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Taku Mizukami Assistant Professor
School of Materials Science

■Degrees

Ph.D.from Kyoto University (1994)

■Specialties

biophysics, photobiology

■Research Keywords

Protein, Water, Molecular Simulation, Data Mining

■Research Interests

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

  • Molecular dynamics study on binding free energy of Azurin–Cytochrome c551 complex,H. Saito, M.Iwayama, T.Mizukami, J. Kang, M. Tateno, H. Nagao,Chemical Physics Letters,556,297-302,2013
  • Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile,H. Saito, M. Iwayama, H.Takagi, M.Nishimura, T. Miyakawa, K.Kawaguchi, M.Takasu, T. Mizukami, H. Nagao,International Journal of Quantum Chemistry,112,3834-3839,2012
  • Solvation effect on the structural change of a globular protein: a molecular dynamics study,Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, and Hidemi Nagao,International Journal of Quantum Chemistry,112,1,344,7,2011/11/19

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◇Lectures and Presentations

  • Molecular dynamic study on solvation free energy of water and model protein,Taku Mizukami, Hiroaki Saito,XXIX IUPAP Conference on Computational PhysicsCCP 2018 July 29 – August 2, 2018,UC Davis, USA,July 29 – August 2, 2018
  • Molecular dynamics study on the free energy profiles of lipid translocation across binary POPC bilayer mixtures,Hiroaki Saito, Taku Mizukami, Hidemi Nagao,XXIX IUPAP Conference on Computational PhysicsCCP 2018 July 29 – August 2, 2018,UC Davis, USA,July 29 – August 2, 2018
  • Solvation free energy in protein docking process: a molecular dynamics study,Taku Mizukami, Hiroaki Saito, and Hidemi Nagao,XXIX IUPAP Conference on Computational PhysicsCCP 2017July, 9th to 13th, 2017,Paris, FRANCE,July, 9th to 13th, 2017

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■Extramural Activities

◇Academic Society Affiliations

  • Society of Molecular Science Japan,A member of the society,2010-
  • Biophysical Society Japan,An editor of BIOPHYSICS,2008-

◇Other Activities

  • Member of The Chemical Society of Japan
  • Member of The Biophysical Society of Japan