Structure and binding efficiency relations of QB site inhibitors of photosynthetic reaction centres*

Abstract

Abstract. Many herbicides employed in agriculture and also some antibiotics bind to a specific site of the reaction centre protein (RC) blocking the photosynthetic electron transport. Crystal structures showed that all these compounds bind at the secondary ubiquinone (Q B ) site albeit to slightly different places. Different herbicide molecules have different binding affinities (evaluated as inhibition constants, K I , and binding enthalpy values, ∆H bind ). The action of inhibitors depends on the following parameters: (i) herbicide molecular structure; (ii) interactions between herbicide and quinone binding site; (iii) protein environment. In our investigations K I and ∆H bind were determined for several inhibitors. Bound herbicide structures were optimized and their intramolecular charge distributions were calculated. Experimental and calculated data were compared to those available from databank crystal structures. We can state that the herbicide inhibition efficiency depends on steric and electronic factors, i.e. geometry of binding with the protein and molecular charge distribution, respectively. Apolar bulky groups on N-7 atom of the inhibitor molecule (like t-buthyl in terbutryn) are preferable for establishing stronger interactions with Q B site, while such substituents are not recommended on N-8. The N-4,7,8 nitrogen atoms maintain a larger electron density so that more effective H-bonds are formed between the inhibitor and the surrounding amino acids of the protein.

An Evaluation of Sensor Performance for Harmful Compounds by Using Photo-Induced Electron Transfer from Photosynthetic Membranes to Electrodes

“…Jones et al reported that the photocurrent was inhibited by atrazine and terbutryn and that the values of detection limits were 49 nM for atrazine and 8.3 nM for terbutryn [ 8 ]. Nagy et al reported inhibition constants for terbutryn and atrazine of 1.3 and 63 μM, respectively, when assayed against the photosynthetic reaction center isolated from R. sphaeroides [ 36 ]. Nagy et al further demonstrated that the three parameters (herbicide molecular structure, interaction between herbicide and quinone binding site, and protein environment) depended on the magnitude of the inhibitory effect of herbicides.…”