Molecular dynamics mechanism to generate species differences in inhibition of protoporphyrinogen oxidase by flumioxazin

- A mechanism of species difference in inhibitory potency of flumioxazin is proposed.
- Amino acid sequence variance induces species difference in global dynamics of PPO.
- Local dynamics of a flumioxazin-binding pocket affects PPO-flumioxazin interaction.
- Species difference in the global dynamics propagates to the local dynamics.

Flumioxazin is an N-phenylimide herbicide and shows a remarkable species difference in developmental toxicity between rats and rabbits. The species difference is corresponded well to the inhibitory potency on protoporphyrinogen oxidase (PPO), an enzyme involved in chlorophyll and heme biosynthesis. In vitro experiments have shown that rat PPO is more sensitive to flumioxazin than human PPO and rabbit PPO. However, it remains unknown how the large difference in sensitivity to flumioxazin is generated in PPOs with highly conserved amino acid sequences. In order to determine the molecular dynamics (MD) mechanism responsible for these species differences, we performed MD simulations of human, rat, and rabbit PPO-flumioxazin complexes and found that rat PPO exhibited a higher binding affinity of flumioxazin than human and rabbit PPOs. A sophisticated comparative analysis of MD trajectories demonstrated that differences in the dynamics of the 107-120 loop region derived from amino acid sequence variants generated differences in the PPO-flumioxazin interactions via changes in the dynamics of Arg97. Moreover, a change in the shape of the flumioxazin-binding pocket in human PPO weakened the van der Waals forces contributing to the human PPO-flumioxazin interaction. Additionally, the positional and orientational shift in flumioxazin weakened the Coulomb force contributing to the rabbit PPO-flumioxazin interaction. These findings support the involvement of an MD mechanism in species differences in flumioxazin sensitivity.