Flavio Augusto Vicente Seixas

The accessory domain changes the accessibility and molecular topography of the catalytic interface in monomeric GH39 β-xylosidases

β-Xylosidases (EC 3.2.1.37) are among the principal glycosyl hydrolases involved in the breakdown of hemicelluloses, catalyzing the reduction of xylooligosaccharides to free xylose. All GH39 β-xylosidases structurally characterized to date display a modular multi-domain organization that assembles a tetrameric quaternary structure. In this work, the crystal structure and the SAXS molecular envelope of a new GH39 β-xylosidase from Caulobacter crescentus (CcXynB2) have been determined. Interestingly, CcXynB2 is a monomer in solution and comparative structural analyses suggest that the shortened C-terminus prevents the formation of a stable tetramer. Moreover, CcXynB2 has a longer loop from the auxiliary domain (the long α-helix-containing loop) which makes a number of polar and hydrophobic contacts with the parental (α/β)(8)-barrel domain, modifying the accessibility and the molecular topography of the catalytic interface. These interactions also maintain the accessory domain tightly linked to the catalytic core, which may be important for enzyme function and stability.

Modeling Based Structural Insights into Biodegradation of the Herbicide Diuron by Laccase-1 from Ceriporiopsis subvermispora.

The herbicide diuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea) is used in many agricultural crops and non-crop areas worldwide, leading to the pollution of the aquatic environment by soil leaching. White rot fungi and its lignin modifying enzymes, peroxidases and laccases, are responsible for its degradation. Therefore, it is of interest to explore the potential use of Ceriporiopsis subvermispora laccase (CersuLac1) in the biotransformation of this herbicide by using its enzyme laccase. However, the structure of laccase from Ceriporiopsis subvermispora is still unknown. Hence, a model of laccase was constructed using homology modeling. The model was further used to dock p-methylbenzoate in the presence of four copper ions to analyze molecular basis of its binding and interaction. The ligand-protein interaction is stereo-chemically favorable in nature. The presence of the single protonated Lys457 was necessary for catalysis, being coordinated by a cupper ion. The best pose of diuron on CersuLac1 has a theoretical Ki of 2.91 mM. This is comparable to the KM values for laccases from other organisms with similar compounds. Thus, we document the insights for the potential use of laccase from Ceriporiopsis subvermispora in the biotransfrormation of diuron.

Evaluation of the potential use of rebaudioside-A as sweetener for diet jam

Sweeteners based on stevia extract contain a series of diterpene glycosides derivatives from steviol, standing out the rebaudioside-A. There is no tabletop sweeteners in the market formulated purely with rebaudioside-A yet, so its use in foods depends on the development of new products followed by physicochemical and sensory evaluations. This work presents the formulation of a diet strawberry jam dyed with cranberry juice and sweetened with rebaudioside-A purified from stevia plants of the lineage UEM-320 developed in the Centro de Estudos de Produtos Naturais da Universidade Estadual de Maringa. Evaluations of physicochemical properties, microbiological and sensory characteristics were carried out for the product in comparison with a control sweetened with equal amount of sucralose. The results showed that the physicochemical characteristics of the sample and the control are not significantly different and the supplementation with cranberry juice increased both color and total phenolic content in both samples. The sensory acceptability indicated a significant preference for the formulation sweetened with 100% of rebaudioside-A, only in the items flavor and purchase intent. We concluded that rebaudioside-A has a better sensory performance than sucralose, even this last one being 1.33 fold sweeter than rebaudioside-A.

