Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Chemistry of Late Quaternary sediments and their interstitial waters of sediment cores from the Nort-West African continental margin

In the sediments of the NW African continental margin the mainly biogenic carbonate constituents become increasingly diluted with terrigenous material as one approaches the coast, as indicated by the carbonate-CO2 content, the Al2O3/SiO2-ratios, and the presence of ammonia fixed to alumino-silicates, predominantly to illites. In the norther area of the investigation - off Cape Blanc and Cape Bojador . the terrigenous constituents are mainly quartz from the Sahara Desert, whereas in the south - off Senegal - more alumino-silicates as clay minerals are admixed with the carbonate constituents. The organic carbon content of the continental slope sediments off Senegal is higher than in samples of the continental rise or of the preservation of organic matter as a result of high production and relatively rapid sedimentation. The zone of manganese-oxide enrichment follows the redox potential of + 330 mV from the surface (0-5 cm) into the sediments (20-30 cm deep) at 2000--3000 m and 3700 m of water depths, respectively. At shallower water depths, low redox potentials preclude deposition of manganese oxides and cause their mobilization from the sediments. About 1/3 of the total sedimentary Zn and 1/4 of the Cu is associated with the carbonate mineral fraction, probably in calcium phosphate overgrowths as a result of the mineralization of phosphorus-containing organic matter. Besides the precipitation of calcium phosphate, the mineralization of organic matter mediated by bacterial sulfate reduction also results in calcium carbonate precipitation and the exchange of ammonia for potassium on illites. Because of these simultaneous reactions, the depth distribution of all mineralization constituents in the interstitial water can be determined using the actual molar carbon-to-nitrogen-to phosphorus ratios of the sedimentary organic matter. The amount of sulfide sulfur in this process indicates the predominance of bacterial sulfate reduction in the sediments off NW Africa. This process also preferentially decomposes nitrogen- and phosphorus-containing organic compounds so organic matter deficient in these elements is characteristic for the rapidly accumulating sediments than today, indicating there was increased production of organic carbon compounds and more favorable conditions of their preservations. During the last interglacial times conditions were similar to those to today. This differentiation with time has also been observed in sediments from the Argentine Basin and from slope off South India indicating perhaps world-wide environmental changes throughout Late Quaternary times.

Novel imprinted polymers as artificial enzymes

Derivatives of L-histidine were investigated as suitable models for the Asp-His couple found in the catalytic triad of serine proteases. A combination of molecular dynamics and IH NMR spectroscopy suggested that the most populous conformations of N-acetyl-L-histidine and the N-acetyl-L-histidine anion were predominated by those in which the carboxylate group was gauche to the imidazole ring overcoming steric and electrostatic repulsion, suggesting there is an interaction between the carboxylate group and the imidazole ring. Kinetic studies, using imidazole, N-acetyl-L-histidine and the N-acetyl-L-histidine anion showed that in a DMSO/H20 9: 1 v/v solution, the N-acetyl-L-histidine anion catalysed the hydrolysis of p-nitrophenyl acetate at a greater rate than using either imidazole or N-acetyl-L-histidine as catalyst. This indicates that the carboxylate group affects the nucleophilicity of the unprotonated imidazole ring. 31P MAS NMR spectroscopy was investigated as a new technique for the study of the template molecule environment within the polymer networks. It was found that it was possible to distinguish between template associated with the polymer and that which was precipitated onto the surface, though it was not possible to distinguish between polymer within imprinted cavities and that which was not. Attempts to study the effect of the carboxylate group/imidazole ring interaction in the imprinted cavity of a molecularly imprinted polymer network were hindered by the method used to follow the reaction. It was found though that in a pH 8.0 buffered solution the presence of imprinted cavities increased the rate of reaction for those polymers derived from L-histidine. Some preliminary investigations into the design and synthesis of an MIP which would catalyse the oxy-Cope rearrangement were carried out but the results were inconclusive.

