MIZUKAMI, Taku Assistant Professor
School of Materials Science
◆Degrees
Ph.D.from Kyoto University (1994)
◆Professional Experience
2016 - : 石川高専 , 情報科学 , 非常勤講師
◆Specialties
Other
◆Research Keywords
Protein, Water, Molecular Simulation, Data Mining
◆Research Interests

My interest is the reaction mechanism of biological molecules. Biochemical reaction has aspects of ``controlled'' selectivity and high-efficiency, especially in proteins. To investigate the reaction mechanism, I developed a spectroscopic approach to the biological molecules which were sometimes artificially modified.
1) Signal transduction of photoreceptor proteins:
Visual excitation is caused by a single photon absorption with the chromophore of photoreceptor proteins in visual cell on retina, rhodopsin or iodopsin, results in electrophysiological responses of the cell. The primary process is 11-cis to all-trans isomerization of its chromophore, retinal, with abruptly high quantum yield (0.67). By means of picosecond flash photolysis and ring-modified analog retinal, I have proposed a highly twisted chromophore of primary intermediate (ground state), photorhodopsin, which accelerate photoisomerization of retinal. The result suggests anisotropic and distinct configuration of amino acid residues being located around the chromophore, retinal. Recently, it has been discovered out that the successive photobiological reactions could be described as a series of high-efficient chemical reactions. I am now focusing on the ``controlled'' singularity of the reaction field of protein by means of UV or IR low-temperature spectrophotometry, flash photolysis (from 10-15 to 100 sec) , dichroism, numerical data analysis and cheical or biological modification of the sample.
2) Improvement of spectroscopy for biomolecules:
For a kinetic reaction analysis of biomolecule, a more qualitative method is needed. I propose to design an apparatus which can derive automatically a large number of timeresolved spectral data and decide a reaction scheme simultaneously optimizing its thermodynamic parameters by numerical data analysis methods, singular value decomposition (SVD), etc.
3) Molecular design of biomimetic material:
Some organic compounds bind to retinal and induce a regioselective photoisomerization of its chromophore. I am investigating synthetic photoreceptor-like molecules for application of novel materials.
Mechanisms of protein function expression by means of the fusion of molecular simulation and data-mining methods.
The molecular motion or the functional expression process of protein is described by time resolved-data with 3(N-1)dimension when protein is treated as N-atom cluster. However many kinds of protein have N as over 10^4 ,resulting in a large amount of simulation data. For the purpose to analyze the protein functional expression mechanisms with novel ideas which are free from a "prejudice of physics", I apply data- mining methods, i.e. principal component analysis and support vector machine, to the simulation data. Hi-through-put analysis will be achieved by fusion of simulation and data-mining methods.

■Publications

◆Published Papers
第一原理計算とデータ科学的アプローチ
ダムヒョウチ,水上卓
化学と教育, 67, 2, 62-64, 2019
Free energy profiles of lipid translocation across pure POPC and POPC/CHOL bilayer: all-atom molecular dynamics study (accepted)
Hiroaki Saito, Tetsuya Morishita, Taku Mizukami, Ken-ichi Nishiyama, Kazutomo Kawaguchi, Hidemi Nagao
-, 2019
Molecular dynamics study of binary POPC bilayers: Molecular condensing effects on membrane structure and dynamics
Hiroaki Saito, Tetsuya Morishita, Taku Mizukami, Ken Ichi Nishiyama, Kazutomo Kawaguchi, Hidemi Nagao
Journal of Physics: Conference Series, 1136, -, 2018
Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction
Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, Hidemi NAGAO
JPS Conf. Proc., 012053-, 2014
Molecular Dynamics Simulations of the Hras-GTP Complex and the Hras-GDP Complex
Miyakawa Takeshi, Morikawa Ryota, Takasu Masako, Sugimori Kimikazu, Mizukami Taku, Kawaguchi Kazutomo, Saito Hiroaki, Nagao Hidemi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 113, 21, 2333-2337, 2013
◆Misc
混合脂質膜における脂質分子の膜透過・離脱に関する自由エネルギー曲線
齋藤大明, 森下徹也, 水上卓, 川口一朋, 長尾秀実
分子シミュレーション討論会講演要旨集, 32nd, 132-, 2018
Presence of two rhodopsin intermediates responsible for transducin activation.
Shuji Tachibanaki, Hiroo Imai, Taku Mizukami, Tetsuji Okada, Yasushi Imamoto, Takahiko Matsuda, Yoshitaka Fukada, Akihisa Terakita, Yoshinori Shichida
Biochemistry, 36, 46, 14173-14180, 1997
◆Books
◆Conference Activities & Talks
Machine-learning approach for water dynamics(水のダイナミクスへの機械学習アプローチ)
日本生物物理学会 第57回年会, 2019
Classification and prediction of physicochemical properties by machine-learning approach: molecular dynamic study of hydration water(機械学習アプローチによる物理化学量の予測)
日本生物物理学会 第56回年会, 岡山市,岡山大学, 2018
Molecular dynamics study on the free energy profiles of lipid translocation across binary POPC bilayer mixtures
XXIX IUPAP Conference on Computational PhysicsCCP 2018 July 29 – August 2, 2018, UC Davis, USA, 2018
Molecular dynamic study on solvation free energy of water and model protein
XXIX IUPAP Conference on Computational PhysicsCCP 2018 July 29 – August 2, 2018, UC Davis, USA, 2018
Solvation free energy in protein docking process: a molecular dynamics study
XXIX IUPAP Conference on Computational PhysicsCCP 2017July, 9th to 13th, 2017, Paris, FRANCE, 2017

■Contributions to  Society

◆Academic Society Affiliations
THE CHEMICAL SOCIETY OF JAPAN, Society of Molecular Science Japan, Biophysical Society Japan
◆Social Contribution
・ 欧文誌 Biophysics and Physicobiology 編集委員 (Associate Editor) 2020
・ 欧文誌 Biophysics and Physicobiology 編集委員 2010 - 2019
・ 金沢泉丘高校スーパーサイエンスハイスクール 2019