Molecular Modelling Studies on the Binding of Phenylurea Inhibitors to the D 1 Protein of Photosystem II

Abstract

Abstract A hypothetical molecular model of part of the D 1 protein of photosystem II, based on the analogous portion of the L subunit of the Rhodopseudomonas viridis reaction centre, has been used to study the binding of an extended hydrophobic phenylurea inhibitor (N,N-dimethyl-carbamoyl)4 -amino-4 ′-chloro-trans-stilbene) (I) to the QB site. The inhibitor was fitted by eye into a cleft in the site, and a limited part of the inhibitor/D 1 complex was energy minimized. The gross orientation of the inhibitor placed the dimethylurea moiety towards the predicted binding domain of the plastoquinone head group, and the stilbene moiety directed along the quinone isoprenoid side chain binding domain, suggesting a similar pathway of approach of the two molecules from the membrane into the binding site. Binding interactions of the inhibitor included hydrogen bonds to the side chain hydroxyl of ser 264 and the peptide carbonyl group of ala 251, with the side chain hydroxyl of ser 268 as an alternative ligand. Numerous hydrophobic contacts were also possible. Although phenylureas do not bind to reaction centres of Rp. viridis, many of the binding interactions to D1 could also be detected in Rp. viridis. However, the β-CH2 and δ-CO2 -groups of glu 212 in Rp. viridis are located in the corresponding region of D1 occupied by the dimethylurea moiety of the inhibitor in our model of its binding to D 1. This may explain why diuron (DCMU) does not bind to Rp. viridis reaction centres.