Jack bean urease: the first nickel enzyme

Comparative analysis of Zn(II)-complexes as model metalloenzymes for mimicking Jack bean urease

The inhibitory action of Schiff base complexes of 3d metals against the urease enzyme is well explored in the scientific community. However, the ability of such complexes in mimicking active metallobiosites of urease enzymes, possessing ureolytic behavior, still remains unexplored. With this aim firstly, two Zn(II)-complexes (PPR-HMB-Zn and PZ-HMB-Zn) have been developed from two different Schiff base ligands (HL1 = 2-((E)-(2-(piperidin-1-yl)ethylimino)methyl)-5-methylphenol and HL2 = 2-((E)-(2-(piperizin-1-yl)ethylimino)methyl)-5-methylphenol) and structurally characterized using single crystal XRD. The hydrolytic enzymatic activity of both complexes was demonstrated by the gradual increase in the absorption maxima at 425 nm for the formation of the p-nitrophenolate ion from catalytic hydrolysis mediated by the Zn(II) complexes with a disodium salt of p-nitrophenyl phosphate as a model substrate. Associated kinetic parameters, pH dependency and a relevant hydrolysis mechanism have also been explored. After confirming the hydrolytic ability, the complexes were exploited to mimic the hydrolytic activity of Jack bean urease that catalytically hydrolyses urea into ammonia and CO2. The change in the pH of the solution owing to the formation of ammonia under the complex catalysed hydrolytic action of urea has been monitored spectrophotometrically using the pH dependent structural change of phenol red. The amount of ammonia has been quantified using the Nessler's reagent spectrophotometric method. The ureolytic reaction mechanism has been investigated using density functional theory (DFT) calculations using the B3LYP and TPSSH methods for the systematic calculation of the interaction energy. In contrast to PZ-HMB-Zn, PPR-HMB-Zn functions more effectively as a catalyst due to the existence of a lattice-occluded water molecule in its crystal structure and the protonation of the non-terminal N to attract urea by H-bonding, which was further confirmed by AIM analysis.

In Silico Structural and Functional Insight into the Binding Interactions of the Modeled Structure of Watermelon Urease with Urea

Urease (EC 3.5.1.5) is an amidohydrolase. This nickel-dependent metalloenzyme converts urea into NH3 and CO2. Despite their vital role in plants, the structure and function of watermelon (Citrullus lanatus) urease are unknown. We used third- and fourth-generation gene prediction algorithms to annotate the C. lanatus urease sequence in this investigation. The solved urease structure from Canavalia ensiformis (PDB ID: 4GY7) was utilized as a template model to identify the target 3-D model structure of the unknown C. lanatus urease for the first time. Cluretox, the C. lanatus urease intrinsic disordered area identical to Jaburetox, was also found. The C. lanatus urease structure was docked with urea to study atom interaction, amino acid interactions, and binding analyses in the urease-urea complex at 3.5 Å. This study found that amino acids His517, Gly548, Asp631, Ala634, Thr569, His543, Met635, His407, His490, and Ala438 of C. lanatus urease bind urea. To study the molecular basis and mode of action of C. lanatus urease, molecular dynamics simulation was performed and RMSD, RMSF, Rg, SAS, and H-bond analyses were done. The calculated binding free energy (ΔG) for the urea-urease complex at 100 ns using the MM/PBSA method is -7.61 kJ/mol. Understanding its catalytic principles helps scientists construct more efficient enzymes, tailor fertilization to boost agricultural output, and create sustainable waste management solutions.

[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives as new therapeutic candidates against urease positive microorganisms: design, synthesis, pharmacological evaluations, and in silico studies

Regarding the important role of the urease enzyme as a virulence factor in urease-positive microorganisms in this study, new series of [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives were designed and synthesized. All compounds evaluated against urease enzyme exhibiting IC50 values of 0.87 ± 0.09 to 8.32 ± 1.21 µM as compared with thiourea as the positive control (IC50 = 22.54 ± 2.34 µM). The kinetic evaluations of 6a as the most potent derivative recorded a competitive type of inhibition. Molecular dynamic simulations of the 6a derivative were also conducted, showing that 6a occupied the active site with closed state. Antimicrobial activities of all derivatives were performed, and 6f (R = 3-Cl), 6g (R = 4-Cl), and 6h (R = 3,4-diCl) analogs demonstrated significant antifungal activities with MIC values of 1, 2, and 0.5 µg/mL compared with fluconazole with MIC = 2 µg/mL. Synthesized analogs also exhibited potent urease inhibitory activities against C. neoformans (IC50 = 83.7-118.7 µg/mL) and P. mirabilis (IC50 = 74.5-113.7 µg/mL), confirming their urease inhibitory potential. The results demonstrated that the designed scaffold could be considered a suitable pharmacophore to develop potent urease inhibitors.

