Genetic, structural, and molecular insights into the function of ras of complex proteins domains

Ras of complex proteins (ROC) domains were identified in 2003 as GTP binding modules in large multidomain proteins from Dictyostelium discoideum. Research into the function of these domains exploded with their identification in a number of proteins linked to human disease, including leucine-rich repeat kinase 2 (LRRK2) and death-associated protein kinase 1 (DAPK1) in Parkinson’s disease and cancer, respectively. This surge in research has resulted in a growing body of data revealing the role that ROC domains play in regulating protein function and signaling pathways. In this review, recent advances in the structural informa- tion available for proteins containing ROC domains, along with insights into enzymatic function and the integration of ROC domains as molecular switches in a cellular and organismal context, are explored.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Enzymatic inhibitory activity of hydroxycinnamates (HCs): in silico studies

Diabetes is a worldwide health issue that has been expanding mainly in developed countries. It is characterized by abnormal levels of blood sugar due to several factors. The most common are resistance to insulin and the production of defective insulin which exerts little or no effect. Its most common symptoms include tissue damage to several systems due to elevated levels of blood sugar. One of the key enzymes in hydrocarbon metabolism is α-glucosidase (EC 3.2.1.20). It catalyzes the breakdown of complex carbohydrates into their respective monomers (glucose) which allows them to be absorbed. In this work, caffeoyl quinic acids and their metabolites were analyzed as potential inhibitors for α-glucosidase. The search for the best inhibitor was conducted using molecular docking. The affinity of each compound was compared to the inhibitor present in the crystal structure of the protein. As no inhibitor with a similar affinity was´found, a new approach was used, in situ drug design. It was not possible to achieve an inhibitor capable of competing with the one present in the crystal structure of the enzyme, which is also its current commercial inhibitor. It is possible to draw some conclusions as to which functional groups interact best with certain residues of the active site. This work was divided into three main sections. The first section, Diabetes, serves as an introduction to what is Diabetes, its symptoms and/or side effects and how caffeoyl quinic acids could be used as a treatment. The second section, Caffeoylquinic acids and their metabolites as inhibitors for Alfa-glucosidase, corresponds to the search through molecular docking of caffeoyl quinic acids as inhibitors for α-glucosidase and what was possible to draw from this search. The last section, In situ design of an inhibitor for α-glucosidase (EC 3.2.1.20), corresponds to the in situ drug design study and what it achieved. The representation of each of the molecules used as a ligand can be found in the Annexes.

Harpalycin 2 inhibits the enzymatic and platelet aggregation activities of PrTX-III, a D49 phospholipase A(2) from Bothrops pirajai venom

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Dissociation of enzymatic and pharmacological properties of piratoxins-I and -III, two myotoxic phospholipases A(2) from Bothrops pirajai snake venom

Piratoxins (PrTX) I and III are phospholipases A(2) (PLA(2)s) or PLA(2) homologue myotoxins isolated from Bothrops pirajai snake venom, which also induce myonecrosis, bactericidal activity against Escherichia coli, disruption of artificial membranes, and edema. PrTX-III is a catalytically active hemolytic and anticoagulant Asp49 PLA(2), while PrTX-I is a Lys49 PLA, homologue, which is catalytically inactive on artificial substrates, but promotes blockade of neuromuscular transmission. Chemical modifications of His, Lys, Tyr, and Trp residues of PrTX-I and PrTX-III were performed, together with cleavage of the N-terminal octapeptide by CNBr and inhibition by heparin and EDTA. The lethality, bactericidal activity, myotoxicity, neuromuscular effect, edema inducing effect, catalytic and anticoagulant activities, and the liposome-disruptive activity of the modified toxins were evaluated. A complex pattern of functional differences between the modified and native toxins was observed. However, in general, chemical modifications that significantly affected the diverse pharmacological effects of the toxins did not influence catalytic or membrane disrupting activities. Analysis of structural changes by circular dichroism spectroscopy demonstrated significant changes in the secondary structure only in the case of N-terminal octapeptide cleavage. These data indicate that PrTX-I and PrTX-III possess regions other than the catalytic site, which determine their toxic and pharmacological activities. (C) 2001 Academic Press.

