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General Physiology and Biophysics Vol.34, No.2, p.119–133, 2015 |
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Title: Structure and binding efficiency relations of QB site inhibitors of photosynthetic reaction centres* | ||
Author: Ivan Husu, Melinda Magyar, Tibor Szabó, Béla Fiser, Enrique Gómez-Bengoa, László Nagy | ||
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 (QB) site albeit to slightly different places. Different herbicide molecules have different binding affinities (evaluated as inhibition constants, KI, and binding enthalpy values, ∆Hbind). 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 KI and ∆Hbind 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 QB 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. |
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Keywords: Herbicides — Bacterial reaction centers — Photosynthesis — Molecular modeling | ||
Year: 2015, Volume: 34, Issue: 2 | Page From: 119, Page To: 133 | |
doi:10.4149/gpb_2015003 |
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