The quintessence of metallomics: a harbinger of a different life science based on the periodic table of the bioelements

This year marks the 20th anniversary of the field of metallomics. As a landmark in time, it is an occasion to reflect on the past, present, and future of this integrated field of biometal sciences. A fundamental bias is one reason for having metallomics as a scientific discipline. The focus of biochemistry on the six non-metal chemical elements, collectively known with the acronym SPONCH (sulphur, phosphorus, oxygen, nitrogen, carbon, hydrogen), glosses over the fact that the lower quantities of many other elements have qualities that made them instrumental in the evolution of life and pivotal in numerous life processes. The metallome, alongside the genome, proteome, lipidome, and glycome, should be regarded as a fifth pillar of elemental-vis-à-vis molecular-building blocks in biochemistry. Metallomics as 'global approaches to metals in the biosciences' considers the biological significance of most chemical elements in the periodic table, not only the ones essential for life, but also the non-essential ones that are present in living matter-some at higher concentrations than the essential ones. The non-essential elements are bioactive with either positive or negative effects. Integrating the significance of many more chemical elements into the life sciences requires a transformation in learning and teaching with a focus on elemental biology in addition to molecular biology. It should include the dynamic interactions between the biosphere and the geosphere and how the human footprint is changing the ecology globally and exposing us to many additional chemical elements that become new bioelements.

The Effect of Nucleating Agents on Enzyme-Induced Carbonate Precipitation and Corresponding Microscopic Mechanisms

Plant urease has the advantages of high activity and small size in enzyme-induced calcium carbonate precipitation (EICP). However, there area lack of nucleation sites for calcium carbonate in EICP. Sucrose and sorbitol, which are readily available and inexpensive, have the potential to provide nucleation sites for EICP as nucleating agents. To explore the effects of the two nucleating agents on EICP, the productivity of calcium carbonate, unconfined compressive strength (UCS) and microscopic mechanisms were tested. It is found that the productivity of EICP can be increased as much as 5.1% by the addition of sorbitol with an optimal content of 5%, and the productivity of EICP can be increased as much as 12.3% by the addition of sucrose with an optimal of 4%. The UCS of EICP-treated sand increases by 2.2 times after being improved by sorbitol with a content of 5.2%, the CaCO₃ content of EICP-treated sand with sorbitol added increased by 1.5% compared to conventional EICP-treated sand. These results show that the two nucleating agents are effective for improving EICP. The SEM images verify that sorbitol/sucrose can compensate for the lack of nucleating sites in EICP and explicate the effect of nucleating agents on EICP.

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Urease catalyzes the hydrolysis of urea to form ammonia and carbamate, inducing an overall pH increase that affects both human health and agriculture. Inhibition, mutagenesis, and kinetic studies have provided insights into its enzymatic role, but there have been debates on the substrate binding mode as well as the reaction mechanism. In the present study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) calculations on urease that mainly investigate the binding mode of urea and the mechanism of the urease-catalyzed hydrolysis reaction. Comparison between the experimental data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that urea hydrolysis via a complex with bidentate-bound urea is much more favorable than via that with monodentate-bound urea for both nucleophilic attack and the subsequent proton transfer steps. We also indicate that the bidentate coordination of urea fits the active site with a closed conformation of the mobile flap and can facilitate the stabilization of transition states and intermediates by forming multiple hydrogen bonds with certain active site residues.

Advances in Enzyme Induced Carbonate Precipitation and Application to Soil Improvement: A Review

Climate change and global warming have prompted a notable shift towards sustainable geotechnics and construction materials within the geotechnical engineer’s community. Earthen construction materials, in particular, are considered sustainable due to their inherent characteristics of having low embodied and operational energies, fire resistance, and ease of recyclability. Despite these attributes, they have not been part of the mainstream construction due to their susceptibility to water-induced deterioration. Conventional soil improvement techniques are generally expensive, energy-intensive, and environmentally harmful. Recently, biostabilization has emerged as a sustainable alternative that can overcome some of the limitations of existing soil improvement methods. Enzyme-induced carbonate precipitation (EICP) is a particularly promising technique due to its ease of application and compatibility with different soil types. EICP exploits the urease enzyme as a catalyst to promote the hydrolysis of urea inside the pore water, which, in the presence of calcium ions, results in the precipitation of calcium carbonate. The purpose of this paper is to provide a state-of-the-art review of EICP stabilization, highlighting the potential application of this technique to field problems and identifying current research gaps. The paper discusses recent progress, focusing on the most important factors that govern the efficiency of the chemical reactions and the precipitation of a spatially homogenous carbonate phase. The paper also discusses other aspects of EICP stabilization, including the degree of ground improvement, the prediction of the pore structure of the treated soil by numerical simulations, and the remediation of potentially toxic EICP by-products.

A sample cell for the study of enzyme-induced carbonate precipitation at the grain-scale and its implications for biocementation

Biocementation is commonly based on microbial-induced carbonate precipitation (MICP) or enzyme-induced carbonate precipitation (EICP), where biomineralization of [Formula: see text] in a granular medium is used to produce a sustainable, consolidated porous material. The successful implementation of biocementation in large-scale applications requires detailed knowledge about the micro-scale processes of [Formula: see text] precipitation and grain consolidation. For this purpose, we present a microscopy sample cell that enables real time and in situ observations of the precipitation of [Formula: see text] in the presence of sand grains and calcite seeds. In this study, the sample cell is used in combination with confocal laser scanning microscopy (CLSM) which allows the monitoring in situ of local pH during the reaction. The sample cell can be disassembled at the end of the experiment, so that the precipitated crystals can be characterized with Raman microspectroscopy and scanning electron microscopy (SEM) without disturbing the sample. The combination of the real time and in situ monitoring of the precipitation process with the possibility to characterize the precipitated crystals without further sample processing, offers a powerful tool for knowledge-based improvements of biocementation.

