Theoretical study of the binding site and mode of action for photosystem II herbicides

Several features of a proteinaceous binding site and a molecular mode of action are proposed for photosystem II (PS II) herbicides based upon a variety of experimental and theoretical evidence. Experimental studies have established that PS II herbicides bind non-covalently to a 32 kdalton protein in the PS II complex and inhibit electron transfer between the first quinone (Q) and the second quinone (B) on the reducing side of PS II. The herbicides each contain hydrophobic components as well as a flat polar component with a dipole moment in the range of 3–5 Debyes. The primary function of the hydrophobic components is to increase the lipid solubility of the entire herbicide molecule; the secondary function of the hydrophobic components is to fit the hydrophobic surface of the herbicide binding site. It is proposed that the flat polar component binds electrostatically at a highly polar protein site, probably a protein salt bridge or the terminus of a protein alpha helix. Further, it is proposed that the PS II herbicides shift the equilibrium Q^?Bz?QB^? to the left (i) by reducing the magnitude of an anion-stabilizing electric field across the B-binding site, or (ii) by inhibiting the conformational relaxation or protonation of the PS II protein in response to reduction of B to B^?, or (iii) by displacing the quinone head of B from its binding site. Ab initio molecular quantum mechanical calculations have been carried out to investigate the electrostatic interactions in specific herbicide-binding site models.