Mechanistic study of arsenic uptake, transformation and tolerance in arsenic hyperaccumulator Pteris vittata

Pteris vittata, the first reported arsenic hyperaccumulating plant, is potentially used in phytoremediation of arsenic, as it can accumulate up to 2.3% of arsenic in its fronds. In this study, the mechanisms of arsenic tolerance, uptake and transformation were studied in the plant. Arsenic species were analyzed by HPLC-AFS. Results showed that arsenic was mainly accumulated in leaflets, and inorganic arsenate and arsenite were only species in P. vittata. Arsenite was the predominant species in leaflets, whereas arsenate was the predominant species in roots. Arsenic induced the synthesis of thiol containing compounds in P. vittata. As-induced thiol was purified by a novel method: covalent chromatography following preparative HPLC. The purified thiol was characterized as a phytochelatin with two units (PC2). ^ In P. vittata, enhanced tolerance likely results from unusual intracellular detoxification mechanisms. Although PC-dependent sequestration of arsenic into vacuoles is essential for nonhyperaccumulators, this sequestration is not the major arsenic tolerance mechanisms in this arsenic hyperaccumulator. PC-independent sequestration of arsenic is likely the major arsenic tolerance mechanism. PC-dependent arsenic detoxification is probably a supplement to this major mechanism. ^ Interactions between arsenic and phosphate were studied. Under hydroponic condition, arsenic supply decreased the concentrations of phosphate in roots. In soil, arsenic increased the concentrations of phosphate in roots. Arsenic concentrations in rachises and leaflets were not affected by arsenic supply in either hydroponic or soil system. Phosphate decreased arsenic accumulation in roots, rachises and leaflets in the hydroponic system. ^ The uptake kinetics of arsenate, arsenite, monomethyl arsinic acid (MMA), dimethyl arsonic acid, and phosphate were studied in P. vittata. Phosphate uptake systems in Pteris vittata cannot distinguish phosphate and As(V), resulting in As hyperaccumulation. Arsenic hyperaccumulation in this plant is an inevitable consequence during phosphate acquisition. Arsenate, arsenite and MMA are transported via the phosphate uptake systems. The co-transport of arsenite/phosphate and MMA/phosphate is reported for the first time in plants. These unique phenomena are useful for understanding arsenic hyperaccumulation and the evolution of this capacity in P. vittata. ^

Geochemical and biogeochemical parameters of Black Sea waters and suspended matter

The monograph focuses on the analysis of data addressing the problem of H2S contamination and oxic-anoxic interface in the Black Sea. Regularities of the fine structure of vertical distribution of oxygen, hydrogen sulfide, biogenic elements, organic substances, suspended matter, and metals of the iron-manganese group in the area of contact of aerobic and anaerobic waters have been revealed. Also effects of biochemical, physico-chemical and dynamic processes on their vertical distribution have been examined. Sulfate reduction in seawater and bottom sediments has been studied. Quantitative estimates of H2S fluxes at the water - bottom sediment and O2-H2S interfaces have been done. Features of H2S oxidation have been studied, its budget in the Black Sea has been calculated. Multiyear spatial-temporal variability of the oxic-anoxic interface has been investigated.

Geomicrobiology, bulk sediment characteristics and pore water chemistry of sediment cores from Laguna Potrok Aike, southern Patagonia

Authigenic minerals can form in the water column and sediments of lakes, either abiotically or mediated by biological activity. Such minerals have been used as paleosalinity and paleoproductivity indicators and reflect trophic state and early diagenetic conditions. They are also considered potential indicators of past and perhaps ongoing microbial activity within sediments. Authigenic concretions, including vivianite, were described in late glacial sediments of Laguna Potrok Aike, a maar lake in southernmost Argentina. Occurrence of iron phosphate implies specific phosphorus sorption behavior and a reducing environment, with methane present. Because organic matter content in these sediments was generally low during glacial times, there must have been alternative sources of phosphorus and biogenic methane. Identifying these sources can help define past trophic state of the lake and diagenetic processes in the sediments. We used scanning electron microscopy, phosphorus speciation in bulk sediment, pore water analyses, in situ ATP measurements, microbial cell counts, and measurements of methane content and its carbon isotope composition (d13C CH4) to identify components of and processes in the sediment. The multiple approaches indicated that volcanic materials in the catchment are important suppliers of iron, sulfur and phosphorus. These elements influence primary productivity and play a role in microbial metabolism during early diagenesis. Authigenic processes led to the formation of pyrite framboids and revealed sulfate reduction. Anaerobic oxidation of methane and shifts in pore water ion concentration indicated microbial influence with depth. This study documents the presence of active microbes within the sediments and their relationship to changing environmental conditions. It also illustrates the substantial role played by microbes in the formation of Laguna Potrok Aike concretions. Thus, authigenic minerals can be used as biosignatures in these late Pleistocene maar sediments.