State-of-the-Art Review of the Applicability and Challenges of Microbial-Induced Calcite Precipitation (MICP) and Enzyme-Induced Calcite Precipitation (EICP) Techniques for Geotechnical and Geoenvironmental Applications

The development of alternatives to soil stabilization through mechanical and chemical stabilization has paved the way for the development of biostabilization methods. Since its development, researchers have used different bacteria species for soil treatment. Soil treatment through bioremediation techniques has been used to understand its effect on strength parameters and contaminant remediation. Using a living organism for binding the soil grains to make the soil mass dense and durable is the basic idea of soil biotreatment. Bacteria and enzymes are commonly utilized in biostabilization, which is a common method to encourage ureolysis, leading to calcite precipitation in the soil mass. Microbial-induced calcite precipitation (MICP) and enzyme-induced calcite precipitation (EICP) techniques are emerging trends in soil stabilization. Unlike conventional methods, these techniques are environmentally friendly and sustainable. This review determines the challenges, applicability, advantages, and disadvantages of MICP and EICP in soil treatment and their role in the improvement of the geotechnical and geoenvironmental properties of soil. It further elaborates on their probable mechanism in improving the soil properties in the natural and lab environments. Moreover, it looks into the effectiveness of biostabilization as a remediation of soil contamination. This review intends to present a hands-on adoptable treatment method for in situ implementation depending on specific site conditions.

Managing enzyme promiscuity in plant specialized metabolism: A lesson from flavonoid biosynthesis: Mission of a "body double" protein clarified

Specificities of enzymes involved in plant specialized metabolism, including flavonoid biosynthesis, are generally promiscuous. This enzyme promiscuity has served as an evolutionary basis for new enzyme functions and metabolic pathways in land plants adapting to environmental challenges. This phenomenon may lead, however, to inefficiency in specialized metabolism and adversely affect metabolite-mediated plant survival. How plants manage enzyme promiscuity for efficient specialized metabolism is, thus, an open question. Recent studies of flavonoid biosynthesis addressing this issue have revealed a conserved strategy, namely, a homolog of chalcone isomerase with no catalytic activity binds to chalcone synthase, a key flavonoid pathway enzyme, to narrow (or rectify) the enzyme's highly promiscuous product specificity. Reducing promiscuity via specific protein-protein interactions among metabolic enzymes and proteins may be a solution adopted by land plants to achieve efficient operation of specialized metabolism, while the intrinsic promiscuity of enzymes has likely been retained incidentally.

Forming amorphous calcium carbonate within hydrogels by enzyme-induced mineralization in the presence of N-(phosphonomethyl)glycine

Amorphous inorganic materials have a great potential in material science. Amorphous calcium carbonate (ACC) is a widely useable system, however, its stabilization often turns out to be difficult and the synthesis is mostly limited to precipitation in solution as nanoparticles. Stable ACC in bulk phases would create new composite materials. Previous work described the enzyme-induced mineralization of hydrogels with crystalline calcium carbonate by entrapping urease into a hydrogel and treating this with an aqueous mineralization solution containing urea und calcium chloride. Here, this method was modified using a variety of crystallization inhibitors attached to the hydrogel matrix or added to the surrounding mineralization solution. It was found that only N-(phosphonomethyl)glycine (PMGly) in solution completely inhibits the crystallization of ACC in the hydrogel matrix. The stability of the homogeneously precipitated ACC could be accounted to the combination of stabilizing effects of the additive and stabilization through confinement. The crystallization could be accelerated at higher temperatures up to 60 °C. Here, a combination of Mg ions and PMGly was required to stabilize ACC in the hydrogel. Variation of these two compounds can be used to control a number of different calcium carbonate morphologies within the hydrogel. While the ACC nanoparticles within the hydrogel are stable over weeks even in water, a calcite layer grows on the surface of the hydrogel, which might be used as self-hardening mechanism of a surface.

Heavy Metal Immobilization Studies and Enhancement in Geotechnical Properties of Cohesive Soils by EICP Technique

Soil treatment methods to cope with ever-growing demands of construction industry and environmental aspects are always explored for their suitability in different in-situ conditions. Of late, enzyme induced calcite precipitation (EICP) is gaining importance as a reliable technique to improve soil properties and for contaminant remediation scenarios. In the present work, swelling and permeability characteristics of two native Indian cohesive soils (Black and Red) are explored. Experiments on the sorption and desorption of multiple heavy metals (Cd, Ni and Pb) onto these soils were conducted to understand the sorptive response of the heavy metals. To improve the heavy metal retention capacity and enhance swelling and permeability characteristics, the selected soils were treated with different enzyme solutions. The results revealed that EICP technique could immobilize the heavy metals in selected soils to a significant level and reduce the swelling and permeability. This technique is contaminant selective and performance varies with the nature and type of heavy metal used. Citric acid (C6H8O7) and ethylene diamine tetra-acetic acid (EDTA) were used as extractants in the present study to study the desorption response of heavy metals for different EICP conditions. The results indicate that calcium carbonate (CaCO3) precipitate deposited in the voids of soil has the innate potential in reducing the permeability of soil up to 47-fold and swelling pressure by 4-fold at the end of 21 days of curing period. Reduction in permeability and swell, following EICP treatment can be maintained with one time rinsing of the treated soil in water to avoid dissolution of precipitated CaCO3. Outcomes of this study have revealed that EICP technique can be adopted on selected native soils to reduce swelling and permeability characteristics followed by enhanced contaminant remediation enabling their potential as excellent landfill liner materials.

