MOLECULAR MODELING OF THE INTERACTION OF CYANOACRYLATE INHIBITORS WITH PHOTOSYSTEM-II .1. THE EFFECT OF HYDROPHOBICITY OF INHIBITOR BINDING

The secondary quinone binding site of photosystem II is also the bindi ng site for many different herbicides. The 2-cyanoacrylate inhibitors are a potent class of electron transfer inhibitors which bind at this site and are extremely sensitive to minor structural variation. In ord er to understand their mode of binding, we have studied the interactio n between the inhibitors and receptor in the D 1 protein binding regio n (residues Leu 210 to Val 280) in terms of nonbonded intermolecular f orces. The intermolecular energy was calculated by van der Waals and e lectrostatic interactions after energy minimization of the combined st ructures to reduce inter and intramolecular strain. We have identified specific amino acid residues within the binding protein which are ins trumental in binding the herbicide and have shown that the spatial arr angement of the herbicide functional groups within the binding site ra ther than their lipophilicity is the determining factor in binding eff iciency.