SHIMIZU Hirofumi

FacultyMorphological and Physiological Sciences, Molecular Physiology and Biophysics
Teacher OrganizationMorphological and Physiological Sciences
Education and
 Research Organization
Faculty of Medical Sciences, School of Medicine
PositionSenior Assistant Professor
Last Updated: 19/07/23 18:48

Researcher Profile & Settings


    SHIMIZU Hirofumi


  •  Morphological and Physiological Sciences, Molecular Physiology and Biophysics Senior Assistant Professor


  • 2000The University of Tokyo 生物化学

Research Activities

Published Papers

  • 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
  • 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 Not 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
  • 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
  • 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
  • Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field
    Yamakata, Akira;Shimizu, Hirofumi;Oiki, Shigetoshi
  • Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy
    Furutani Yuji;Shimizu Hirofumi;Asai Yusuke;Oiki Shigetoshi;Kandori Hideki
    Biophysics and Physicobiology 12 37-45 2015
    The X-ray structure of KcsA, a eubacterial potassium channel, displays a selectivity filter composed of four parallel peptide strands. The backbone carbonyl oxygen atoms of these strands solvate multiple K+ ions. KcsA structures show different distributions of ions within the selectivity filter in solutions containing different cations. To assess the interactions of cations with the selectivity filter, we used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Ion-exchange-induced ATR-FTIR difference spectra were obtained by subtracting the spectrum of KcsA soaked in K+ solution from that obtained in Li+, Na+, Rb+, and Cs+ solutions. Large spectral changes in the amide-I and -II regions were observed upon replacing K+ with smaller-sized cations Li+ and Na+ but not with larger-sized cations Rb+ and Cs+. These results strongly suggest that the selectivity filter carbonyls coordinating Rb+ or Cs+ adopt a conformation similar to those coordinating K+ (cage configuration), but those coordinating Li+ or Na+ adopt a conformation (plane configuration) considerably different from those coordinating K+. We have identified a cation-type sensitive amide-I band at 1681 cm−1 and an insensitive amide-I band at 1659 cm–1. The bands at 1650, 1639, and 1627 cm–1 observed for Na+-coordinating carbonyls were almost identical to those observed in Li+ solution, suggesting that KcsA forms a similar filter structure in Li+ and Na+ solutions. Thus, we conclude that the filter structure adopts a collapsed conformation in Li+ solution that is similar to that in Na+ solution but is in clear contrast to the X-ray crystal structure of KcsA with Li+.
  • 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.

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