Molecular Modelling of the Interaction of Cyanoacrylate Inhibitors with Photosystem II Part 1. The Effect of Hydrophobicity of Inhibitor Binding

The secondary quinone binding site of photosystem II is also the binding site for many dif­ ferent herbicides. The 2-cyanoacrylate inhibitors are a potent class of electron transfer inhibi­ tors which bind at this site and are extremely sensitive to minor structural variation. In order to understand their mode of binding, we have studied the interaction between the inhibitors and receptor in the D 1 protein binding region (residues Leu 210 to Val 280) in terms of non­ bonded intermolecular forces. The intermolecular energy was calculated by van der Waals and electrostatic interactions after energy minimization of the combined structures to reduce inter and intramolecular strain. We have identified specific amino acid residues within the binding protein which are instrumental in binding the herbicide and have shown that the spatial arrangement of the herbicide functional groups within the binding site rather than their lipo­ philicity is the determining factor in binding efficiency.