Building and Evaluating Force Field Parameters around Transition Metal-including Active Site in 4-Hydroxyphenylpyruvate Dioxygenase (HPPD)

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.