanino, Shun Sakuraba, Romain Amyot, Holger Flechsig, Atsushi Matsumoto, Hidetoshi Kono, Leonardo Puppulin, Mikihiro Shibata, Hiroshi Aoyama, Tsuyoshi Inoue, Kunio Matsumoto*, & Katsuya Sakai*, “Ligand binding to the membrane-distal domain of the Met receptor induces dimerization at the membrane-proximal domain.” ACS Nano, in press.
  2. 柴田幹大, “高速AFMを利用したタンパク質１分子のナノ動態観察”, 実験医学増刊「構造生命科学AlphaFold時代にどう活かす？」Vol. 43, No. 15 (増刊) pp183-188 (2025).
  3. Hiroki Tanaka, Joao Diogo Dias, Basile Jay, Shunsuke Kita, Mina Sasaki, Hiroyuki Takeda, Naoki Kishimoto, Shogo Misumi, Masashi Mizokami, Christine Neuveut, Takashi Sumikama, Mikihiro Shibata, Katsumi Maenaka, & Shinichi Machida*, “Structural basis of the hepatitis B virus x protein in complex with DDB1.” Proc. Natl. Acad. Sci. USA, 122 (24) e2421325122 (2025).
  4. Keisuke Matsushima, Takashi Sumikama, Taisei Suzuki, Mizuho Ito, Yutaro Nagasawa, Ayumi Sumino, Holger Flechsig, Tomoki Ogoshi, Kenichi Umeda, Noriyuki Kodera, Hideji Murakoshi*, & Mikihiro Shibata*, “Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM.” bioRxiv, (2025) doi: https://doi.org/10.1101/2025.04.24.650392
  5. Takayuki Yamaguchi†, Kei Okatsu†, Masato Kubota, Ayuka Mitsumori, Atsushi Yamagata, Yuko Fukata, Masaki Fukata, Mikihiro Shibata*, & Shuya Fukai*, “Structural insights into heterohexameric assembly of epilepsy-related ligand–receptor complex LGI1–ADAM22.” eLife, 14:RP105918 (2025).
  6. Ayumi Sumino*, “High-speed atomic force microscopy of ion channels.” Jpn. J. Appl. Phys., 24 020802 (2025).

2024

  1. Ayumi Sumino†, Takashi Sumikama†, Yimeng Zhao†, Holger Flechsig, Kenichi Umeda, Noriyuki Kodera, Hiroki Konno, Motoyuki Hattori*, & Mikihiro Shibata*, “High-speed atomic force microscopy reveals fluctuations and dimer splitting of the N-terminal domain of GluA2 ionotropic glutamate receptor-auxiliary subunit complex.” ACS Nano, 18, 36, 25018-25035 (2024).
  2. Shin Morioka†, Takumi Oishi†, Suguru Hatazawa, Takahiro Kakuta, Tomoki Ogoshi, Kenichi Umeda, Noriyuki Kodera, Hitoshi Kurumizaka*, & Mikihiro Shibata*, “High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes.” Nano Lett., 24, 17, 5246–5254 (2024).

2023

  1. Ayumi Sumino*, Takashi Sumikama*, Mikihiro Shibata, & Katsumasa Irie*, “Voltage sensors of a Na+ channel dissociate from the pore domain and form inter-channel dimers in the resting state.” Nat. Commun. 14, 7835 (2023).
  2. Shotaro Tsujioka†, Ayumi Sumino†, Yutaro Nagasawa†, Takashi Sumikama, Holger Flechsig, Leonardo Puppulin, Takuya Tomita, Yudai Baba, Takahiro Kakuta, Tomoki Ogoshi, Kenichi Umeda, Noriyuki Kodera, Hideji Murakoshi*, & Mikihiro Shibata*, “Imaging single CaMKII holoenzymes at work by high-speed atomic force microscopy.” Sci. Adv. 9 (26), eadh1069 (2023).
  3. Ayumi Sumino†,*, Yimeng Zhao†, Daichi Mukai, Takashi Sumikama, Leonardo Puppulin, Motoyuki Hattori* & Mikihiro Shibata, “Antithetic effects of agonists and antagonists on the structural fluctuations of TRPV1 channel.” Proc. Natl. Acad. Sci. USA, 120 (20) e2301013120 (2023).
  4. Leonardo Puppulin*, Junichiro Ishikawa, Ayumi Sumino, Arin Marchesi, Holger Flechsig, Kenichi Umeda, Noriyuki Kodera, Hiroshi Nishimasu, & Mikihiro Shibata*, “Dynamics of target DNA binding and cleavage by Staphylococcus aureus Cas9 as revealed by high-speed atomic force microscopy.” ACS Nano, 17, 5, 4629-4641 (2023).
  5. Shin Morioka, Shoko Sato, Naoki Horikoshi, Tomoya Kujirai, Takuya Tomita, Yudai Baba, Takahiro Kakuta, Tomoki Ogoshi, Leonardo Puppulin, Ayumi Sumino, Kenichi Umeda, Noriyuki Kodera, Hitoshi Kurumizaka, & Mikihiro Shibata*, “High-speed atomic force microscopy reveals spontaneous nucleosome sliding of H2A.Z at the subsecond timescale.” Nano Lett., 23, 5, 1696-1704 (2023).

