期刊
GENERAL PHYSIOLOGY AND BIOPHYSICS
卷 34, 期 2, 页码 119-133出版社
GENERAL PHYSIOL AND BIOPHYSICS
DOI: 10.4149/gpb_2015003
关键词
Herbicides; Bacterial reaction centers; Photosynthesis; Molecular modeling
资金
- Switzerland through the Swiss Contribution [SH/7/2/20]
- European Union [TAMOP-4.2.2.A-11/1/KONV-2012-0060]
- European Social Fund
- FP7 Marie Curie Actions of the European Commission via the ITN ECHONET Network [MCITN-2012-316379]
- University of the Basque Country/UPV-EHU
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, Delta 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 Delta 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.
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