Prediction of biodegradability of aromatics in water using QSAR modeling.

The study was aimed at developing models for predicting the biodegradability of aromatic water pollutants. For that purpose, 36 single-benzene ring compounds, with different type, number and position of substituents, were used. The biodegradability was estimated according to the ratio of the biochemical (BOD5) and chemical (COD) oxygen demand values determined for parent compounds ((BOD5/COD)0), as well as for their reaction mixtures in half-life achieved by UV-C/H2O2 process ((BOD5/COD)t1/2). The models correlating biodegradability and molecular structure characteristics of studied pollutants were derived using quantitative structure-activity relationship (QSAR) principles and tools. Upon derivation of the models and calibration on the training and subsequent testing on the test set, 3- and 5-variable models were selected as the most predictive for (BOD5/COD)0 and (BOD5/COD)t1/2, respectively, according to the values of statistical parameters R2 and Q2. Hence, 3-variable model predicting (BOD5/COD)0 possessed R2=0.863 and Q2=0.799 for training set, and R2=0.710 for test set, while 5-variable model predicting (BOD5/COD)1/2 possessed R2=0.886 and Q2=0.788 for training set, and R2=0.564 for test set. The selected models are interpretable and transparent, reflecting key structural features that influence targeted biodegradability and can be correlated with the degradation mechanisms of studied compounds by UV-C/H2O2.

Roles of the SH2 and SH3 domains in the regulation of neuronal Src kinase functions.

Previous studies demonstrated that intra-domain interactions between Src family kinases (SFKs), stabilized by binding of the phosphorylated C-terminus to the SH2 domain and/or binding of the SH2 kinase linker to the SH3 domain, lock the molecules in a closed conformation, disrupt the kinase active site, and inactivate SFKs. Here we report that the up-regulation of N-methyl-D-aspartate receptors (NMDARs) induced by expression of constitutively active neuronal Src (n-Src), in which the C-terminus tyrosine is mutated to phenylalanine (n-Src/Y535F), is significantly reduced by dysfunctions of the SH2 and/or SH3 domains of the protein. Furthermore, we found that dysfunctions of SH2 and/or SH3 domains reduce auto-phosphorylation of the kinase activation loop, depress kinase activity, and decrease NMDAR phosphorylation. The SH2 domain plays a greater regulatory role than the SH3 domain. Our data also show that n-Src binds directly to the C-terminus of the NMDAR NR2A subunit in vitro, with a K(D) of 108.2 ± 13.3 nM. This binding is not Src kinase activity-dependent, and dysfunctions of the SH2 and/or SH3 domains do not significantly affect the binding. These data indicate that the SH2 and SH3 domains may function to promote the catalytic activity of active n-Src, which is important in the regulation of NMDAR functions.

Photooxidation processes for an azo dye in aqueous media: modeling of degradation kinetic and ecological parameters evaluation.

Three photooxidation processes, UV/H(2)O(2), UV/S(2)O(8)(2-) and UV/O(3) were applied to the treatment of model wastewater containing non-biodegradable organic pollutant, azo dye Acid Orange 7 (AO7). Dye degradation was monitored using UV/VIS and total organic carbon (TOC) analysis, determining decolorization, the degradation/formation of naphthalene and benzene structured AO7 by-products, and the mineralization of model wastewater. The water quality during the treatment was evaluated on the bases of ecological parameters: chemical (COD) and biochemical (BOD(5)) oxygen demand and toxicity on Vibrio fischeri determining the EC(50) value. The main goals of the study were to develop an appropriate mathematic model (MM) predicting the behavior of the systems under investigation, and to evaluate the toxicity and biodegradability of the model wastewater during treatments. MM developed showed a high accuracy in predicting the degradation of AO7 when considering the following observed parameters: decolorization, formation/degradation of by-products and mineralization. Good agreement of the data predicted and the empirically obtained was confirmed by calculated standard deviations. The biodegradability of model wastewater was significantly improved by three processes after mineralizing a half of the initially present organic content. The toxicity AO7 model wastewater was decreased as well. The differences in monitored ecological parameters during the treatment indicated the formation of different by-products of dye degradation regarding the oxidant type applied.

The comparison of photooxidation processes for the minimization of organic load of colored wastewater applying the response surface methodology.

In this comparative study, the effectiveness of three photooxidation processes (UV/H(2)O(2), UV/S(2)O(8)(2-) and UV/O(3)) for degradation of an azo dye model pollutant was investigated using several process parameters. The process parameters such as initial pH, the concentrations of oxidant in the reactor inlet stream and the type of oxidant were considered. In order to investigate the influence of cross-factor effects of process parameters, the full factorial design was applied with three factors (two numeric and one categorical) at three levels combined with response surface modeling. The ANOVA results (R(2), F, p) showed high accuracy of developed quadratic model for the zero-order mineralization rate constants of AO7 model wastewater. Among process parameters studied, the type of oxidant and the concentration of oxidant were shown to be the most influential parameters of studied photooxidation processes. The highest rate of mineralization of AO7 model wastewater, k(obs)=7.507×10(-7) M s(-1), was obtained for UV/O(3) process at the initial pH 10 and oxidant reactor input rate of 0.6 mM min(-1). However, when comparing the operating costs for each process studied, it was evident that UV/H(2)O(2) process is 1.6 times less expensive than UV/O(3) process considering the mineralization of organic content of AO7 model wastewater.

Characterization of neuronal Src kinase purified from a bacterial expression system.

