Development and application of the AMBER Molecular Mechanics force field to investigate herbicide interaction in plants

Photosystem II is the photosynthetic water-splitting enzyme, responsible of the release of oxygen into the air that we breathe. During photosynthetic electron transport, a plastoquinone molecule is reduced at the QB binding site of Photosystem II. This site is a common target for herbicides, but unfortunately there is a lack of understanding of the engineering rules that dictate their mode of action. An understanding of their precise binding mechanisms and interactions would however facilitate rational herbicide design. The determination of the crystal structure of Photosystem II from T. vulcanus with a resolution of 1.9Å is a spectacular achievement, and has enabled the application of standard force field based Molecular Mechanics calculations. To probe herbicide interaction, it is however necessary to have a fully parameterised molecular mechanics force field for all of the components constituting Photosystem II and its environment.

This project with therefore develop parameters for key components constituting Photosystem II, and a range of herbicides to be investigated. The results from this work with clearly aid the rational design of herbicides, and will therefore directly feed into the industrial agrochemical pipeline.