SHIMIZU Hirofumi

FacultyMorphological and Physiological Sciences, Integrative Systems Physiology
Teacher OrganizationMorphological and Physiological Sciences
Education and
 Research Organization
Faculty of Medical Sciences, School of Medicine
PositionSenior Assistant Professor
Last Updated: 20/10/06 16:36

Researcher Profile & Settings

Name

    SHIMIZU Hirofumi

Affiliation

  •  Morphological and Physiological Sciences, Integrative Systems Physiology Senior Assistant Professor

Education

  • 2000The University of Tokyo 生物化学

Research Activities

Published Papers

  • Single-Molecule Twisting Motions During Gating of the Human TRPV1 Channel Recorded with Sub-Millisecond Time Resolution
    Hirofumi Shimizu, Takuya Kobayashi, Masayuki Iwamoto, Kentaro Kajiwara, Nagomi Kurebayashi, Haruo Ogawa, Takashi Murayama.
    Biophysical Journal Vol. 118(Issue 3) p22a Feb.  2020 Refereed
  • Microfabricated Solution Chamber for High Resolution Diffracted X-Ray Tracking Method to Observe Ion-Channel Gating Motion
    Ikkei Yamauchi, Tomoki Tabuchi, Yoshikazu Hirai, Masayuki Iwamoto, Toshiyuki Tsuchiya, Hirofumi Shimizu, Osamu Tabata
    2019 20th International Conference on Solid-State Sensors, Actuators and Microsystems & Eurosensors XXXIII (TRANSDUCERS & EUROSENSORS XXXIII) 25-28 2019 Refereed
  • A Landscape for Structural Stabilities during Gating Transitions in the KcsA Potassium Channel.
    Shimizu, H., Iwamoto, M.
    J. Physiol. Sci. 68 s169 2018 Refereed
  • Microchannel Fabrication Using A Photo-Patternable Adhesive Material for Recording Conformational Changes of KcsA Channel with the Diffracted X-ray Tracking Method†
    Yoshikazu Hirai,Yasuaki Mori ,Tomoki Tabuchi ,Hirofumi Shimizu,Toshiyuki Tsuchiya and Osamu Tabata
    Proceedings 2 972 Dec.  2018 Refereed
  • Structural Analysis of KcsA by Cryo-EM Single Particle Analysis
    Takazaki Hiroko、Shimizu Hirofumi、Yasunaga Takuo
    Microscopy 67 i35 2018 Refereed
  • Hexameric and pentameric complexes of the ExbBD energizer in the Ton system
    Maki-Yonekura Saori、Matsuoka Rei、Yamashita Yoshiki、Shimizu Hirofumi、Tanaka Maiko、Iwabuki Fumie、Yonekura Koji
    eLife 7 e35419 2018 Refereed
  • Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
    Maki-Yonekura Saori;Matsuoka Rei;Yamashita Yoshiki;Shimizu Hirofumi;Tanaka Maiko;Iwabuki Fumie;Yonekura Koji
    eLife 7 2018
    :Gram-negative bacteria import essential nutrients such as iron and vitamin B12 through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force.
  • Photoresist Micro-Chamber for the Diffracted X-ray Tracking Method Recording Single-Molecule Conformational Changes
    Kio Tahara, Yoshikazu Hirai, Hirofumi Shimizu, Toshiyuki Tsuchiya, Osamu Tabata
    Procedia Engineering 163 1394-1397 2016 Refereed
  • Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field
    Yamakata, Akira;Shimizu, Hirofumi;Oiki, Shigetoshi
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17(33) 21104-21111 2015 Refereed
  • Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy
    Y. Furutani, H. Shimizu, Y. Asai, S. Oiki, H. Kandori
    Biophys and Physicobiology 12 37-45 2015 Refereed
  • Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field
    A. Yamakata, H. Shimizu, S. Oiki
    Phys Chemistry Chemical Physics 17 21104-21111 2015 Refereed
  • pH-dependent promotion of phospholipid flip-flop by the KcsA potassium channel
    Nakao, H., Ikeda, K., M.Iwamoto, H.Shimizu, S.Oiki, Ishihara, Y, Nakano, M.
     1848 145-150 2015 Refereed
  • pH-dependent promotion of phospholipid flip-flop by the KcsA potassium channel
    Nakao, Hiroyuki;Ikeda, Keisuke;Iwamoto, Masayuki;Shimizu, Hirofumi;Oiki, Shigetoshi;Ishihama, Yasushi;Nakano, Minoru
    BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1848(1) 145-150 2015 Refereed
  • Structural changes of the KcsA potassium channel upon application of the electrode potential studied by surface-enhanced IR absorption spectroscopy
    A.Yamakata, H.Shimizu, M.Osawa, S.Oiki
    Chemical Physics 419 224-228 2013 Refereed
  • Single Molecular Gating Dynamics for KcsA Potassium Channel
    S.Oiki, H.Shimizu, M.Iwamoto, T.Konno
    Adv. Chem. Phys. 146 147-194 Nov.  2011 Refereed
  • A cytotoxic peptide from a marine sponge exhibits ion channel activity through vectorial-insertion into the membrane
    M.Iwamoto, H.Shimizu, I.Muramatsu, S.Oiki
    FEBS Lett. 584(18) 3995-3999 Sep.  2010 Refereed
  • A Cytotoxic Peptide from a Marine Sponge, Polytheonamide B: I. Channel Activity and Vectorial-Insertion Into the Membrane
    M.Iwamoto, H.Shimizu, I.Muramatsu, S.Matsunaga, S.Oiki
     98(3) 110a Jan.  2010
  • A Cytotoxic Peptide from a Marine Sponge, Polytheonamide B; II. Properties for Ion Conduction and Voltage Dependent Gating
    M.Iwamoto, H.Shimizu, I.Muramatsu, S.Matsunaga, S.Oiki
     98(3) 109a Jan.  2010
  • pH-Dependent gating of KcsA potassium channel
    Y.Matsuki, M.Iwamoto, H.Shimizu, S.Oiki
     98(3suppliment1) 314a Jan.  2010 Not refereed
  • Ion distribution in the open KcsA channel evaluated by the streaming potential
    M.Iwamoto, H.Shimizu, S.Oiki
     59 suppl 256 2009
  • The water-ion coupling ratio for ion permeation through the KcsA potassium channel: Dependencies on concentration and species of permeating ions
    M.Iwamoto, H.Shimizu, S.Oiki
     96 suppl 179a 2009
  • Topological mapping of the asymmetric drug binding to the human ether-a-go-go-related gene product (HERG) potassium channel by use of tandem dimers
    T.Myokai, H.Shimizu, S.Ryu, S.Oiki
    Mol Phaemacol 73(6) 1643-51 Jun.  2008 Refereed
  • Global Twisting Motion of Single Molecular KcsA Potassium Channel Upon Gating
    H. Shimizu, M. Iwanoto, T. Konnno, A. Nihei, Yuji C, Sasaki, S. Oiki
    Cell 132(1) 67-78 Jan.  2008 Refereed
  • Flux coupling between ion and water in the K+ selective pore
    M.Iwamoto, H.Shimizu, S.Oiki
     58 suppl s77 2008 Not refereed
  • Surface structure and its dynamic rearrangements of the KcsA potassium channel upon gating and tetrabutylammonium blocking
    M.Iwamoto, H.Shimizu, F.Inoue, T.Konno, Y.C.Sasaki, S.Oiki
     281 28379-28386 Sep.  2006 Refereed
  • Conformational changes in the cytoplasmic domain of KcsA potassium channel upon gating
    M.Iwamoto, H.Shimizu, F.Inoue, T.Konno, A.Nihei, Y.C.Sasaki, S.Oiki
     56 suppl s157 2006 Not refereed
  • Paradoxical inhibition of protein aggregation and precipitation by transglutaminase-catalyzed intermolecular aross-lonking
    Konno,T., Morii,T., Shimizu, H., Oiki,S., Ikura,K.
     280(17) 17520 -17525 Apr.  2005 Refereed
  • Coupled K+-Water Flux through the HERG Potassium Channel Measured by an Osmotic Pulse Method
    H.Ando, M.Kuno, H.Shimizu, I.Muramatsu, S.Oiki
     126(5) 529-538 Jan.  2005 Refereed
  • Interaction between Tetraethylammonium and Permeant Cations at the Inactivation Gate of the HERG Potassium Channel
    Shimizu,H., Toyoshima,C., Oiki,S.
     53(1) 25-34 Feb.  2003 Refereed