Efficacy of Enzymatically Induced Calcium Carbonate Precipitation in the Retention of Heavy Metal Ions

This study evaluated the efficacy of enzyme induced calcite precipitation (EICP) in restricting the mobility of heavy metals in soils. EICP is an environmentally friendly method that has wide ranging applications in the sustainable development of civil infrastructure. The study examined the desorption of three heavy metals from treated and untreated soils using ethylene diamine tetra-acetic acid (EDTA) and citric acid (C6H8O7) extractants under harsh conditions. Two natural soils spiked with cadmium (Cd), nickel (Ni), and lead (Pb) were studied in this research. The soils were treated with three types of enzyme solutions (ESs) to achieve EICP. A combination of urea of one molarity (M), 0.67 M calcium chloride, and urease enzyme (3 g/L) was mixed in deionized (DI) water to prepare enzyme solution 1 (ES1); non-fat milk powder (4 g/L) was added to ES1 to prepare enzyme solution 2 (ES2); and 0.37 M urea, 0.25 M calcium chloride, 0.85 g/L urease enzyme, and 4 g/L non-fat milk powder were mixed in DI water to prepare enzyme solution 3 (ES3). Ni, Cd, and Pb were added with load ratios of 50 and 100 mg/kg to both untreated and treated soils to study the effect of EICP on desorption rates of the heavy metals from soil. Desorption studies were performed after a curing period of 40 days. The curing period started after the soil samples were spiked with heavy metals. Soils treated with ESs were spiked with heavy metals after a curing period of 21 days and then further cured for 40 days. The amount of CaCO3 precipitated in the soil by the ESs was quantified using a gravimetric acid digestion test, which related the desorption of heavy metals to the amount of precipitated CaCO3. The order of desorption was as follows: Cd > Ni > Pb. It was observed that the average maximum removal efficiency of the untreated soil samples (irrespective of the load ratio and contaminants) was approximately 48% when extracted by EDTA and 46% when extracted by citric acid. The soil samples treated with ES2 exhibited average maximum removal efficiencies of 19% and 10% when extracted by EDTA and citric acid, respectively. It was observed that ES2 precipitated a maximum amount of calcium carbonate (CaCO3) when compared to ES1 and ES3 and retained the maximum amount of heavy metals in the soil by forming a CaCO3 shield on the heavy metals, thus decreasing their mobility. An approximate improvement of 30% in the retention of heavy metal ions was observed in soils treated with ESs when compared to untreated soil samples. Therefore, the study suggests that ESs can be an effective alternative in the remediation of soils contaminated with heavy metal ions.

Microbial insights from Antarctic and Mediterranean shallow-water bone-eating worms

Bone-eating worms of the genus Osedax (Annelida, Siboglinidae) form unique holobionts (functional entity comprising host and associated microbiota), highly adapted to inhabit bone tissue of marine vertebrates. These gutless worms have developed nutritional symbioses housing intracellular, horizontally acquired, heterotrophic bacteria hypothesised to harness nutrients from organic compounds, sequestered within the bone. Despite previous efforts, critical mechanisms mediating activity and acquisition of diverse bacterial assemblages remain unclear. Using 16S rRNA amplicon sequencing, we performed detailed taxonomic and predicted functional analyses shedding light on the microbial communities of two shallow-water Osedax species (Osedax deceptionensis and Osedax ‘mediterranea’) from contrasting habitats (Antarctic and Mediterranean Sea), in two tissue types (roots and palps). Comparative assessments between host species revealed distinct microbial assemblages whilst, within host species and body tissue, relative symbiont frequencies retained high variability. We reported relatively high abundances of microbes previously classified as primary endosymbionts, Ribotype 1 (order Oceanospirillales), and diverse likely secondary epibionts warranting further exploration as recurrent Osedax associates. Surprisingly, O. ‘mediterranea’ exhibited relatively low abundance of Oceanospirillales, but increased abundance of other potentially hydrocarbon degrading bacteria from the family Alteromonadaceae. We hypothesise the presence of functionally similar, non-Oceanospirillales primary endosymbionts within O. ‘mediterranea’. Functional metagenomic profiling (using 16S rRNA sequences) predicted broad metabolic capabilities, encompassing relatively large abundances of genes associated with amino acid metabolism. Comparative analyses between host body tissue communities highlighted several genes potentially providing critical functions to the Osedax host or that confer adaptations for intracellular life, housed within bone embedded host root tissues.

