研究成果

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, 25018-25035 (2024).

Mohammad Shahidul Alam, Marcos Penedo*, Takashi Sumikama*, Keisuke Miyazawa, Kaori Hirahara, Takeshi Fukuma*, "Revealing the Mechanism Underlying 3D‐AFM Imaging of Suspended Structures by Experiments and Simulations" Small Methods 8, 2400287 (2024).

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" Nature Communications 14, 7835 (2023).

Takehisa Dewa*, Komei Kimoto, Genki Kasagi, Hiromi Harada, Ayumi Sumino, Masaharu Kondo, "Functional Coupling of Biohybrid Photosynthetic Antennae and Reaction Center Complexes: Quantitative Comparison with Native Antennae"  Journal of Physical Chemistry B 127, 10315-10325 (2023).

Takashi Sumikama*, "Computation of topographic and three-dimensional atomic force microscopy images of biopolymers by calculating forces" Biophysical Reviews 15, 2059-2064 (2023).

Katsumasa Irie*, Yoshinori Oda, Takashi Sumikama, Atsunori Oshima, Yoshinori Fujiyoshi, "The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel" Nature Communications 14, 4236 (2023).

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" Science Advances 9, eadh1069 (2023).

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" Proceedings of the National Academy of Sciences of the United States of America 120, e2301013120 (2023).

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,  4629-4641 (2023).

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 Time Scale" Nano Letters 23, 1696-1704 (2023).

Takashi Sumikama*, Filippo Federici Canova, David Z. Gao, Marcos Penedo, Keisuke Miyazawa, Adam S. Foster, Takeshi Fukuma*, "Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality" Journal of Physical Chemistry Letters 13, 5365-5371 (2022).  [chosen for the cover art]

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, 31831-31842 (2021).

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, 54817-54829 (2021).

Ayhan Yurtsever*, Sandip Das#,*, Tatsuya Nishimura, Rafael Rodríguez, Daisuke Hirose, Kazuki Miyata, Ayumi Sumino, Takeshi Fukuma, Katsuhiro Maeda*, "Visualisation of helical structures of poly(diphenylacetylene)s bearing chiral amide pendants by atomic force microscopy" Chemical Communications 57, 12266-12269 (2021).

Mahroof Kalathingal, Takashi Sumikama, Shigetoshi Oiki, Shinji Saito*, "Vectorial insertion of a β-helical peptide into membrane: A theoretical study on polytheonamide B" Biophysical Journal 120, 4786-4797 (2021).

Tetsuo Komori, Heri Satria, Kyohei Miyamura, Ai Ito, Magoto Kamiya, Ayumi Sumino, Takakazu Onishi, Kazuaki Ninomiya, Kenji Takahashi, Jared L. Anderson, Takuya Uto*, Kosuke Kuroda*, "Essential Requirements of Biocompatible Cellulose Solvents" ACS Sustainable Chemistry & Engineering 9, 11825-11836 (2021).

Kenichiro Mita, Takashi Sumikama#, Masayuki Iwamoto, Yuka Matsuki, Kenji Shigemi, Shigetoshi Oiki*, "Conductance selectivity of Na+ across the K+ channel via Na+ trapped in a tortuous trajectory" Proceedings of the National Academy of Sciences of the United States of America 118, e2017168118 (2021).

Shigekuni Hosogi, Yoshinori Marunaka, Eishi Ashihara, Tadaaki Yamada, Ayumi Sumino, Hideo Tanaka, Leonardo Puppulin*, "Plasma membrane anchored nanosensor for quantifying endogenous production of H2O2 in living cells" Biosensors & bioelectronics 179, 113077-113077 (2021).

Ryosuke Fukuda, Mio Saito#, Shiori Shibukawa, Ayumi Sumino, Minoru Nakano, Tatsuya Murakami*, "Urea-Assisted Reconstitution of Discoidal High-Density Lipoprotein" Biochemistry 59, 1455-1464 (2020).

Takashi Sumikama*, Adam S. Foster, Takeshi Fukuma*, "Computed Atomic Force Microscopy Images of Chromosomes by Calculating Forces with Oscillating Probes" Journal of Physical Chemistry C 124, 2213-2218 (2020). [chosen for the cover art]

Takashi Sumikama, Shigetoshi Oiki*, "Queueing arrival and release mechanism for K+ permeation through a potassium channel" Journal of Physiological Sciences 69, 919-930 (2019).

Ayumi Sumino*, Takashi Sumikama#, Takayuki Uchihashi*, Shigetoshi Oiki*, "High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit" Science Advances 5, eaax0495 (2019).

Masataka Inada, Masanao Kinoshita, Ayumi Sumino, Shigetoshi Oiki, Nobuaki Matsumori*, "A concise method for quantitative analysis of interactions between lipids and membrane proteins" Analytica Chimica Acta 1059, 103-112 (2019).

