Professor Mikihiro Shibata
Faculty, Affiliation
WPI Nano Life Science Institute Institute for Frontier Science Initiative, WPI-NanoLSI
College and School Educational Field
Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology
Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology
Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology
Course in Physics, School of Mathematics and Physics, College of Science and Engineering
Laboratory
Biophysics TEL:076-264-5927 FAX:076-264-5739
Academic Background
【Academic background(Doctoral/Master's Degree)】
Nagoya Institute of Technology Doctor Department of Materials Science and Engineering Department of Materials Science and Engineering 200703 Completed
Nagoya Institute of Technology Master Department of Materials Science and Engineering Department of Materials Science and Engineering 200503 Completed
【Academic background(Bachelor's Degree)】
Nagoya Institute of Technology Applied Chemistry 200303
【Degree】
Ph. D (Engineering)
Career
Kanazawa University Department of Physics Tenure Track Associate Professor(2016/03/01-)
Kanazawa University Department of Physics Postdoctoral Fellow(2015/08/01-2016/02/29)
Max Planck Florida Institute for Neuroscience Neuronal Signal Transduction Postdoctoral Fellow(2013/04/01-2015/07/31)
Duke University Medical Center Department of Neurobiology Postdoctoral Fellow(2011/04/01-2013/03/31)
JSPS Postdoctoral Fellowship for Research Abroad(2011/04/01-2013/02/28)
JSPS Research Fellowship for Young Scientists (SPD)(2008/04/01-2011/03/31)
JSPS Research Fellowship for Young Scientists (PD)(2007/04/01-2008/03/31)
JSPS Research Fellowship for Young Scientists (DC1)(2005/04/01-2007/03/31)
Year & Month of Birth
1980/08
Academic Society
The Biophysical Society of Japan
The Molecular Biology Society of Japan
Biophysical Society
Award
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
○The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology The Young Scientists’ Prize(2018/04/17)
Specialities
Biophysics、Nanobioscience
Speciality Keywords
atomic force microscopy, membraneproteins, single-molecules
Research Themes
Investigations of molecular mechanism of genome editing tools by high-speed AFM
High-speed atomic force microscopy for Neuroscience
Bio-nano-imaging using high-speed atomic force microscopy
Books
- T. Ando, T. Uchihashi, N. Kodera, M. Shibata, D. Yamamoto, H. Yamashita Atomic force microscopy in liquid (Arturo M Baró ed.) Wiley-VCH Verlag GmbH (Chapter 7: High-speed AFM for observing dynamic processes in liquid) 2012
Papers
- High thermal stability of oligomeric assemblies of Thermophilic rhodopsin in a lipid environment. T. Shionoya, M. Mizuno, T. Tsukamoto, K. Ikeda, H. Seki, K. Kojima, M. Shibata, I. Kawamura, Y, Sudo, and Y, Mizutani J. Phys. Chem. B 122 27 6945-6953 2018/07/12
- Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. M. Shibata+, K. Inoue+, K. Ikeda, M. Konno, M. Singh, C. Kataoka, R. Abe-Yoshizumi, H. Kandori*, and T. Uchihashi* Sci. Rep. 8 8262 11 2018/05/29
- Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy. M. Shibata*+, H. Nishimasu*+, N. Kodera, S. Hirano, T. Ando, T. Uchihashi, and O. Nureki* Nature Communications 8 1430 2017/11/10
- High-speed atomic force microscopy imaging of live mammalian cells. M. Shibata*, H. Watanabe, T. Uchihashi, T. Ando, and R. Yasuda Biophys. Physicobiol. 14 127-135 2017/07/26
- Fast Adsorption of Soft Hydrogel Microspheres on Solid Surfaces in Aqueous Solutions. S. Matsui, S. Hiroshige, T. Kureha, M. Shibata, T. Uchihashi,* and D. Suzuki Angew. Chem. Int. Ed. 56 40 12146–12149 2017/08/25