Real-time monitoring of the enzymatic reaction of urease by using whispering gallery mode lasing

A new strategy is reported here to monitor the enzymatic reactions in real time by using whispering gallery mode (WGM) lasing. The optical microcavity is formed via the self-assembly of an ultraviolet (UV)-treated nematic liquid crystal (LC) 4-cyano-4'-pentylbiphenyl (5CB). The single UV-treated 5CB microdroplet serves as both optical resonator and sensing reactor. The microdroplet configuration transitions induced wavelength shift in the WGM lasing spectra can be used as an indicator for the enzymatic reaction. The proposed sensor has a sub-microgram detection limit of urease (∼0.5 µg/ml), which is lower than the detection limit of currently available urease sensor based on LC materials. Our experimental results demonstrate that WGM lasing has unique advantages in the real-time monitoring of enzymatic reactions compared, for instance, with observation of the optical appearance under a polarized optical microscope.

The Maturation Pathway of Nickel Urease

Maturation of urease involves post-translational insertion of nickel ions to form an active site with a carbamylated lysine ligand and is assisted by urease accessory proteins UreD, UreE, UreF and UreG. Here, we review our current understandings on how these urease accessory proteins facilitate the urease maturation. The urease maturation pathway involves the transfer of Ni2+ from UreE → UreG → UreF/UreD → urease. To avoid the release of the toxic metal to the cytoplasm, Ni2+ is transferred from one urease accessory protein to another through specific protein–protein interactions. One central theme depicts the role of guanosine triphosphate (GTP) binding/hydrolysis in regulating the binding/release of nickel ions and the formation of the protein complexes. The urease and [NiFe]-hydrogenase maturation pathways cross-talk with each other as UreE receives Ni2+ from hydrogenase maturation factor HypA. Finally, the druggability of the urease maturation pathway is reviewed.

Synthesis of β-Ketosulfone Derivatives As New Non-Cytotoxic Urease Inhibitors In Vitro

BACKGROUND

Peptic ulcer and urolithiasis are largely due to infection caused by ureaseproducing bacteria. Therefore, the discovery of urease inhibitors is an important area of medicinal chemistry research.

OBJECTIVE

The main aim of the work was to identify novel urease inhibitors with no cytotoxicity.

METHODS

During the current study, a series of β-ketosulfones 1-26 was synthesized in two steps and evaluated for their in vitro urease inhibition potential.

RESULTS

Out of twenty-six compounds, seventeen have shown good to significant urease inhibitory activity with IC50 values ranging between 49.93-351.46 µM, in comparison to standard thiourea (IC50 = 21 ± 0.11 µM). Moreover, all compounds found to be non-cytotoxic against normal 3T3 cell line.

CONCLUSION

This study has identified β-ketosulfones as novel and non-cytotoxic urease inhibitors.

Synthesis, Magnetic Properties, and Catalytic Properties of a Nickel(II)-Dependent Biomimetic of Metallohydrolases

A dinickel(II) complex of the ligand 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol (HL1) has been prepared and characterized to generate a functional model for nickel(II) phosphoesterase enzymes. The complex, [Ni2(L1)(μ-OAc)(H2O)2](ClO4)2·H2O, was characterized by microanalysis, X-ray crystallography, UV-visible, and IR absorption spectroscopy and solid state magnetic susceptibility measurements. Susceptibility studies show that the complex is antiferromagnetically coupled with the best fit parameters J = -27.4 cm-1, g = 2.29, D = 28.4 cm-1, comparable to corresponding values measured for the analogous dicobalt(II) complex [Co2(L1)(μ-OAc)](ClO4)2·0.5 H2O (J = -14.9 cm-1 and g = 2.16). Catalytic measurements with the diNi(II) complex using the substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) demonstrated activity toward hydrolysis of the phosphoester substrate with K m ~10 mM, and k cat ~0.025 s-1. The combination of structural and catalytic studies suggests that the likely mechanism involves a nucleophilic attack on the substrate by a terminal nucleophilic hydroxido moiety.

Benzylidine indane-1,3-diones: As novel urease inhibitors; synthesis, in vitro, and in silico studies

Current study deals with the evaluation of indane-1,3-dione based compounds as new class of urease inhibitors. For that purpose, benzylidine indane-1,3-diones (1-30) were synthesized and fully characterized by different spectroscopic techniques including EI-MS, HREI-MS, ¹H, and ¹³C NMR. All synthetic molecules 1-30 were evaluated for urease inhibitory activity and showed good to moderate inhibitory potential within the range of (IC₅₀ = 11.60 ± 0.3-257.05 ± 0.7 µM) as compared to the standard acetohydroxamic acid (IC₅₀ = 27.0 ± 0.5 µM). Compound 1 (IC₅₀ = 11.60 ± 0.3 µM) was found to be most potent inhibitor amongst all derivatives. The key binding interactions of most active compounds within the enzyme pocket were evaluated through in silico studies.

