Taku Mizukami
Japan Advanced Institute of Science and Technology
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Publication
Featured researches published by Taku Mizukami.
FLOW DYNAMICS: The Second International Conference on Flow Dynamics | 2006
Ayumu Sugiyama; Yuichiro Takamatsu; Acep Purqon; Taku Mizukami; Hidemi Nagao; Kiyoshi Nishikawa
We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein azurin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules , which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B‐factor of these residues which indicates the fluctuation of hydration residues in each temperature. B‐factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature.
COMPLEX SYSTEMS: 5th International Workshop on Complex Systems | 2008
Keigo Nishikawa; Tetsunori Yamamoto; Ayumu Sugiyama; Acep Purqon; Taku Mizukami; Hidemi Nagao; Kiyoshi Nishikawa
We investigate the docking stability of Azurin(I)—Cytochrome C551(III) complex by molecular dynamic simulations. The charge distribution around the active sites for Azurin(I) and Cytochrome C551(III) is estimated by quantum chemical calculation to simulate the complex system by molecular dynamic simulations. We estimete some physical properties such as the root square mean deviation, distance between iron ion in active site of Cytochrome C551(III) and copper ion in active site of Azurin(I), the dynamical cross‐correlation map and free energy in the energetic representation. We discuss the stability of the complex system of Azurin(I)—Cytochrome C551(III) from these properties.
COMPLEX SYSTEMS: 5th International Workshop on Complex Systems | 2008
Tetsunori Yamamoto; Keigo Nishikawa; Ayumu Sugiyama; Acep Purqon; Taku Mizukami; Hidemi Nagao; Kiyoshi Nishikawa
The docking structure of the Azurin‐Cytochrome C551 is presented. We investigate a complex system of Azurin(II)‐Cytochrome C551(II) by using molecular dynamics simulation. We estimate some physical properties, such as root‐mean‐square deviation (RMSD), binding energy between Azurin and Cytochrome C551, distance between Azurin(II) and Cytochrome C551(II) through center of mass and each active site. We also discuss docking stability in relation to the configuration by free energy between Azurin(II)‐Cytochrome C551(II) and Azurin(I)‐Cytochrome C551(III).
Biochemistry | 2001
Yasushi Imamoto; Hisatsugu Koshimizu; Ken'ichi Mihara; Osamu Hisatomi; Taku Mizukami; Kazuo Tsujimoto; Mikio Kataoka; Fumio Tokunaga
Chemical Physics Letters | 2013
Hiroaki Saito; Masashi Iwayama; Taku Mizukami; Jiyoung Kang; Masaru Tateno; Hidemi Nagao
International Journal of Quantum Chemistry | 2012
Taku Mizukami; Hiroaki Saito; Shuhei Kawamoto; Takeshi Miyakawa; Masashi Iwayama; Masako Takasu; Hidemi Nagao
International Journal of Quantum Chemistry | 2012
Hiroaki Saito; Masashi Iwayama; Hiroyuki Takagi; Megumi Nishimura; Takeshi Miyakawa; Kazutomo Kawaguchi; Masako Takasu; Taku Mizukami; Hidemi Nagao
International Journal of Quantum Chemistry | 2013
Takeshi Miyakawa; Ryota Morikawa; Masako Takasu; Kimikazu Sugimori; Taku Mizukami; Kazutomo Kawaguchi; Hiroaki Saito; Hidemi Nagao
Chemistry Letters | 1997
Kazuo Tsujimoto; Yasuhiro Shirasaka; Taku Mizukami; Mamoru Ohashi
Chemistry Letters | 1997
Hikaru Urano; Taku Mizukami; Kazuo Tsujimoto