Produção enzimática de biodiesel a partir de resíduos agro-industriais usando a lipase imobilizada de origem microbiana

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Purificação e caracterização parcial de uma B-D glicosidase de Artemia franciscana com ação sobre celobiose e lactose

-D-glucosidase (EC 3.2.1.21) is one of the most interesting glycosidases, especially for hydrolysis cellobiose releasing glucose, is last step degradation of cellulose. This function makes the -D-glucosidase is of great interest as a versatile industrial biocatalyst, being critical to various bio-treatment / biorefinery processes, such as bioethanol production. Hen in the report, a -D-glucosidase was extracts from protein extracted of the invertebrate marine Artemia franciscana was purified and characterized with a combination of precipitation with ammonium sulfate (0 - 30%, 30 to 50%, 50 to 80%), the fraction saturated in the range of 30 to 50% (called F-II) was applied in a molecular exclusion chromatography, in Sephacryl S-200, the fractions corresponding to the first peak of activity of -D-glucosidase were gathered and applied in a chromatography of ion exchange in Mono Q; the third peak this protein obtained chromatography, which coincides with the peak of activity of -D-glucosidase was held and applied in a gel filtration chromatography Superose 12 where the first peak protein, which has activity of -D-glucosidase was rechromatography on Superose 12. This enzyme is probably multimerica, consisting of three subunit molecular mass of 52.7 kDa (determined by SDS-PAGE) with native molecular mass of 157 kDa (determined by gel filtration chromatography on Superose 12 under the system FPLC). The enzyme was purified 44.09 times with a recovery of 1.01%. Using up p-nitrophenyl-β-D-glucopiranoside as substrate obtained a Km apparent of 0.229 mM and a Vmax of 1.109 mM.60min-1.mL-1mM. The optimum pH and optimum temperature of catalysis of the synthetic substrate were 5.0 and 45 °C, respectively. The activity of the -D-glucosidase was strongly, inhibited by silver nitrate and N- etylmaleimide, this inhibition indicates the involvement of radical sulfidrila the hydrolysis of synthetic substrate. The -D-glucosidase of Artemia franciscana presented degradativa action on celobiose, lactose and on the synthetic substrate -nitrophenyl-β-D-glucopiranoside indicating potential use of this enzyme in the industry mainly for the production of bioethanol (production of alcohol from the participating cellulose), and production hydrolysate milk (devoid of milk lactose)

Isolamento de uma quitinase extraída do cefalotórax do camarão marinho Litopenaeus schmitti (BURKENROAD, 1936) : avaliação de suas atividades antimicrobiana e larvicida

Chitinases are enzymes involved in degradation of chitin and are present in a range of organisms, including those that do not contain chitin, such as bacteria, viruses, plants and animals, and play important physiological and ecological roles. Chitin is hydrolyzed by a chitinolytic system classified as: endo-chitinases, exo-chitinases and N-acetyl-b-D-glucosaminidases. In this study a Litochitinase1 extracted from the cephalotorax of the shrimp Litopenaeus Schmitt was purified 987.32 times using ionexchange chromatography DEAE-Biogel and molecular exclusion Sephacryl S-200. These enzyme presented a molecular mass of about 28.5 kDa. The results, after kinetic assay with the Litochitinase1 using as substrate p-nitrophenyl-N-acetyl-b-Dglucosaminideo, showed apparent Km of 0.51 mM, optimal activity at pH ranging from 5.0 to 6.0, optimum temperature at 55°C and stability when pre-incubated at temperatures of 25, 37, 45, 50 and 55°C. The enzyme showed a range of stability at pH 4.0 to 5.5. HgCl2 inhibited Litochitinase1 while MgCl2 enhances its activity. Antimicrobial tests showed that Litochitinase1 present activity against gram-negative bacterium Escherichia coli in the 800 μg/mL concentration. The larvicidal activity against Aedes aegypti was investigated using crude extracts, F-III (50-80%) and Litochitinase1 at 24 and 48 hours. The results showed larvicidal activity in all these samples with EC50 values of 6.59 mg/mL for crude extract, 5.36 mg/mL for F-III and 0.71 mg/mL for Litochitinase1 at 24 hours and 3.22 and 0.49 mg/mL for the F-III and Litochitinase1 at 48 hours, respectively. Other experiments confirmed the presence of chitin in the midgut of Aedes aegypti larvae, which may be suffering the action of Litochitinase1 killing the larvae, but also the absence of contaminating proteins as serine proteinase inhibitors and lectins in the crude extract, F-III and Litochitinase1, indicating that the death of the larvae is by action of the Litochitinase1. We also observed that the enzymes extracted from intestinal homogenate of the larvae no have activity on Litochitinase1. These results indicate that the enzyme can be used as an alternative to control of infections caused by Escherichia coli and reducing the infestation of the mosquito vector of dengue.