Neuronal Src (n-Src) is an alternative isoform of Src kinase containing a 6-amino acid insert in the SH3 domain that is highly expressed in neurons of the central nervous system (CNS). To investigate the function of n-Src, wild-type n-Src, constitutively active n-Src in which the C-tail tyrosine 535 was mutated to phenylalanine (n-Src/Y535F) and inactive n-Src in which the lysine 303 was mutated to arginine in addition to the mutation of Y535F (n-Src/K303R/Y535F), were expressed and purified from Escherichia coli BL21(DE3) cells. We found that all three types of n-Src constructs expressed at very high yields (∼500 mg/L) at 37°C, but formed inclusion bodies. In the presence of 8M urea these proteins could be solubilized, purified under denaturing conditions, and subsequently refolded in the presence of arginine (0.5M). These Src proteins were enzymatically active except for the n-Src/K303R/Y535F mutant. n-Src proteins expressed at 18°C were soluble, albeit at lower yields (∼10-20 mg/L). The lowest yields were for n-Src/Y535F (∼10 mg/L) and the highest for n-Src/K303R/Y535F (∼20 mg/L). We characterized the purified n-Src proteins expressed at 18°C. We found that altering n-Src enzyme activity either pharmacologically (e.g., application of ATP or a Src inhibitor) or genetically (mutation of Y535 or K303) was consistently associated with changes in n-Src stability: an increase in n-Src activity was coupled with a decrease in n-Src stability and vice versa. These findings, therefore, indicate that n-Src activity and stability are interdependent. Finally, the successful production of functionally active n-Src in this study indicates that the bacterial expression system may be a useful protein source in future investigations of n-Src regulation and function.

Sequence of ligand binding and structure change in the diphtheria toxin repressor upon activation by divalent transition metals.

The diphtheria toxin repressor (DtxR) is an Fe(II)-activated transcriptional regulator of iron homeostatic and virulence genes in Corynebacterium diphtheriae. DtxR is a two-domain protein that contains two structurally and functionally distinct metal binding sites. Here, we investigate the molecular steps associated with activation by Ni(II)Cl(2) and Cd(II)Cl(2). Equilibrium binding energetics for Ni(II) were obtained from isothermal titration calorimetry, indicating apparent metal dissociation constants of 0.2 and 1.7 microM for two independent sites. The binding isotherms for Ni(II) and Cd(II) exhibited a characteristic exothermic-endothermic pattern that was used to infer the metal binding sequence by comparing the wild-type isotherm with those of several binding site mutants. These data were complemented by measuring the distance between specific backbone amide nitrogens and the first equivalent of metal through heteronuclear NMR relaxation measurements. Previous studies indicated that metal binding affects a disordered to ordered transition in the metal binding domain. The coupling between metal binding and structure change was investigated using near-UV circular dichroism spectroscopy. Together, the data show that the first equivalent of metal is bound by the primary metal binding site. This binding orients the DNA binding helices and begins to fold the N-terminal domain. Subsequent binding at the ancillary site completes the folding of this domain and formation of the dimer interface. This model is used to explain the behavior of several mutants.

Prolylpeptide binding by the prokaryotic SH3-like domain of the diphtheria toxin repressor: a regulatory switch.

Diphtheria toxin repressor (DtxR) regulates the expression of iron-sensitive genes in Corynebacterium diphtheriae, including the diphtheria toxin gene. DtxR contains an N-terminal metal- and DNA-binding domain that is connected by a proline-rich flexible peptide segment (Pr) to a C-terminal src homology 3 (SH3)-like domain. We determined the solution structure of the intramolecular complex formed between the proline-rich segment and the SH3-like domain by use of NMR spectroscopy. The structure of the intramolecularly bound Pr segment differs from that seen in eukaryotic prolylpeptide-SH3 domain complexes. The prolylpeptide ligand is bound by the SH3-like domain in a deep crevice lined by aliphatic amino acid residues and passes through the binding site twice but does not adopt a polyprolyl type-II helix. NMR studies indicate that this intramolecular complex is present in the apo-state of the repressor. Isothermal equilibrium denaturation studies show that intramolecular complex formation contributes to the stability of the apo-repressor. The binding affinity of synthetic peptides to the SH3-like domain was determined using isothermal titration calorimetry. From the structure and the binding energies, we calculated the enhancement in binding energy for the intramolecular reaction and compared it to the energetics of dimerization. Together, the structural and biophysical studies suggest that the proline-rich peptide segment of DtxR functions as a switch that modulates the activation of repressor activity.

Genetic and biophysical studies of diphtheria toxin repressor (DtxR) and the hyperactive mutant DtxR(E175K) support a multistep model of activation.

The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is the prototypic member of a superfamily of transition metal ion-activated transcriptional regulators that have been isolated from Gram-positive prokaryotes. Upon binding divalent transition metal ions, the N-terminal domain of DtxR undergoes a dynamic structural organization leading to homodimerization and target DNA binding. We have used site-directed mutagenesis and NMR analysis to probe the mechanism by which apo-DtxR transits from an inactive to a fully active repressor upon metal ion binding. We demonstrate that the ancillary metal-binding site mutant DtxR(H79A) requires higher concentrations of metal ions for activation both in vivo and in vitro, providing a functional correlation to the proposed cooperativity between ancillary and primary binding sites. We also demonstrate that the C-terminal src homology 3 (SH3)-like domain of DtxR functions to modulate repressor activity by (i) binding to the polyprolyl tether region between the N- and C-terminal domains, and (ii) destabilizing the ancillary binding site, leading to full inactivation of the repressor. Finally, we show by NMR analysis that the hyperactive phenotype of DtxR(E175K) results from the stabilization of a structural intermediate in the activation process. Taken together, the data presented support a multistep model for the activation of apo-DtxR by transition metal ions.