Conference Activities & Talks

  • Single-Molecule Fluctuations and Conformational Changes of the Human Transient Receptor Potential Vanilloid 1 (TRPV1) Channel Recorded using Diffracted X-ray Tracking
    Shimizu Hirofumi,Kobayashi Takuya ,Iwamoto Masayuki ,Kajiwara Kentaro ,Kurebayashi Nagomi ,Ogawa Haruo,Murayama Takashi
    第97回日本生理学会大会 Mar.  2020
  • Single-Molecule Twisting Motions during Gating of the Human TRPV1 channel Recorded with Sub-Millisecond Time Resolution.
    Hirofumi Shimizu, Takuya Kobayashi, Masayuki Iwamoto, Kentaro Kajiwara, Nagomi Kurebayashi, Haruo Ogawa, Takashi Murayama
    64th Annual Meeting of Biophysical Society Feb.  2020
  • Microchannel Fabrication using a Photo Patternable Adhesive Material for Recording Conformational Changes of KcsA Channel with the Diffracted X-ray Tracking Method
    Yoshikazu Hirai, Yasuaki Mori, Tomoki Tabuchi, Hirofumi Shimizu, Toshiyuki Tsuchiya, Osamu Tabata
    The EUROSENSORS 2018
  • Structural Analysis of KcsA by Cryo-EM Single Particle Analysis
    Hiroko Takazaki, Hirofumi Shimizu, Kaoru Mitsuoka, Takuo Yasunaga
    第55回日本生物物理学会年会 2018
  • Method to Record Single-Molecule Fluctuations and Conformational Changes in Proteins
    Hirofumi Shimizu, Masayuki Iwamoto, Kentaro Kajiwara, Yoshikazu Hirai, Osamu Tabata
    9th FAOPS CONGRESS (Federation of the Asian and Oceanian Physiological Societies) Mar.  2019

Awards & Honors

  •  Ministry of Education,Culture,Sports,Science & Technology in Japan The Young Scientists’ Prize, The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and TechnologyApr. 2010


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