[Published online Journal of Computer Chemistry, Japan Vol.21, 82-84, by J-STAGE]
<Title:> 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
<Author(s):> 宗井 陽平, 堀 優太, Hengphasatporn Kowit, 原田 隆平, 重田 育照
<Corresponding author E-Mill:> shigeta(at)ccs.tsukuba.ac.jp
<Abstract:> Metalloproteins such as 4-hydroxyphenylpyruvate dioxygenase (HPPD) and Cytochrome P450 are important for agrochemical research. In classical mechanics, to reproduce the metal-coordination environment of metalloproteins, various models (Nonbonded model, Bonded model, Nonbonded/Bonded Hybrid model etc.) for metal complexes have been developed. In this study, we built force field parameters for the molecular dynamics simulation of HPPD and evaluated the Fe2+-coordination environment. The result revealed that the hybrid model is suitable for the simulation of HPPD and able to simulate the metal-ligand (water) exchange process.
<Keywords:> Molecular dynamics, Metalloprotein, Force field, 4-Hydroxyphenylpyruvate dioxygenase, Agrochemical
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0003/_article/-char/ja/
<Title:> 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
<Author(s):> 宗井 陽平, 堀 優太, Hengphasatporn Kowit, 原田 隆平, 重田 育照
<Corresponding author E-Mill:> shigeta(at)ccs.tsukuba.ac.jp
<Abstract:> Metalloproteins such as 4-hydroxyphenylpyruvate dioxygenase (HPPD) and Cytochrome P450 are important for agrochemical research. In classical mechanics, to reproduce the metal-coordination environment of metalloproteins, various models (Nonbonded model, Bonded model, Nonbonded/Bonded Hybrid model etc.) for metal complexes have been developed. In this study, we built force field parameters for the molecular dynamics simulation of HPPD and evaluated the Fe2+-coordination environment. The result revealed that the hybrid model is suitable for the simulation of HPPD and able to simulate the metal-ligand (water) exchange process.
<Keywords:> Molecular dynamics, Metalloprotein, Force field, 4-Hydroxyphenylpyruvate dioxygenase, Agrochemical
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0003/_article/-char/ja/