2022

  1. Katsuya Sakai, Nozomi Sugano-Nakamura, Emiko Mihara, Nichole Marcela Rojas-Chaverra, Sayako Watanabe, Hiroki Sato, Ryu Imamura, Dominic Chih-Cheng Voon, Itsuki Sakai, Chihiro Yamasaki, Chise Tateno, Mikihiro Shibata, Hiroaki Suga, Junichi Takagi & Kunio Matsumoto, “Designing receptor agonists with enhanced pharmacokinetics by grafting macrocyclic peptides into fragment crystallizable regions.” Nat. Biomed. Eng., 7, 164-176 (2023).
  2. Koichiro E. Kishi, Yoon Seok Kim, Masahiro Fukuda, Masatoshi Inoue, Tsukasa Kusakizako, Peter Y. Wang, Charu Ramakrishnan, Eamon F.X. Byrne, Elina Thadhani, Joseph M. Paggi, Toshiki E. Matsui, Keitaro Yamashita, Takashi Nagata, Masae Konno, Sean Quirin, Maisie Lo, Tyler Benster, Tomoko Uemura, Kehong Liu, Mikihiro Shibata, Norimichi Nomura, So Iwata, Osamu Nureki, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, & Hideaki E. Kato, “Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine.” Cell, 185, 4, 672-689 (2022).

2021

  1. Leonardo Puppulin*, Daiki Kanayama, Naohiro Terasaka, Katsuya Sakai, Noriyuki Kodera, Kenichi Umeda, Ayumi Sumino, Arin Marchesi, Wei Weilin, Hideo Tanaka, Takeshi Fukuma, Hiroaki Suga, Kunio Matsumoto, & Mikihiro Shibata*, “Macrocyclic peptide-conjugated tip for fast and selective molecular recognition imaging by high-speed atomic force microscopy.” ACS　Applied　Materials　&　Interfaces, 13, 46, 54817–54829 (2021).
  2. Rina Hirano, Yasuhiro Arimura, Tomoya Kujirai, Mikihiro Shibata, Aya Okuda, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, & Hitoshi Kurumizaka, “Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome.” Commun. Biol. 4, 191 (2021).
  3. Tetsuo Komori, Heri Satria, Kyohei Miyamura, Ai Ito, Magoto Kamiya, Ayumi Sumino, Takakazu Onishi, Kazuaki, Ninomiya, Kenji Takahashi, Jared L. Anderson, Takuya Uto, and Kosuke Kuroda, “Essential requirements of biocompatible cellulose solvents.” ACS Sustainable Chem. Eng. 9, 35, 11825–11836 (2021).
  4. Hatsuo Yamamura, Tatsuya Hagiwara, Yuma Hayashi, Kayo Osawa, Hisato Kato, Takashi Katsu, Kazufumi Masuda, Ayumi Sumino, Hayato Yamashita, Ryo Jinno, Masayuki Abe, & Atsushi Miyagawa, “Antibacterial activity of membrane-permeabilizing bactericidal cyclodextrin derivatives.” ACS Omega, 6, (47), 31831-31842 (2021).

2020

  1. Tetsuya Ueta, Keiichi Kojima, Tomoya Hino, Mikihiro Shibata, Shingo Nagano, & Yuki Sudo, “Applicability of styrene-maleic acid copolymer for two microbial rhodopsins, RxR and HsSRI.” Biophys. J. 119 (9) 1760-1770 (2020).

2019

  1. Ayumi Sumino*,Takashi Sumikama, Takayuki Uchihashi*, & Shigetoshi Oiki*, “High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit.” Sci. Adv. 5(7) eaax0495 (2019).
  2. Wataru Shihoya, Keiichi Inoue, Manish Singh, Masae Konno, Shoko Hososhima, Keitaro Yamashita, Kento Ikeda, Akimitsu Higuchi, Tamaki Izume, Sae Okazaki, Masanori Hashimoto, Ritsu Mizutori, Sahoko Tomida, Yumeka Yamauchi, Rei Abe-Yoshizumi, Kota Katayama, Satoshi P Tsunoda, Mikihiro Shibata, Yuji Furutani, Alina Pushkarev, Oded Béjà, Takayuki Uchihashi, Hideki Kandori, & Osamu Nureki, “Crystal structure of heliorhodopsin.” Nature 574 (7776) 132-136 (2019).
  3. Katsuya Sakai, Toby Passioura, Hiroki Sato, Kenichiro Ito, Hiroki Furuhashi, Masataka Umitsu, Junichi Takagi, Yukinari Kato, Hidefumi Mukai, Shota Warashina, Maki Zouda, Yasuyoshi Watanabe, Seiji Yano, Mikihiro Shibata, Hiroaki Suga, & Kunio Matsumoto, “Macrocyclic peptide-based inhibition and imaging of hepatocyte growth factor.” Nat. Chem. Biol. 15 (6) 598-606 (2019).

2018

  1. Mikihiro Shibata, Keiichi Inoue, Kento Ikeda, Masae Konno, Manish Singh, Chihiro Kataoka, Rei Abe-Yoshizumi, Hideki Kandori, & Takayuki Uchihashi, “Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy.” Sci. Rep. 8(1) 8262 (11 pages) (2018).
  2. Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, & Yasuhisa Mizutani, “High thermal stability of oligomeric assemblies of thermophilic rhodopsin in a lipid environment.” J. Phys. Chem. B 122(27) 6945-6953 (2018).

2017

  1. Mikihiro Shibata*, Hiroshi Nishimasu*, Noriyuki Kodera, Seiichi Hirano, Toshio Ando, Takayuki Uchihashi, & Osamu Nureki*, “Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy.” Nat. Commun. 8(1) 1430 (9 pages) (2017).
  2. Mikihiro Shibata*, Hiroshi Watanabe, Takayuki Uchihashi, Toshio Ando, & Ryohei Yasuda, “High-speed atomic force microscopy imaging of live mammalian cells.” Biophys. Physicobiol. 14 127-135 (2017).