Urease-aided calcium carbonate mineralization for engineering applications: A review

Inducing calcium carbonate precipitation is another important function of urease in nature. The process takes advantage of the supply of carbonate ions derived from urea hydrolysis and of an increase in pH generated by the reaction, effects that in the presence of Ca²⁺ ions lead to the precipitation of CaCO₃. Further to its importance in nature, if performed in a biomimetic manner, the urease-aided CaCO₃ mineralization offers enormous potential in innovative engineering applications as an eco-friendly technique operative under mild conditions, to be used for remediation and cementation/deposition in field applications in situ. These include among others, the strengthening and consolidation of soil/sand, the protection and restoration of stone and concrete structures, conservation of stone cultural heritage materials, cleaning waste- and groundwater of toxic metals and radionuclides, and plugging geological formations for the enhancement of oil recovery and geologic CO₂ sequestration. In view of the potential of this newly emerging interdisciplinary branch of engineering, this article presents the principles of urease-aided calcium carbonate mineralization apposed to other biomineralization processes, and reviews the advantages and limitations of the technique compared to the conventional techniques presently in use. Further, it presents areas of its existing and potential applications, notably in geotechnical, construction and environmental engineering, and its future perspectives.

Nitrous Oxide Emissions from Open-Lot Cattle Feedyards: A Review

Nitrous oxide (NO) emissions from concentrated animal feeding operations, including cattle feedyards, have become an important research topic. However, there are limitations to current measurement techniques, uncertainty in the magnitude of feedyard NO fluxes, and a lack of effective mitigation methods. The objective of this review was to assess NO emission from cattle feedyards, including comparison of measured and modeled emission rates, discussion of measurement methods, and evaluation of mitigation options. Published annual per capita flux rates for beef cattle feedyards and open-lot dairies were highly variable and ranged from 0.002 to 4.3 kg NO animal yr. On an area basis, published emission rates ranged from 0 to 41 mg NO m h. From these studies and Intergovernmental Panel on Climate Change emission factors, calculated daily per capita NO fluxes averaged 18 ± 10 g NO animal d (range, 0.04-67 g NO animal d). This variation was due to inconsistency in measurement techniques as well as irregularity in NO production and emission attributable to management, animal diet, and environmental conditions. Based on this review, it is clear that the magnitude and dynamics of NO emissions from open-lot cattle systems are not well understood. Further research is required to quantify feedyard NO fluxes and develop cost-effective mitigation methods.

Chitosan Membrane-Immobilized Urease. Kinetic Behavior in Phosphate Buffer in the pH Range 5.76-8.19

The effect of phosphate buffer on the kinetic behavior of jack bean urease covalently immobilized on chitosan membrane was studied in the pH range 5.76-8.19, and compared with that of the free enzyme in an attempt to elucidate the effects of heterogeneity of the system on its kinetics. The chemical inhibition by the buffer, occurring between pH 5.76 and 7.50, was found to consist of two antagonistic effects: a decrease in the intrinsic enzyme activity and a reduction in the degree of environment-related inhibition. The apparent kinetic constants of the immobilized urease: v xmax., K x M and K i,buffer exhibited both pH- and buffer concentration-dependence, anomalous as compared to the free enzyme: the optimum pH and the pK i,buffer values were displaced toward more acidic pH values, and the p K x M values were leveled off. The anomalies were gradually suppressed by increasing the buffer concentration. The anomalous behavior of chitosan membrane-immobilized urease was accounted for by a combined effect of: a) the increase in local pH on the membrane produced by both the enzymatic reaction and the electric charge of the support, and b) diffusional limitations imposed on substrate and product in the external solution.

Microbially-induced Carbonate Precipitation for Immobilization of Toxic Metals

Rapid urbanization and industrialization resulting from growing populations contribute to environmental pollution by toxic metals and radionuclides which pose a threat to the environment and to human health. To combat this threat, it is important to develop remediation technologies based on natural processes that are sustainable. In recent years, a biomineralization process involving ureolytic microorganisms that leads to calcium carbonate precipitation has been found to be effective in immobilizing toxic metal pollutants. The advantage of using ureolytic organisms for bioremediating metal pollution in soil is their ability to immobilize toxic metals efficiently by precipitation or coprecipitation, independent of metal valence state and toxicity and the redox potential. This review summarizes current understanding of the ability of ureolytic microorganisms for carbonate biomineralization and applications of this process for toxic metal bioremediation. Microbial metal carbonate precipitation may also be relevant to detoxification of contaminated process streams and effluents as well as the production of novel carbonate biominerals and biorecovery of metals and radionuclides that form insoluble carbonates.

Effect of ohmic heating of soymilk on urease inactivation and kinetic analysis in holding time

To verify the effect of the ohmic heating on the urease activity in the soymilk, the ohmic heating methods with the different electrical field conditions (the frequency and the voltage ranging from 50 to 10 kHz and from 160 to 220 V, respectively) were employed. The results showed that if the value of the urease activity measured with the quantitative spectrophotometry method was lower than 16.8 IU, the urease activity measured with the qualitative method was negative. The urease activity of the sample ohmically heated was significantly lower than that of the sample conventionally heated (P < 0.01) at the same target temperature. It was concluded that the electrical field enhanced the urease inactivation. In addition, the inactivation kinetics of the urease in the soymilk could be described with a biphasic model during holding time at a target temperature. Thus, it was concluded that the urease in the soymilk would contain 2 isoenzymes, one is the thermolabile fraction, the other the thermostable fraction, and that the thermostable isoenzyme could not be completely inactivated when the holding time increased, whether the soymilk was cooked with the conventional method or with the ohmic heating method. Therefore, the electric field had no effect on the inactivation of the thermostable isoenzyme of the urease.