Mutations in catalase-peroxidase KatG from isoniazid resistant Mycobacterium tuberculosis clinical isolates: insights from molecular dynamics simulations

The current multidrug therapy for tuberculosis (TB) is based on the use of isoniazid (INH) in combination with other antibiotics such as rifampin, ethambutol and pyrazinamide. Literature reports have shown that Mycobacterium tuberculosis, the causative agent of TB, has become resistant to this treatment by means of point mutations in the target enzymes of these drugs, such as catalase-peroxidase (KatG). By means of equilibrium molecular dynamics in the presence of the ligand, this work evaluated ten point mutations described in the enzyme KatG that are related to resistance to INH . The results showed that the resistance mechanism is related to stereochemical modifications at the N-terminal domain of the protein, which restrict INH access to its catalytic site, not involving mechanisms of electrostatic nature. These results show insights that can be useful for the identification of new anti-TB drugs which may be able to circumvent this mechanism of resistance.

Enzymes from Basidiomycetes—Peculiar and Efficient Tools for Biotechnology

Abstract Basidiomycetes are considered to be a very interesting group of fungi given their exceptional adjustment abilities to accommodate themselves to the detrimental conditions of the environment where they constantly act as natural lignocellulose destroyers. Basidiomycetes possess the two types of extracellular enzymatic systems necessary to degrade the vegetal biomass: (1) a hydrolytic system responsible for polysaccharide degradation, consisting mainly of xylanases and cellulases and (2) a unique oxidative ligninolytic system, which degrades lignin and opens phenyl rings; this systemcomprises mainly laccases, ligninases, and peroxidases. Recent genomic studies of basidiomycetes have provided valuable information about the various ecological groups including white rot and brown rot fungi. The ability of basidiomycetes to degrade the complex structure of lignocellulose makes them potentially useful in the exploration of the lignocellulosic biomass for the production of fuel ethanol and other value-added commodity chemicals. No less important is their potential in biodegradation and bioremediation processes, thanks to the capability of their ligninolytic system in degrading a wide range of xenobiotic compounds. In this chapter, special attention is devoted to those enzymes typically produced by basidiomycetes with a high potential for biotechnological applications.

Depletion of the xynB2 Gene Upregulates β-Xylosidase Expression in C . crescentus

Caulobacter crescentus is able to express several enzymes involved in the utilization of lignocellulosic biomasses. Five genes, xynB1–5, that encode β-xylosidases are present in the genome of this bacterium. In this study, the xynB2 gene, which encodes β-xylosidase II (CCNA_02442), was cloned under the control of the PxylX promoter to generate the O-xynB2 strain, which overexpresses the enzyme in the presence of xylose. In addition, a null mutant strain, Δ-xynB2, was created by two homologous recombination events where the chromosomal xynB2 gene was replaced by a copy that was disrupted by the spectinomycin-resistant cassette. We demonstrated that C. crescentus cells lacking β-xylosidase II upregulates the xynB genes inducing β-xylosidase activity. Transcriptional analysis revealed that xynB1 (RT-PCR analysis) and xynB2 (lacZ transcription fusion) gene expression was induced in the Δ-xynB2 cells, and high β-xylosidase activity was observed in the presence of different agro-industrial residues in the null mutant strain, a characteristic that can be explored and applied in biotechnological processes. In contrast, overexpression of the xynB2 gene caused downregulation of the expression and activity of the β-xylosidase. For example, the β-xylosidase activity that was obtained in the presence of sugarcane bagasse was 7-fold and 16-fold higher than the activity measured in the C. crescentus parental and O-xynB2 cells, respectively. Our results suggest that β-xylosidase II may have a role in controlling the expression of the xynB1 and xynB2 genes in C. crescentus.

The Water Effect on the Kinetics of the Bovine Liver Catalase

Catalase is an enzyme that occurs in almost all aerobic organisms. Its main metabolic function is to prevent oxidative damage to tissues induced by hydrogen peroxide which is a strong oxidizing agent. Catalase is very effective in performing this task, since it has the highest turnover rate among all the enzymes. The properties of catalase have been investigated extensively for many years; however, the role of the solvent molecules in the catalytic reaction of this enzyme has not yet been investigated. Therefore, the objective of this work was to investigate the contribution of the solvent molecules on the catalytic reaction of bovine liver catalase with its substrate H2O2 by the osmotic stress method. As a probe for protein structural changes in solution, the differential number of water molecules released during the transition from free to bound form of the enzyme was measured. These assays were correlated with protein structural data provided by the SAXS technique and crystallographic structures of free and CN(-) bonded enzymes. The results showed that the difference in surface accessible area of the crystal structures does not reflect the variation that is observed in solution. Moreover, catalase is not influenced by the solvent during the catalytic reaction, which represents a lower energy barrier to be crossed in the overall energetics of the reaction, a fact that contributes to the high turnover rate of catalase.