Xylo-oligosaccharides from lignocellulosic materials: Chemical structure, health benefits and production by chemical and enzymatic hydrolysis

Currently, there is worldwide interest in the technological use of agro-industrial residues as a renewable source of food and biofuels. Lignocellulosic materials (LCMs) are a rich source of cellulose and hemicellulose. Hemicellulose is rich in xylan, a polysaccharide used to develop technology for producing alcohol, xylose, xylitol and xylo-oligosaccharides (XOSs). The XOSs are unusual oligosaccharides whose main constituent is xylose linked by β 1-4 bonds. The XOS applications described in this paper highlight that they are considered soluble dietary fibers that have prebiotic activity, favoring the improvement of bowel functions and immune function and having antimicrobial and other health benefits. These effects open a new perspective on potential applications for animal production and human consumption. The raw materials that are rich in hemicellulose include sugar cane bagasse, corncobs, rice husks, olive pits, barley straw, tobacco stalk, cotton stalk, sunflower stalk and wheat straw. The XOS-yielding treatments that have been studied include acid hydrolysis, alkaline hydrolysis, auto-hydrolysis and enzymatic hydrolysis, but the breaking of bonds present in these compounds is relatively difficult and costly, thus limiting the production of XOS. To obviate this limitation, a thorough evaluation of the most convenient methods and the opportunities for innovation in this area is needed. Another challenge is the screening and taxonomy of microorganisms that produce the xylanolytic complex and enzymes and reaction mechanisms involved. Among the standing out microorganisms involved in lignocellulose degradation are Trichoderma harzianum, Cellulosimicrobium cellulans, Penicillium janczewskii, Penicillium echinulatu, Trichoderma reesei and Aspergillus awamori. The enzyme complex predominantly comprises endoxylanase and enzymes that remove hemicellulose side groups such as the acetyl group. The complex has low β-xylosidase activities because β-xylosidase stimulates the production of xylose instead of XOS; xylose, in turn, inhibits the enzymes that produce XOS. The enzymatic conversion of xylan in XOS is the preferred route for the food industries because of problems associated with chemical technologies (e.g., acid hydrolysis) due to the release of toxic and undesired products, such as furfural. The improvement of the bioprocess for XOS production and its benefits for several applications are discussed in this study. © 2012 Elsevier Ltd.

Electrochemical Properties of Oxo-Manganese Complex Biomimicking Enzyme Active Sites and Its Electrocatalytic Application for Dopamine Determination

This work describes the characterization of the [Mn2 IV,IVO2(terpy)2(H2O)2]4+ complex in aqueous solution by UV-vis spectrophotometry, cyclic voltammetry, and linear sweep voltammetry with a rotating disk electrode. The pH effect, potential scan rate, effect of perfluorosulfonate polymer, and anion of supporting electrode on the electrochemical behavior of the modified electrode for better performance were investigated. The potential peak of the modified electrode was linearly dependent upon the ratio [ionic charge]/[ionic radius]. The modified electrode exerted an electrocatalytic effect on dopamine oxidation in aqueous solution with a decrease in the overpotential compared with the unmodified glassy carbon electrode. This way, the modified electrode showed an enzymatic biomimicking behavior. Tafel plot analyses were used to elucidate the kinetics and mechanism of dopamine oxidation. © 2013 Springer Science+Business Media New York.

Enzymatic transesterification of soybean oil with ethanol using lipases immobilized on highly crystalline PVA microspheres

Polyvinyl alcohol (PVA) microspheres with different degree of crystallinity were used as solid supports for Rhizomucor miehei lipase immobilization, and the enzyme-PVA complexes were used as biocatalysts for the transesterification of soybean oil to fatty acid ethyl esters (FAEE). The amounts of immobilized enzyme on the polymeric supports were similar for both the amorphous microspheres (PVA4) and the high crystalline microspheres (PVA25). However, the enzymatic activity of the immobilized enzymes was depended on the crystallinity degree of the PVA microspheres: enzymes immobilized on the PVA4 microspheres have shown low enzymatic activity (6.13 U mg-1), in comparison with enzymes immobilized on the high crystalline PVA25 microspheres (149.15 U mg-1). A synergistic effect was observed for the enzyme-PVA25 complex during the transesterification reaction of soybean oil to FAEE: transesterification reactions with free enzyme with the equivalent amount of enzyme that were immobilized onto the PVA25 microspheres (5.4 U) have yielded only 20% of FAEE, reactions with the pure highly crystalline microsphere PVA25 have not yielded FAEE, however reactions with the enzyme-PVA25 complexes have yielded 66.3% of FAEE. This synergistic effect of an immobilized enzyme on a polymeric support has not been observed before for transesterification reaction of triacylglycerides into FAEE. Based on ATR-FTIR, 23Na- and 13C-NMR-MAS spectroscopic data and the interaction of the polymeric network intermolecular hydrogen bonds with the lipases residual amino acids a possible explanation for this synergistic effect is provided. © 2013 Elsevier Ltd. All rights reserved.