Urease-induced calcification of segmented polymer hydrogels - a step towards artificial biomineralization

Natural organic/inorganic composites, such as nacre, bones and teeth, are perfectly designed materials with exceptional mechanical properties. Numerous approaches have been taken to synthetically prepare such composites. The presented work describes a new way of mineralizing bulk materials on a large scale following the approach of bioinduced mineralization. To this end, a series of polymer conetworks with entrapped urease were prepared. After polymerization, the entrapped urease shows high enzymatic activity. The bioactive polymer conetworks were then treated with an aqueous mixture of urea and CaCl2. The urease-induced calcification indeed allows formation of carbonate crystals exclusively within the hydrogel even at room temperature. The influence of network composition, degree of cross-linking, immobilized urease concentration and temperature of calcification were investigated. By varying these parameters, spherical, monolithic clusters, as well as bar-like nanocrystals with different aspect ratios in spherical or dendritic arrays, are formed. The grown nanocrystals improve the stiffness of the starting material by up to 700-fold, provided that the microstructure shows a dense construction without pores and strong interaction between crystals and network. The process has the potential to generate a new class of hybrid materials that would be available on the macroscopic scale for use in lightweight design and medicine.

Selective enrichment and production of highly urease active bacteria by non-sterile (open) chemostat culture

In general, bioprocesses can be subdivided into naturally occurring processes, not requiring sterility (e.g., beer brewing, wine making, lactic acid fermentation, or biogas digestion) and other processes (e.g., the production of enzymes and antibiotics) that typically require a high level of sterility to avoid contaminant microbes overgrowing the production strain. The current paper describes the sustainable, non-sterile production of an industrial enzyme using activated sludge as inoculum. By using selective conditions (high pH, high ammonia concentration, and presence of urea) for the target bacterium, highly active ureolytic bacteria, physiologically resembling Sporosarcina pasteurii were reproducibly enriched and then continuously produced via chemostat operation of the bioreactor. When using a pH of 10 and about 0.2 M urea in a yeast extract-based medium, ureolytic bacteria developed under aerobic chemostat operation at hydraulic retention times of about 10 h with urease levels of about 60 μmol min−1 ml−1 culture. For cost minimization at an industrial scale the costly protein-rich yeast extract medium could be replaced by commercial milk powder or by lysed activated sludge. Glutamate, molasses, or glucose-based media did not result in the enrichment of ureolytic bacteria by the chemostat. The concentration of intracellular urease was sufficiently high such that the produced raw effluent from the reactor could be used directly for biocementation in the field.

Acetohydroxamate Inhibition of the Activity of Urease from Dehusked Seeds of Water Melon(Citrullus vulgaris)

Urease from the seeds of watermelon (Citrullus vulgaris) was purified to apparent homogeneity, using two acetone fractionation steps, heat treatment at 48 degrees C and gel filtration through Sephadex G-200. Effect of acetohydroxamic acid (AHA) on the activity of the homogeneous enzyme preparation (sp. act. 3000 +/- 550U/mg protein) was investigated. AHA exhibited a concentration-dependent inhibition both in the presence and absence of the substrate. The inhibition was uncompetitive and the Ki was 2.5 mM. Binding of AHA with the enzyme was reversible, as 63% activity could be restored by dialysis. Time-dependent inhibition revealed a monophasic inhibition of the activity. Addition of beta-mercaptoethanol (ME) gradually abolished the inhibition. Pre-treatment of native enzyme with 8.0 mM ME for 5 min at 30 degrees C exhibited protection against AHA-induced inhibition. The significance of these observations is discussed.

