The topology of the 32 kDa herbicide binding protein of photosystem ii in the thylakoid membrane

The 32 kDa herbicide binding protein is a membrane bound protein which is implicated in the binding of many photosystem II herbicides as well as in the binding of the endogenous quinone QB which serves as the secondary electron acceptor on the reducing side of photosystem II. The topology of the 32 kDa protein has been predicted using a combination of hydrophobic moment analysis, membrane propensity analysis and empirical secondary structure predictions. Our model consists of five transmembrane helices. The loop connecting the fourth and fifth transmembrane helices is thought to form part of the herbicide binding site. Our analysis suggests that this loop also contains a helical segment which may seek the surface of the membrane by virtue of its relatively high hydrophobic moment. Our topology is compared with several others which have been proposed in the literature as well as with the topology of the L and M proteins of the bacterial reaction center of R. viridis. The significance of mutagenesis and photo-affinity labeling experiments is also discussed in terms of our model.