Sulfated polysaccharide extracted of the green algae Caulerpa racemosa increase the enzymatic activity and paw edema induced by sPLA2 from Crotalus durissus terrificus venom

Sulfated polysaccharides derived from seaweed have shown great potential for use in the development of new drugs. In this study, we observed that a low-molecular-weight sulfated polysaccharide from Caulerpa racemosa, termed CrSP, could interact with secretory phospholipase A2 (sPLA2) isolated from Crotalus durissus terrificus venom. When native sPLA2 (14 kDa) was incubated with CrSP, they formed a molecular complex (sPLA2:CrSP) with a molecular mass of 32 kDa, approximately. Size exclusion chromatography experiments suggested that CrSP formed a stable complex with sPLA2. We belived that sPLA2 and SPCr are involved an ionic interaction between negatively charged CrSP and the positively charged basic amino acid residues of sPLA2, because this interaction induced significant changes in sPLA2 enzymatic and pharmacological activities. CrSP caused a significant increase in sPLA2 enzymatic and bactericidal activity and increased its edematogenic effect. A pharmacological assay showed that the myotoxic activity of sPLA2:CrSP is unrelated to its enzymatic activity and that sPLA2:CrSP may have a practical application as a natural antibacterial agent for use in humans and commercially raised animals.

Chicken fat and inorganic nitrogen source for lipase production by Fusarium sp. (Gibberella fujikuroi complex)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+

Abstract Background Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. Leptospira interrogans is a spirochaete parasitic bacterium capable of infecting humans and mammals in general. Leptospira interrogans FNR (LepFNR) displays low sequence identity with plant (34% with Zea mays) and bacterial (31% with Escherichia coli) FNRs. However, LepFNR contains all consensus sequences that define the plastidic class FNRs. Results The crystal structures of the FAD-containing LepFNR and the complex of the enzyme with NADP+, were solved and compared to known FNRs. The comparison reveals significant structural similarities of the enzyme with the plastidic type FNRs and differences with the bacterial enzymes. Our small angle X-ray scattering experiments show that LepFNR is a monomeric enzyme. Moreover, our biochemical data demonstrate that the LepFNR has an enzymatic activity similar to those reported for the plastidic enzymes and that is significantly different from bacterial flavoenzymes, which display lower turnover rates. Conclusion LepFNR is the first plastidic type FNR found in bacteria and, despite of its low sequence similarity with plastidic FNRs still displays high catalytic turnover rates. The typical structural and biochemical characteristics of plant FNRs unveiled for LepFNR support a notion of a putative lateral gene transfer which presumably offers Leptospira interrogans evolutionary advantages. The wealth of structural information about LepFNR provides a molecular basis for advanced drugs developments against leptospirosis.