Katsuhiro Ajito*, Yuko Ueno, Jae-Young Kim, Takashi Sumikama#,*, "Capturing the Freeze-Drying Dynamics of NaCl Nanoparticles Using THz Spectroscopy" Journal of the American Chemical Society 140, 13793-13797 (2018).

Tomoyasu Noji, Mikano Matsuo#, Nobutaka Takeda, Ayumi Sumino, Masaharu Kondo, Mamoru Nango, Shigeru Itoh, Takehisa Dewa*, "Lipid-Controlled Stabilization of Charge-Separated States (P+QB–) and Photocurrent Generation Activity of a Light-Harvesting–Reaction Center Core Complex (LH1-RC) from Rhodopseudomonas palustris" Journal of Physical Chemistry B 122, 1066-1080 (2018).

Mahroof Kalathingal, Takashi Sumikama, Toshifumi Mori, Shigetoshi Oiki, Shinji Saito*, "Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study" Physical Chemistry Chemical Physics 20, 3334-3348 (2018).

Masayuki Iwamoto, Ayumi Sumino, Eri Shimada, Masanao Kinoshita, Nobuaki Matsumori, Shigetoshi Oiki*, "Channel Formation and Membrane Deformation via Sterol-Aided Polymorphism of Amphidinol 3" Scientific Reports 7, 10782 (2017).

Ayumi Sumino, Takayuki Uchihashi, Shigetoshi Oiki*, "Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging" Journal of Physical Chemistry Letters 8, 785-793 (2017).

Takashi Yokoyama, Daisuke Yoshida, Hiroya Mori, Masaya Okabe, Zameer Shervani*, Keijiro Taga, Yasushi Yamamoto, Ayumi Sumino, Takehisa Dewa, Mamoru Nango, Masato Yamamoto, "MorphologicaObservation of Specific Condensation Effect of Cholesterol on Dipalmitoyl Phosphatidyl Choline (DPPC) Monolayer by Dropping Method" Journal of Biophysical Chemistry 7, 98-109 (2016).

Takashi Sumikama, Shigetoshi Oiki*, "Digitalized K+ Occupancy in the Nanocavity Holds and Releases Queues of K+ in a Channel" Journal of the American Chemical Society 138, 10284-10292 (2016).

Takashi Sumikama*, "Origin of the Shape of Current-Voltage Curve through Nanopores: A Molecular Dynamics Study" Scientific Reports 6, 25750 (2016).

Chiasa Uragami, Yuko Sugai#, Kohei Hanjo, Ayumi Sumino, Ritsuko Fujii, Takanori Nishioka, Isamu Kinoshita, Takehisa Dewa, Mamoru Nango, Alastair T. Gardiner, Richard J. Cogdell, Hideki Hashimoto*, "Observation of hybrid artificial photosynthetic membranes using peripheral and core antennae from two different species of photosynthetic bacteria by AFM and fluorescence micro-spectroscopy" Journal of Photochemistry and Photobiology A: Chemistry 313, 60-71 (2015).

Takehisa Dewa*, Ayumi Sumino, Natsuko Watanabe, Tomoyasu Noji, Mamoru Nango, "Structure-function relationships of the supramolecular assembly of the bacterial photosynthetic antenna complexes in lipid membranes" Research on Chemical Intermediates 40, 3243-3256 (2014).

Ayumi Sumino, Daisuke Yamamoto, Masayuki Iwamoto, Takehisa Dewa, Shigetoshi Oiki*, "Gating-Associated Clustering-Dispersion Dynamics of the KcsA Potassium Channel in a Lipid Membrane" Journal of Physical Chemistry Letters 5, 578-584 (2014).

Takashi Sumikama*, Shinji Saito*, Iwao Ohmine*, "Mechanism of ion permeation through a model channel: Roles of energetic and entropic contributions" Journal of Chemical Physics 139, 165106 (2013).

Ayumi Sumino, Takehisa Dewa*, Tomoyasu Noji, Yuki Nakano, Natsuko Watanabe, Richard Hildner, Nils Boesch, Juergen Koehler, Mamoru Nango*, "Influence of Phospholipid Composition on Self-Assembly and Energy-Transfer Efficiency in Networks of Light-Harvesting 2 Complexes" Journal of Physical Chemistry B 117, 10395-10404 (2013).

Shuhei Koeda, Katsunari Umezaki, Ayumi Sumino, Tomoyasu Noji, Atsushi Ikeda, Yasushi Yamamoto, Takehisa Dewa, Keijiro Taga, Mamoru Nango, Toshiki Tanaka, Toshihisa Mizuno*, "Creation of Cross-Linked Bilayer Membranes That Can Incorporate Membrane Proteins from Oligo-Asp-Based Peptide Gemini Surfactants" Langmuir 29, 11695-11704 (2013).