Purificação e caracterização parcial de duas N-acetil-ß-hexosaminidases do Equinoderma marinho Echinometra lucunter

Two b-N-acetylhexosaminidases (F11 e F15) were purified from Echinometra lucunter gonads extracts. The purified enzymes were obtained using ammonium sulfate fractionation, followed by gel filtration chromatographies (Sephacryl S-200, Sephadex G-75 and Sephacryl S-200). The F11 fraction was purified 192.47 -fold with a 28.5% yield, and F15 fraction 85.41 -fold with a 32.3% yield. The molecular weights of the fractions were 116 kDa for F11 and 42 kDa for F15 using SDS-PAGE. In Sephacryl S-200, F15 was 84 kDa, indicating that it is a dimeric protein. When p-nitrophenyl-β-D-glycosaminide was used as substrate, we determined an apparent Km of 0.257 mM and Vmax of 0.704 for F11 and for F15 the Km was 0.235 mM and Vmax of 0.9 mM of product liberated by hour. Both enzymes have optimum pH and temperature respectively at 5.0 and 45 °C. The enzymes showed inhibition by silver nitrate, while the glucuronic acid was a potent activator. The high inhibition of F15 by N-etylmaleimide indicates that sulphydril groups are involved in the catalysis of synthetic substrate

Purificação e caracterização parcial de uma B-D glicosidase de Artemia franciscana com ação sobre celobiose e lactose

-D-glucosidase (EC 3.2.1.21) is one of the most interesting glycosidases, especially for hydrolysis cellobiose releasing glucose, is last step degradation of cellulose. This function makes the -D-glucosidase is of great interest as a versatile industrial biocatalyst, being critical to various bio-treatment / biorefinery processes, such as bioethanol production. Hen in the report, a -D-glucosidase was extracts from protein extracted of the invertebrate marine Artemia franciscana was purified and characterized with a combination of precipitation with ammonium sulfate (0 - 30%, 30 to 50%, 50 to 80%), the fraction saturated in the range of 30 to 50% (called F-II) was applied in a molecular exclusion chromatography, in Sephacryl S-200, the fractions corresponding to the first peak of activity of -D-glucosidase were gathered and applied in a chromatography of ion exchange in Mono Q; the third peak this protein obtained chromatography, which coincides with the peak of activity of -D-glucosidase was held and applied in a gel filtration chromatography Superose 12 where the first peak protein, which has activity of -D-glucosidase was rechromatography on Superose 12. This enzyme is probably multimerica, consisting of three subunit molecular mass of 52.7 kDa (determined by SDS-PAGE) with native molecular mass of 157 kDa (determined by gel filtration chromatography on Superose 12 under the system FPLC). The enzyme was purified 44.09 times with a recovery of 1.01%. Using up p-nitrophenyl-β-D-glucopiranoside as substrate obtained a Km apparent of 0.229 mM and a Vmax of 1.109 mM.60min-1.mL-1mM. The optimum pH and optimum temperature of catalysis of the synthetic substrate were 5.0 and 45 °C, respectively. The activity of the -D-glucosidase was strongly, inhibited by silver nitrate and N- etylmaleimide, this inhibition indicates the involvement of radical sulfidrila the hydrolysis of synthetic substrate. The -D-glucosidase of Artemia franciscana presented degradativa action on celobiose, lactose and on the synthetic substrate -nitrophenyl-β-D-glucopiranoside indicating potential use of this enzyme in the industry mainly for the production of bioethanol (production of alcohol from the participating cellulose), and production hydrolysate milk (devoid of milk lactose)