Evaluation of the (haem)Fe--Nepsilon(2)(HisF8) bond distances from haemoglobin structures deposited in the Protein Data Bank.

Scientists working on the structure and function of proteins use haemoglobin as a model of allosteric proteins. In this molecule, the (haem)Fe-N(2)(His) bond is one of the most significant because the length of this bond provides relevant information about the mechanism of cooperativity and affinity for O(2). Thus, the aim of the present study was to evaluate the quality of the structural models of Hb deposited in the Protein Data Bank (PDB), in particular the reliability of the Fe-N(2) bond distance. To achieve this, 329 Hb structures solved by X-ray diffraction were downloaded from the PDB. The Fe-N(2) bond distance was computed and compared with the ideal value determined using the spectroscopic techniques of X-ray absorption and EXAFS. This investigation showed the presence of crystallographic structures of native haemoglobins deposited in the PDB in which the Fe-N(2) bond distance was far beyond the ideal value found for this length, a fact that makes their use in studies that correlate haemoglobin structure and function questionable.

Multiple resistance to pirimiphos-methyl and bifenthrin in Tribolium castaneum involves the activity of lipases, esterases, and laccase2 ☆

Several recent studies have elucidated the molecular mechanisms that confer insecticide resistance on insect pests. However, little is known about multiple resistance in red flour beetle (Tribolium castaneum) at molecular level. The multiple resistance is characterized as resistance to different classes of insecticides that have different target sites, and is mediated by several enzymatic systems. In this study, we investigated the biochemical and molecular mechanisms involved in multiple resistance of T. castaneum to bifenthrin (pyrethroid [Pyr]) and pirimiphos-methyl (organophosphate [Org]). We used artificial selection, biochemical and in silico approaches including structural computational biology. After five generations of artificial selection in the presence of bifenthrin (F5Pyr) or pirimiphos-methyl (F5Org), we found high levels of multiple resistance. The hierarchical enzymatic cluster revealed a pool of esterases (E), lipases (LIPs) and laccase2 (LAC2) potentially contributing to the resistance in different ways throughout development, after one or more generations in the presence of insecticides. The enzyme-insecticide interaction network indicated that E2, E3, LIP3, and LAC2 are enzymes potentially required for multiple resistance phenotype. Kinetic analysis of esterases from F5Pyr and F5Org showed that pirimiphos-methyl and specially bifenthrin promote enzyme inhibition, indicating that esterases mediate resistance by sequestering bifenthrin and pirimiphos-methyl. Our computational data were in accordance with kinetic results, indicating that bifenthrin has higher affinity at the active site of esterase than pirimiphos-methyl. We also report the capability of these insecticides to modify the development in T. castaneum. Our study provide insights into the biochemical mechanisms employed by T. castaneum to acquire multiple resistance.

The structure of viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus as a target against grasserie: Docking and molecular dynamics simulations

The viral cathepsin from Bombyx mori Nucleopolyhedrosis virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by Bombyx mori Nucleopolyhedrosis virus (BmNPV), there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin BmNPV-Cath was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of ΔGbinding by the molecular mechanics Poisson-Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The in vivo infection models of B. mori caterpillars with BmNPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of BmNPV-Cath in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.Abstract The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin BmNPV-Cath was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of ΔGbinding by the molecular mechanics Poisson–Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The in vivo infection models of B. mori caterpillars with BmNPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of BmNPV-Cath in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.