Takehisa Dewa*, Ayumi Sumino, Natsuko Watanabe, Tomoyasu Noji, Mamoru Nango*, "Energy transfer and clustering of photosynthetic light-harvesting complexes in reconstituted lipid membranes" Chemical Physics 419, 200-204 (2013).

Ayumi Sumino, Takehisa Dewa*, Nobuaki Sasaki, Masaharu Kondo, Mamoru Nango*, "Electron Conduction and Photocurrent Generation of a Light-Harvesting/Reaction Center Core Complex in Lipid Membrane Environments" Journal of Physical Chemistry Letters 4, 1087-1092 (2013).

Naoya Okiyama, Eriko Ota, Ayumi Sumino, Tomoyasu Noji, Katsuhiro Yamamoto, Jun-Ichi Oku, Takehisa Dewa, Toshiki Tanaka, Toshihisa Mizuno*, "Creation of fibrous nanotubes of green fluorescent protein by conjugation with pH-responsive polymer, poly(2-vinylpyridine), and use of microfluidic synthesis" Chemistry Letters 42, 495-497 (2013).

Ayumi Sumino, Takashi Sumikama, Masayuki Iwamoto, Takehisa Dewa*, Shigetoshi Oiki*, "The Open Gate Structure of the Membrane-Embedded KcsA Potassium Channel Viewed From the Cytoplasmic Side" Scientific Reports 3, 1063 (2013).

Shunsuke Sakai, Akito Hiro, Ayumi Sumino, Toshihisa Mizuno, Toshiki Tanaka, Hideki Hashimoto, Takehisa Dewa*, Mamoru Nango*, "Reconstitution and Organization of Photosynthetic Antenna Protein Complex Bearing Functional Hydrophilic Domains" Chemistry Letters 40, 1280-1282 (2011).

Daisuke Uchiyama, Hajime Hoshino, Kohei Otomo, Taro Kato, Ken-ichi Onda, Akira Watanabe, Hiroyuki Oikawa, Satoru Fujiyoshi, Michio Matsushita*, Mamoru Nango, Natsuko Watanabe, Ayumi Sumino, Takehisa Dewa, "Single-protein study of photoresistance of pigment–protein complex in lipid bilayer" Chemical Physics Letters 511, 135-137 (2011).

Ayumi Sumino, Takehisa Dewa*, Toshikazu Takeuchi, Ryuta Sugiura, Nobuaki Sasaki, Nobuo Misawa, Ryugo Tero, Tsuneo Urisu, Alastair T. Gardiner, Richard J. Cogdell, Hideki Hashimoto, Mamoru Nango*, "Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis" Biomacromolecules 12, 2850-2858 (2011).

Ayumi Sumino, Takehisa Dewa*, Masaharu Kondo, Takashi Morii, Hideki Hashimoto, Alastair T. Gardiner, Richard J. Cogdell, Mamoru Nango*, "Selective Assembly of Photosynthetic Antenna Proteins into a Domain-Structured Lipid Bilayer for the Construction of Artificial Photosynthetic Antenna Systems: Structural Analysis of the Assembly Using Surface Plasmon Resonance and Atomic Force Microscopy" Langmuir 27, 1092-1099 (2011).

Ayumi Sumino, Takehisa Dewa*, Nobuaki Sasaki, Natsuko Watanabe, Masaharu Kondo, Takashi Morii, Hideki Hashimoto, Mamoru Nango*, "Reconstitution and AFM observation of photosynthetic membrane protein assembly in planar lipid bilayers" e-Journal of Surface Science and Nanotechnology 9, 15-20 (2011).

Shigetoshi Oiki,* Masayuki Iwamoto, Takashi Sumikama, "Cycle Flux Algebra for Ion and Water Flux through the KcsA Channel Single-File Pore Links Microscopic Trajectories and Macroscopic Observables" PLoS ONE 6, e16578 (2011).

Shigetoshi Oiki*, Masayuki Iwamoto, Takashi Sumikama, "A mesoscopic approach to understanding the mechanisms underlying the ion permeation on the discrete-state diagram" Journal of General Physiology 136, 363-365 (2010).

Takehisa Dewa*, Tomohiro Asai, Yuka Tsunoda, Kiyoshi Kato, Daisukc Baba, Misa Uchida, Ayumi Sumino, Kayoko Niwata, Takuya Umemoto, Kouji Iida, Naoto Oku, Mamoru Nango*, "Liposomal Polyamine−Dialkyl Phosphate Conjugates as Effective Gene Carriers: Chemical Structure, Morphology, and Gene Transfer Activity" Bioconjugate Chemistry 21, 844-852 (2010).

Takashi Sumikama, Shinji Saito, Iwao Ohmine*, "Mechanism of ion permeation in a model channel: Free energy surface and dynamics of K+ ion transport in an anion-doped carbon nanotube" Journal of Physical Chemistry B 110, 20671-20677 (2006).