- A natural light-driven inward proton pump. Keiichi Inoue, Shota Ito, Yoshitaka Kato, Yurika Nomura, Mikihiro Shibata, Takayuki Uchihashi, Satoshi P. Tsunoda & Hideki Kandori Nature Communications 7 13415 2016/11/17
- Functional extension of high-speed AFM for wider biological applications. T. Uchihashi, H. Watanabe, S. Fukuda, M. Shibata and T. Ando Ultramicroscopy 160 182-196 2016/01
- Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells. M. Shibata*, T. Uchihashi, T. Ando and R. Yasuda* Sci. Rep. 5 8724 2015
- Wide-area scanner for high-speed atomic force microscopy. H. Watanabe, T. Uchihashi, T. Kobashi, M. Shibata, J. Nishiyama, R. Yasuda and T. Ando Rev. Sci. Instrum. 84 053702 2013
- Role of trimer-trimer interaction of Bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy. H. Yamashita, K. Inoue, M. Shibata, T. Uchihashi, J. Sasaki, H. Kandori, T. Ando J. Struct. Biol. 184 2-11 2013
- Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps. K. Muroda, K. Nakashima, M. Shibata, M. Demura and H. Kandori Biochemistry 51 4677-4684 2012
- Structural changes in bacteriorhodopsin in response to alternate illumination observed by high-speed atomic force microscopy. M. Shibata, T. Uchihashi, H. Yamashita, H. Kandori and T. Ando Angew. Chem. Int. Ed. 50 4410-4413 2011
- High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. D. Yamamoto, T. Uchihashi, N. Kodera, H. Yamashita, S. Nishikori, T. Ogura, M. Shibata, and T. Ando Methods in Enzymol. (Part B) 475 541-564 2010
- Low-frequency dynamics of bacteriorhodopsin studied by terahertz time-domain spectroscopy. S. Kawaguchi, O. Kambara, M. Shibata, H. Kandori and K. Tominaga Phys. Chem. Chem. Phys. 12 10255-10262 2010
- High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. M. Shibata, H. Yamashita, T. Uchihashi, H. Kandori and T. Ando Nature Nanotech. 5 208-212 2010
- Picosecond time-resolved ultraviolet resonance raman spectroscopy of bacteriorhodopsin: Primary protein response to the photoisomerization of retinal. M. Mizuno, M. Shibata, J. Yamada, H. Kandori and Y. Mizutani J. Phys. Chem. B 113 12121-12128 2009
- Property of anion binding site of pharaonis halorhodopsin studied by ultrafast pump-probe spectroscopy and low-temperature FTIR spectroscopy. K. Nakashima, T. Nakamura, S. Takeuchi, M. Shibata, M. Demura, T. Tahara and H. Kandori J. Phys. Chem. B 113 8429-8434 2009
- Ultrafast pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: Halide-ion dependence and isomerization dynamics. T. Nakamura, S. Takeuchi, M. Shibata, M. Demura, H. Kandori and T. Tahara J. Phys. Chem B 112 12795-12800 2008
- Color change of proteorhodopsin by a single amino acid replacement at a distant cytoplasmic loop. M. Yoshitsugu, M. Shibata, D. Ikeda, Y. Furutani and H. Kandori Angew. Chem. Int. Ed. 47 3923-3926 2008
- Halide Binding by the D212N Mutant of Bacteriorhodopsin Affects Hydrogen-bonding of Water in the Active Site. M. Shibata, M. Yoshitsugu, N. Mizuide, K. Ihara and H. Kandori Biochemistry 46 7525-7535 2007
- Deprotonation of Glu234 during the photocycle of Natronomonas pharaonis halorhodopsin. M. Shibata, Y. Saito, M. Demura and H. Kandori Chem. Phys. Lett. 432 545-547 2006
- Structural changes in bacteriorhodopsin following retinal photoisomerization from the 13-cis form. N. Mizuide, M. Shibata, N. Friedman, M. Sheves, M. Belenky, J. Herzfeld and H. Kandori Biochemistry 45 10674-10681 2006