Essential roles and hazardous effects of nickel in plants

With the world's ever increasing human population, the issues related to environmental degradation of toxicant chemicals are becoming more serious. Humans have accelerated the emission to the environment of many organic and inorganic pollutants such as pesticides, salts, petroleum products, acids, heavy metals, etc. Among different environmental heavy-metal pollutants, Ni has gained considerable attention in recent years, because of its rapidly increasing concentrations in soil, air, and water in different parts of the world. The main mechanisms by which Ni is taken up by plants are passive diffusion and active transport. Soluble Ni compounds are preferably absorbed by plants passively, through a cation transport system; chelated Ni compounds are taken up through secondary, active-transport-mediated means, using transport proteins such as permeases. Insoluble Ni compounds primarily enter plant root cells through endocytosis. Once absorbed by roots, Ni is easily transported to shoots via the xylem through the transpiration stream and can accumulate in neonatal parts such as buds, fruits, and seeds. The Ni transport and retranslocation processes are strongly regulated by metal-ligand complexes (such as nicotianamine, histidine, and organic acids) and by some proteins that specifically bind and transport Ni. Nickel, in low concentrations, fulfills a variety of essential roles in plants, bacteria, and fungi. Therefore, Ni deficiency produces an array of effects on growth and metabolism of plants, including reduced growth, and induction of senescence, leaf and meristem chlorosis, alterations in N metabolism, and reduced Fe uptake. In addition, Ni is a constituent of several metallo-enzymes such as urease, superoxide dismutase, NiFe hydrogenases, methyl coenzyme M reductase, carbon monoxide dehydrogenase, acetyl coenzyme-A synthase, hydrogenases, and RNase-A. Therefore, Ni deficiencies in plants reduce urease activity, disturb N assimilation, and reduce scavenging of superoxide free radical. In bacteria, Ni participates in several important metabolic reactions such as hydrogen metabolism, methane biogenesis, and acetogenesis. Although Ni is metabolically important in plants, it is toxic to most plant species when present at excessive amounts in soil and in nutrient solution. High Ni concentrations in growth media severely retards seed germinability of many crops. This effect of Ni is a direct one on the activities of amylases, proteases, and ribonucleases, thereby affecting the digestion and mobilization of food reserves in germinating seeds. At vegetative stages, high Ni concentrations retard shoot and root growth, affect branching development, deform various plant parts, produce abnormal flower shape, decrease biomass production, induce leaf spotting, disturb mitotic root tips, and produce Fe deficiency that leads to chlorosis and foliar necrosis. Additionally, excess Ni also affects nutrient absorption by roots, impairs plant metabolism, inhibits photosynthesis and transpiration, and causes ultrastructural modifications. Ultimately, all of these altered processes produce reduced yields of agricultural crops when such crops encounter excessive Ni exposures.

Identification of novel urease inhibitors by high-throughput virtual and in vitro screening

Ureases are important in both agriculture and human health. Bacterial ureases are directly involved in many farm-field problems and pathological conditions. Here, we report a structure-based virtual screening of an in-house compound bank of about 6000 molecular entities by computational docking and binding free energy calculations followed by in vitro screening. Applied protocol leads to the identification of novel urease inhibitors, which can serve as starting points for structural optimization.

Inactivation of jack bean urease by N-ethylmaleimide: pH dependence, reversibility and thiols influence

N-Ethylmaleimide (NEM) was studied as an inactivator of jack bean urease at 25 degrees C in 20 mM phosphate buffer, pHs 6.4, 7.4, and 8.3. The inactivation was investigated by incubation procedure in the absence of a substrate. It was found that NEM acted as a time and concentration dependent inactivator of urease. The dependence of urease residual activity on the incubation time showed that the activity decreased with time until the total loss of enzyme activity. The process followed a pseudo-first-order reaction. A monophasic loss of enzyme activity was observed at pH 7.4 and 8.4, while a biphasic reaction occurred at pH 6.4. Moreover, the alkaline pH promoted the inactivation. The presence of thiol-compounds, such as L-cysteine, glutathione or dithiothreitol (DTT), in the incubation mixture significantly slowed down the rate of inactivation. The interaction test showed that the decrease of inactivation was an effect of NEM-thiol interaction that lowered NEM concentration in the incubation mixture. The reactivation of NEM-blocked urease by DTT application and multidilution did not result in an effective activity regain. The applied DTT reacted with the remaining inactivator and could stop the progress of enzyme activity loss but did not cause the reactivation. This confirmed the irreversibility of inactivation. Similar results obtained at pH 6.4, 7.4 and 8.4 indicated that the mechanism of urease inactivation by NEM was pH-independent. However, the pH value significantly influenced the process rate.

Inactivation of Jack Bean Urease by Allicin

Allicin--diallyl thiosulfinate--is the main biologically active component of freshly crushed garlic. Allicin was synthesized as described elsewhere and was tested for its inhibitory ability against jack bean urease in 20 mM phosphate buffer, pH 7.0 at 22 degrees C. The results indicate that allicin is an enzymatic inactivator. The loss of urease activity was irreversible, time- and concentration dependent and the kinetics of the inactivation was biphasic; each phase, obeyed pseudo-first-order kinetics. The rate constants for inactivation were measured for the fast and slow phases and for several concentrations of allicin. Thiol reagents, and competitive inhibitor (boric acid) protected the enzyme from loss of enzymatic activity. The studies demonstrate that urease inactivation results from the reaction between allicin and the SH-group, situated in the urease active site (Cys592).

Structural characteristics of phosphoramide derivatives as urease inhibitors. Requirements for activity

Taking as a reference the structural characteristics of a set of compounds that act as jack bean ( Canavalia ensiformis) urease inhibitors, namely, phenylphosphorodiamidate (PPD), N- n-butylthiophosphorictriamide (NBPT), and N- n-butylphosphorictriamide (NBPTO), we have studied the structure-activity relationships of a series of phosphoramide derivatives for which the activity as urease inhibitors in both in vitro and in vivo assays is known. Molecular modeling studies were carried out, and the results highlighted the relevance of characteristics such as the presence of intramolecular hydrogen bonds, the volume of the fragment involved in the enzyme interaction, and the degree of conformational freedom as well as the HOMO orbital and atomic orbital contributions to the HOMO orbital, electron density, and PEM distributions on the activity of these compounds as urease inhibitors. These data, along with the preliminary docking study carried out, allow us to propose a union mode to the active site of the enzyme for these compounds.