Structures and binding sites of phenolic herbicides in the Q(B) pocket of photosystem II.

Herbicides targeting photosystem II (PSII) block the electron transfer beyond Q(A) by binding to the Q(B) site. Upon binding, the redox potential of Q(A) shifts differently depending on the types of herbicides. In this study, we have investigated the structures, interactions, and locations of phenolic herbicides in the Q(B) site to clarify the molecular mechanism of the Q(A) potential shifts by herbicides. Fourier transform infrared (FTIR) difference spectra upon photoreduction of the preoxidized non-heme iron (Fe(2+)/Fe(3+) difference) were measured with PSII membranes in the presence of bromoxynil or ioxynil. The CN and CO stretching vibrations of these phenolic herbicides were identified at 2215-2200 and 1516-1505 cm(-1), respectively, in the Fe(2+)/Fe(3+) difference spectra. Comparison with the spectra of bromoxynil in ethanol solutions along with density functional theory analysis strongly suggests that the phenolic herbicides take a deprotonated form in the binding pocket. In addition, the CN stretching, NH bending, and NH stretching vibrations of a His side chain, which were found at 1109-1101, 1187-1185, and 3000-2500 cm(-1), respectively, in the Fe(2+)/Fe(3+) difference spectra, showed characteristic features in the presence of phenolic herbicides. These signals are probably attributed to D1-His215, one of the ligands to the non-heme iron. Docking calculations for herbicides to the Q(B) pocket confirmed the binding of deprotonated bromoxynil to D1-His215 at the CO group, whereas the protonated form of bromoxynil and DCMU were found to bind to the opposite side of the pocket without an interaction with D1-His215. From these results, it is proposed that a strong hydrogen bond of the phenolate CO group with D1-His215 induces the change in the hydrogen bond strength of the Q(A) CO group through the Q(A)-His-Fe-His-phenolate bridge causing the downshift of the Q(A) redox potential.