Showing papers on "Urea published in 2007"

Interactions between Hydrophobic and Ionic Solutes in Aqueous Guanidinium Chloride and Urea Solutions: Lessons for Protein Denaturation Mechanism

Abstract: In order to clarify the mechanism of denaturant-induced unfolding of proteins we have calculated the interactions between hydrophobic and ionic species in aqueous guanidinium chloride and urea solutions using molecular dynamics simulations. Hydrophobic association is not significantly changed in urea or guanidinium chloride solutions. The strength of interaction between ion pairs is greatly diminished by the guanidinium ion. Although the changes in electrostatic interactions in urea are small, examination of structures, using appropriate pair functions, of urea and water around the solutes show strong hydrogen bonding between urea's carbonyl oxygen and the positively charged solute. Our results strongly suggest protein denaturation occurs by the direct interaction model according to which the most commonly used denaturants unfold proteins by altering electrostatic interactions either by solvating the charged residues or by engaging in hydrogen bonds with the protein backbone. To further validate the direct interaction model we show that, in urea and guanidinium chloride solutions, unfolding of an unusually stable helix (H1) from mouse PrPC (residues 144-153) occurs by hydrogen bonding of denaturants to charged side chains and backbone carbonyl groups.

Interaction of urea with amino acids: Implications for urea-induced protein denaturation

Abstract: The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.

Synthesis of High-Temperature Stable Anatase TiO2 Photocatalyst

Abstract: In the absence of a dopant or precursor modification, anatase to rutile transformation in synthetic TiO2 usually occurs at a temperature of 600−700 °C. Conventionally, metal oxide dopants (e.g., Al2O3 and SiO2) are used to tune the anatase to rutile transformation. A simple methodology is reported here to extend the anatase rutile transformation by employing various concentrations of urea. XRD and Raman spectroscopy were used to characterize various phases formed during thermal treatment. A significantly higher anatase phase (97%) has been obtained at 800 °C with use of a 1:1 Ti(OPr)4:urea composition and 11% anatase composition is retained even after calcining the powder at 900 °C. By comparison a sample that has been prepared without urea showed that rutile phases started to form at a temperature as low as 600 °C. The effect of smaller amounts of urea such as 1:0.25 and 1:0.5 Ti(OPr)4:urea has also been studied and compared. The investigation concluded that the stoichiometric modification by urea 1:1 Ti...

Anatomy of energetic changes accompanying urea-induced protein denaturation

Abstract: Because of its protein-denaturing ability, urea has played a pivotal role in the experimental and conceptual understanding of protein folding and unfolding. The measure of urea's ability to force a protein to unfold is given by the m value, an experimental quantity giving the free energy change for unfolding per molar urea. With the aid of Tanford's transfer model [Tanford C (1964) J Am Chem Soc 86:2050-2059], we use newly obtained group transfer free energies (GTFEs) of protein side-chain and backbone units from water to 1 M urea to account for the m value of urea, and the method reveals the anatomy of protein denaturation in terms of residue-level free energy contributions of groups newly exposed on denaturation. The GTFEs were obtained by accounting for solubility and activity coefficient ratios accompanying the transfer of glycine from water to 1 M urea. Contrary to the opinions of some researchers, the GTFEs show that urea does not denature proteins through favorable interactions with nonpolar side chains; what drives urea-induced protein unfolding is the large favorable interaction of urea with the peptide backbone. Although the m value is said to be proportional to surface area newly exposed on denaturation, only approximately 25% of the area favorably contributes to unfolding (because of newly exposed backbone units), with approximately 75% modestly opposing urea-induced denaturation (originating from side-chain exposure). Use of the transfer model and newly determined GTFEs achieves the long-sought goal of predicting urea-dependent cooperative protein unfolding energetics at the level of individual amino acid residues.

Aqueous Urea Solutions: Structure, Energetics, and Urea Aggregation

Abstract: Urea is ubiquitously used as a protein denaturant. To study the structure and energetics of aqueous urea solutions, we have carried out molecular dynamics simulations for a wide range of urea concentrations and temperatures. The hydrogen bonds between urea and water were found to be significantly weaker than those between water molecules, which drives urea self-aggregation due to the hydrophobic effect. From the reduction of the water exposed urea surface area, urea was found to exhibit an aggregation degree of ca. 20% at concentrations commonly used for protein denaturation. Structurally, three distinct urea pair conformations were identified and their populations were analyzed by translational and orientational pair distribution functions. Furthermore, urea was found to strengthen water structure in terms of hydrogen bond energies and population of solvation shells. Our findings are consistent with a direct interaction between urea and the protein as the main driving force for protein denaturation. As an additional, more indirect effect, urea was found to enhance water structure, which would suggest a weakening of the hydrophobic effect.

Ammonia volatilisation from urease inhibitor-treated urea applied to sugarcane trash blankets.

