herbicide binding niche of photosystem II--a model

The Q(B) binding niche of photosystem II is also the binding site for many different herbicides. In order to understand the mode of binding of the herbicides, a 3-dimensional model of the binding niche was constructed. The model was based upon a comparison of the known structure of the Q(B) binding niche in purple bacteria with sequence and mutant data of the D-1 protein of photosystem II. Plastoquinone builds up hydrogen bonds to phenylalanine 265 backbone amide nitrogen, to serine 264 hydroxyl, and to histidine 215 delta-1 nitrogen. In addition to these hydrogen bond donors and acceptors, herbicides call build up hydrogen bonds to backbone carbonyl of alanine 263 and to serine 268 hydroxyl. This is supported by binding data of inhibitors in Chlamydomonas reinhardtii chloroplasts of wild type and of five D-I protein mutants (Ser264Ala, Ala251 Val, Phe255Tyr, Val2l9Ile, Leu275Phe).