Hundertneunundzwanzig Xe NMR for investigations of complex and dynamic systems

In this work, the remarkable versatility and usefulness of applications of Xe-129 NMR experiments is further extended. The application of Xe-129 NMR spectroscopy to very different system is studied, including dynamic and static, solid and liquid, porous and non-porous systems. Using the large non-equilibrium polarization created by hyperpolarization of Xe-129, time-resolved NMR measurements can be used for the online-monitoring of dynamic systems. In the first part of this work, several improvements for medical applications of hyperpolarized Xe-129 are achieved and their feasibility shown experimentally. A large gain in speed and reproducibility of the accumulation process of Xe-129 as ice and an enhancement of the usable polarization in any experiment requiring prior accumulation are achieved. An enhancement of the longitudinal relaxation time of Xe-129 is realized by admixture of a buffer gas during the storage of hyperpolarized Xe-129. Pursuing the efforts of simplifying the accumulation process and enhancing the storage time of hyperpolarized Xe-129 will allow for a wider use of the hyperpolarized gas in (medical) MRI experiments. Concerning the use of hyperpolarized Xe-129 in MRI, the influence of the diffusion coefficient of the gas on parameters of the image contrast is experimentally demonstrated here by admixture of a buffer gas and thus changing the diffusion coefficient. In the second part of this work, a polymer system with unique features is probed by Xe-129 NMR spectroscopy, proving the method to be a valuable tool for the characterization of the anisotropic properties of semicrystalline, syndiotactic polystyrene films. The polymer films contain hollow cavities or channels with sizes in the sub-nanometer range, allowing for adsorption of Xe-129 and subsequent NMR measurements. Despite the use of a ’real-world’ system, the transfer of the anisotropic properties from the material to adsorbed Xe-129 atoms is shown, which was previously only known for fully crystalline materials. The anisotropic behavior towards atomar guests inside the polymer films is proven here for the first time for one of the phases. For the polymer phase containing nanochannels, the dominance of interactions between Xe-129 atoms in the channels compared to interactions between Xe atoms and the channel walls are proven by measurements of a powder sample of the polymer material and experiments including the rotation of the films in the external magnetic field as well as temperature-dependent measurements. The characterization of ’real-world’ systems showing very high degrees of anisotropy by Xe-129 are deemed to be very valuable in future applications. In the last part of this work, a new method for the online monitoring of chemical reactions has been proposed and its feasibility and validity are experimentally proven. The chemical shift dependence of dissolved Xe-129 on the composition of a reaction mixture is used for the online monitoring of free-radical miniemulsion polymerization reactions. Xe-129 NMR spectroscopy provides an excellent method for the online monitoring of polymerization reactions, due to the simplicity of the Xe-129 NMR spectra and the simple relationship between the Xe-129 chemical shift and the reaction conversion. The results of the time-resolved Xe-129 NMR measurements are compared to those from calorimetric measurements, showing a good qualitative agreement. The applicability of the new method to reactions other than polymerization reactions is investigated by the online monitoring of an enzymatic reaction in a miniemulsion. The successful combination of the large sensitivity of Xe-129, the NMR signal enhancements due to hyperpolarization, and the solubility of Xe-129 gives access to the large new field of investigations of chemical reaction kinetics in dynamic and complex systems like miniemulsions.

Enzymatic formation of modular cell-instructive fibrin analogs for tissue engineering

The molecular engineering of cell-instructive artificial extracellular matrices is a powerful means to control cell behavior and enable complex processes of tissue formation and regeneration. This work reports on a novel method to produce such smart biomaterials by recapitulating the crosslinking chemistry and the biomolecular characteristics of the biopolymer fibrin in a synthetic analog. We use activated coagulation transglutaminase factor XIIIa for site-specific coupling of cell adhesion ligands and engineered growth factor proteins to multiarm poly(ethylene glycol) macromers that simultaneously form proteolytically sensitive hydrogel networks in the same enzyme-catalyzed reaction. Growth factor proteins are quantitatively incorporated and released upon cell-derived proteolytic degradation of the gels. Primary stromal cells can invade and proteolytically remodel these networks both in an in vitro and in vivo setting. The synthetic ease and potential to engineer their physicochemical and bioactive characteristics makes these hybrid networks true alternatives for fibrin as provisional drug delivery platforms in tissue engineering.

Impact of beta-galactosidase mutations on the expression of the canine lysosomal multienzyme complex

beta-galactosidase (GLB1) forms a functional lysosomal multienzyme complex with lysosomal protective protein (PPCA) and neuraminidase 1 (NEU1) which is important for its intracellular processing and activity. Mutations in the beta-galactosidase gene cause the lysosomal storage disease G(M1)-gangliosidosis. In order to identify additional molecular changes associated with the presence of beta-galactosidase mutations, the expression of canine lysosomal multienzyme complex components in GLB1(+/+), GLB1(+/-) and GLB1(-/-) fibroblasts was investigated by quantitative RT-PCR, Western blot and enzymatic assays. Quantitative RT-PCR revealed differential regulation of total beta-galactosidase, beta-galactosidase variants and protective protein for beta-galactosidase gene (PPGB) in GLB1(+/-) and GLB1(-/-) compared to GLB1(+/+) fibroblasts. Furthermore, it was shown that PPGB levels gradually increased with the number of mutant beta-galactosidase alleles while no change in the NEU1 expression was observed. This is the first study that simultaneously examine the effect of GLB1(+/+), GLB1(+/-) and GLB1(-/-) genotypes on the expression of lysosomal multienzyme complex components. The findings reveal a possible adaptive process in GLB1 homozygous mutant and heterozygous individuals that could facilitate the design of efficient therapeutic strategies.