GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms.

Metals are present in >30% of proteins found in nature and assist them to perform important biological functions, including storage, transport, signal transduction and enzymatic activity. Traditional and experimental techniques for metal-binding site prediction are usually costly and time-consuming, making computational tools that can assist in these predictions of significant importance. Here we present Genetic Active Site Search (GASS)-Metal, a new method for protein metal-binding site prediction. The method relies on a parallel genetic algorithm to find candidate metal-binding sites that are structurally similar to curated templates from M-CSA and MetalPDB. GASS-Metal was thoroughly validated using homologous proteins and conservative mutations of residues, showing a robust performance. The ability of GASS-Metal to identify metal-binding sites was also compared with state-of-the-art methods, outperforming similar methods and achieving an MCC of up to 0.57 and detecting up to 96.1% of the sites correctly. GASS-Metal is freely available at https://gassmetal.unifei.edu.br. The GASS-Metal source code is available at https://github.com/sandroizidoro/gassmetal-local.

Degradation of Direct Red 81 mediated by Fenton reactions: multivariate optimization, effect of chloride and sulfate, and acute ecotoxicity assessment.

The role of different operational parameters related to Fenton reactions (pH, concentration of Fe2+ and H2O2, and reaction time) and of Cl- and SO 4- was investigated in the degradation of the azo dye Direct Red 81, expressed in terms of its decolorization. The factorial design and Pareto's charts showed that only Fe2+ concentration and pH influence the decolorization under the conditions evaluated. So, only these parameters were optimized using the response surface model. Under the best experimental conditions (initial pH 2.5, 11 mg L-1 Fe2+, 78 mg L-1 H2O2, and 20 min of reaction), 94 % of decolorization was achieved. However, even under the these conditions, but in the presence of Cl- and SO 4- , a striking loss of efficiency was observed as the concentration of these ions was increased, due the formation of chloride- and sulfate-iron complexes and less reactive inorganic radicals (Cl2•- and SO4•-). The results show that the presence of Cl- is more deleterious, since sulfate-iron complexes are more reactive towards H2O2, and the SO4•- turns out to favor the degradation. On the other hand, the  negative effect of Cl- can be compensated by increasing the chloride concentration up to 300 mmol L-1. In addition, although a high degradation level has been obtained by monitoring the dye absorbance and by HPLC-UV, a low mineralization occurred, being generated degradation products of higher ecotoxicity to Vibrio fischeri, showing the need of subsequent studies to identify these compounds as well as the application of additional treatments aiming the complete mineralization of the dye.