Universal geometrical factor of protein conformations as a consequence of energy minimization

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A)) of the van der Waals volume V to the surface area A and average atomic radius of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.Comment: 6 pages, 1 table, 4 figure

Antimicrobial interest of essential oils extracted from Tunisian plants

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Electro-Fenton removal of TNT: Evidences of the electro-chemical reduction contribution

International audienceThis study aims in analyzing, at laboratory scale, the mechanisms and performances of 2,4,6-Trinitrotoluene (TNT) removal from contaminated water using electro-Fenton process. This treatment belongs to the group of advanced oxidation processes (AOPs), regarded as the most effective approach to decontaminate wastewater from persistent and toxic organic pollutants. In this study, the TNT degradation was investigated through high resolution LC–ESI–MS/MS to tentatively identify the aromatic by-products. The proposed degradation scheme shows a complex alternation of oxidation and reduction mechanisms, evidencing the importance of the electrochemical reduction in the whole process. Furthermore, oxidative opening of the highly reduced/oxidized TNT aromatic ring occurred rapidly during the treatment, leading to the transient accumulation of short chain carboxylic acids such as malonic, glyoxylic, oxalic and formic acids. Mineralization occurred but was delayed in front of TNT and carboxylic acids, showing the persistence of some recalcitrant by-product