Coupled substitution of niobium and silicon in potassium titanyl phosphate and arsenate (KTiOPO4 and KTiOAsO4. Synthesis and nonlinear optical properties of KTi1-xNbxOX1-xSixO4 (X = P, As)

Coupled substitution of Nb(V) and Si(IV) for Ti(IV) and P(V)/As(V) in KTiOP04 (KTP) and KTiOAsO4 (KTA) giving new series of nonlinear optical materials, KTi1-xNbxOX1-xSixO4 (X=P,As), has been investigated. Substitution up to x = 0.40 readily occurs, the members retaining the orthorhombic (Pna2(1)) structure of KTP. The second harmonic generation (SHG) property of the parent KTP and KTA is not adversely affected by the coupled substitution. SHG intensity of the powder samples of the X = P series shows a slight increase with x up to x = 0.15; for 0.15 < x less-than-or-equal-to 0.40, there is a decrease in SHG intensity as compared to that for KTP. A similar trend in SHG intensity is seen for the arsenic analogs.

The C-terminal domain of the Salmonella enterica WbaP (UDP-galactose:Und-P galactose-1-phosphate transferase) is sufficient for catalytic activity and specificity for undecaprenyl monophosphate

Two families of membrane enzymes catalyze the initiation of the synthesis of O-antigen lipopolysaccharide. The Salmonella enterica Typhimurium WbaP is a prototypic member of one of these families. We report here the purification and biochemical characterization of the WbaP C-terminal (WbaP(CT)) domain harboring one putative transmembrane helix and a large cytoplasmic tail. An N-terminal thioredoxin fusion greatly improved solubility and stability of WbaP(CT) allowing us to obtain highly purified protein. We demonstrate that WbaP(CT) is sufficient to catalyze the in vitro transfer of galactose (Gal)-1-phosphate from uridine monophosphate (UDP)-Gal to the lipid carrier undecaprenyl monophosphate (Und-P). We optimized the in vitro assay to determine steady-state kinetic parameters with the substrates UDP-Gal and Und-P. Using various purified polyisoprenyl phosphates of increasing length and variable saturation of the isoprene units, we also demonstrate that the purified enzyme functions highly efficiently with Und-P, suggesting that the WbaP(CT) domain contains all the essential motifs to catalyze the synthesis of the Und-P-P-Gal molecule that primes the biosynthesis of bacterial surface glycans.

Factors influencing the dissolution of phosphate rock in a range of high P-fixing soils from Cameroon

A laboratory incubation experiment was conducted to evaluate the soil factors that influence the dissolution of two phosphate rocks (PRs) of different reactivity (Gafsa, GPR, reactive PR; and Togo-Hahotoe, HPR, low reactivity PR) in seven agricultural soils from Cameroon having variable phosphorus (P)- sorption capacities, organic carbon (C) contents, and exchangeable acidities. Ground PR was mixed with the soils at a rate of 500 mg P kg 21 soil and incubated at 30 degrees C for 85 days. Dissolution of the PRs was determined at various intervals using the Delta NaOH-P method ( the difference of the amount of P extracted by 0.5 M NaOH between the PR-treated soils and the control). Between 4 and 27% of HPR and 33 and 50% of GPR were dissolved in the soils. Calcium (Ca) saturation of cation exchange sites and proton supply strongly affected PR dissolution in these soils. Acid soils with pH-(H2O), < 5 (NKL, ODJ, NSM, MTF) dissolved more phosphate rock than those with pH-(H2O) > 5 (DSC, FGT, BAF). However, the lack of a sufficient Ca sink in the former constrained the dissolution of both PRs. The dissolution of GPR in the slightly acidic soils was limited by increase in Ca saturation and that of HPR was constrained by limited supply in protons. Generally, the dissolution of GPR was higher than that of HPR for each soil. The kinetics of dissolution of PR in the soils was best described by the power function equation P At B. More efficient use of PR in these soils can be achieved by raising the soil cation exchange capacity, thereby increasing the Ca sink size. This could be done by amending such soils with organic materials.