- Hydrogen-bonding interaction of the protonated Schiff base with halides in a chloride-pumping bacteriorhodopsin mutant. M. Shibata, K. Ihara and H. Kandori Biochemistry 45 10633-10340 2006
- Strongly hydrogen-bonded water molecule is observed only in the alkaline form of proteorhodopsin. Y. Furutani, D. Ikeda, M. Shibata and H. Kandori Chem. Phys. 324 705-708 2006
- Internal water molecules of the proton-pumping halorhodopsin in the presence of azide. N. Muneda, M. Shibata, M. Demura and H. Kandori J. Am. Chem. Soc. 128 6294-6295 2006
- Hydrogen-bonding alterations of the protonated Schiff base and water molecule in the chloride pump of Natronobacterium pharaonis. M. Shibata, N. Muneda, T. Sasaki, K. Shimono, N. Kamo, M. Demura and H. Kandori Biochemistry 44 12279-12286 2005
- FTIR studies of internal water molecules in the Schiff base region of bacteriorhodopsin. M. Shibata and H. Kandori Biochemistry 44 7406-7413 2005
- Internal water molecules of light-driven chloride pump proteins. M. Shibata, N. Muneda, K. Ihara, T. Sasaki, M. Demura and H. Kandori Chem. Phys. Lett. 392 330-333 2004
- Altered hydrogen bonding of Arg82 during the proton pump cycle of bacteriorhodopsin: A low-temperature polarized FTIR spectroscopic study. T. Tanimoto, M. Shibata, M. Belenky, J. Herzfeld and H. Kandori Biochemistry 43 9439-9447 2004
- Water molecules in the Schiff base region of bacteriorhodopsin. M. Shibata, T. Tanimoto and H. Kandori J. Am. Chem. Soc. 125 13312-13313 2003
Conference Presentations
- High-speed AFM visualized DNA cleavage reaction of CRISPR-Cas9.(conference：International Symposium on Atomic Force Microscopy at Solid-Liquid Interfaces)(2017/11/08)
- High-speed AFM imaging of membrane proteins in lipid nanodiscs.(2017/09/19)
- High-speed atomic force microscopy imaging of oligomeric states of microbial rhodopsins.(conference：International Symposium on Biophysics of Rhodopsin)(2017/05/11)
- Nanoscale Visualization of Membrane Proteins by High-Speed Atomic Force Microscopy(conference：International Symposium on Molecular Science – Physical Chemistry/Theoretical Chemistry, Chemoinformatics, Computational Chemistry)(2017/03/16)
- Visualization of protein molecules in action by high-speed atomic force microscopy.(2016/11/25)
- Nanoscale imaging of living cells by high-speed AFM.(conference：OIIB Retreat 2016 )(2016/11/21)
- Nanoscale visualization of morphological dynamics of living neurons by high-speed atomic force microscopy.(2016/09/25)
- High-speed atomic force microscopy for nano-scale imaging in live cells.(conference：OptoBioTechnology Symposium on “Membrane Protein Dynamics”)(2016/07/12)
Others
Arts and Fieldwork
Patent
Theme to the desired joint research
Grant-in-Aid for Scientific Research
○「高速AFMによるゲノム編集ツールCRISPR-Casの分子作動機構の網羅的解析」(2018-2020)
○「高速AFMを用いたCaMKIIの多量体構造内における記憶のメカニズム解明」(2016-2018)
Competitive research funding,Contribution
Collaborative research,Consignment study
Classes (Bachelors)
○Exercise in Electromagnetic 1(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Freshman Seminar I(2017)
○Physics Experiments 1(2017)
○Biophysics(2017)
○Exercise in Mathematics and Physics A(2017)
○Exercise in Mathematics and Physics B(2017)
○Physics Experiments 2(2017)
Classes (Graduate Schools)
○Exercise B(2017)
○Seminar B(2017)
○Research Work B(2017)
○Structure and dynamics of biological molecules(2017)
○Introduction to Molecular and Biophysics a(2017)
○Introduction to Molecular and Biophysics b(2017)
○Biophysics a(2017)
○Biophysics b(2017)