Molecular modelling of the interaction between DCMU and QB-binding site of photosystem II

The preferred binding orientations for the herbicide DCMU within the QB-binding of the D1 protein model from a photosystem II reaction centre have been determined. Calculation of the intermolecular energy between the herbicide and the binding site has been instrumental in obtaining optimum positions reinforced by experimental results from mutation studies and herbicide binding to analogous bacterial reaction centres. We have shown that two binding sites are possible, one involving a hydrogen bond to the His 215 residue of the QB-binding site and the other to the Ser 264 residue. In both cases, it appears to be the van der Waals forces which are more important for the stabilization of the interactions.