Abstract: Legal restrictions from burning sugarcane prior to harvest are causing a sharp increase in acreage which is harvested as green cane. The presence of a thick sugarcane trash mulch left after harvest makes it difficult to incorporate fertilisers in the soil. Since large losses of ammonia may occur when urea is surface applied to trash, it is important to find ways to improve urea-N use efficiency. The urease inhibitor NBPT slows down urea hydrolysis and thus may help decrease ammonia losses. Ammonia traps were set up in seven sugarcane fields covered with trash and fertilised with ammonium sulfate or ammonium nitrate, urea, and NBPT-treated urea. All N fertilisers were surface-applied at rates of 80 or 100 kg N ha-1. Very little N was lost when ammonium nitrate or ammonium sulfate were used. However, volatilisation losses as ammonia from the urea treatments varied from 1% (rainy days after fertilisation) to 25% of the applied N. The percentage of reduction in volatilisation due to NBPT application ranged from 15% to 78% depending on the weather conditions during the days following application of N. Addition of NBPT to urea helped to control ammonia losses, but the inhibitor was less effective when rain sufficient to incorporate urea into the soil occurred only 10 to 15 days or latter after fertiliser application.

Hydrogen‐Bond‐Induced Inclusion Complex in Aqueous Cellulose/LiOH/Urea Solution at Low Temperature

Abstract: It was puzzling that cellulose could be dissolved rapidly in 4.6 wt % LiOH/15 wt % urea aqueous solution precooled to -12 degrees C, whereas it could not be dissolved in the same solvent without prior cooling. To clarify this important phenomenon, the structure and physical properties of LiOH and urea in water as well as of cellulose in the aqueous LiOH/urea solution at different temperatures were investigated by means of laser light scattering, 13C NMR spectroscopy, differential scanning calorimetry, Fourier transform infrared spectroscopy, wide-angle X-ray diffraction, and transmission electron microscopy (TEM). The results reveal that a hydrogen-bonded network structure between LiOH, urea, and water can occur, and that it becomes more stable with decreasing temperature. The LiOH hydrates cleave the chain packing of cellulose through the formation of new hydrogen bonds at low temperatures, which result in a relatively stable complex associated with LiOH, water clusters, and cellulose. A channel inclusion complex (IC) hosted by urea could encage the cellulose macromolecule in LiOH/urea solution with prior cooling and therefore provide a rationale for forming a good dispersion of cellulose. TEM observations, for the first time, showed the channel IC in dry form. The low-temperature step played an important role in shifting hydrogen bonds between cellulose and small molecules, leading to the dissolution of macromolecules in the aqueous solution.

Metabolic effects of two low protein diets in chronic kidney disease stage 4–5—a randomized controlled trial

Abstract: BACKGROUND International guidelines have not reached a complete agreement about the optimal amount of dietary proteins in chronic kidney disease(CKD). The aim of this study was to compare, with a randomized-controlled design, the metabolic effects of two diets with different protein content (0.55 vs 0.80 g/kg/day) in patients with CKD stages 4-5. METHODS Study design and sample size calculations were based on previously published experience of our group with low protein diet. The primary outcome of the study was the modification of serum urea nitrogen concentration. From 423 patients randomly assigned to the two diets 392 were analysed: 200 for the 0.55-Group and 192 for the 0.8-Group. The follow-up ranged 6-18 months. RESULTS Mean age was 61+/-18 years, 44% were women, mean eGFR was 18+/-7 ml/min/month. Three months after the dietary assignment and throughout the study period the two groups had a significantly different protein intake (0.72 vs 0.92 g/kg/day). The intention-to-treat analysis did not show any difference between the two groups. Compliance to the two test diets was significantly different (P < 0.05): 27% in the 0.55-Group and 53% in the 0.8-Group, with male gender and protein content (0.8 g/kg/day) predicting adherence to the assigned diet. The per protocol analysis, conversely, showed that serum urea nitrogen, similar at the time of randomization, significantly increased in the 0.8-Group vs 0.55-Group by 15% (P < 0.05). Serum phosphate, PTH and bicarbonate resulted similar in the two groups throughout the study. The 24 h urinary urea nitrogen significantly decreased after the first 3 months in 0.55-Group (P < 0.05), as well as the excretion of creatinine, sodium and phosphate (P < 0.05 vs baseline) and were significantly lower than the 0.8-Group. The prescription of phosphate binders, allopurinol, bicarbonate supplements and diuretics resulted significantly less frequent in the 0.55-Group (P < 0.05). CONCLUSIONS This study represents the first evidence that in CKD patients a protein intake of 0.55 g/kg/day, compared with a 0.8 g/kg/day, guarantees a better metabolic control and a reduced need of drugs, without a substantial risk of malnutrition.

AtDUR3 represents the major transporter for high‐affinity urea transport across the plasma membrane of nitrogen‐deficient Arabidopsis roots

Abstract: Summary Despite the fact that urea is a ubiquitous nitrogen source in soils and the most widespread form of nitrogen fertilizer used in agricultural plant production, membrane transporters that might contribute to the uptake of urea in plant roots have so far been characterized only in heterologous systems. Two T-DNA insertion lines, atdur3-1 and atdur3-3, that showed impaired growth on urea as a sole nitrogen source were used to investigate a role of the H+/urea co-transporter AtDUR3 in nitrogen nutrition in Arabidopsis. In transgenic lines expressing AtDUR3-promoter:GFP constructs, promoter activity was upregulated under nitrogen deficiency and localized to the rhizodermis, including root hairs, as well as to the cortex in more basal root zones. Protein gel blot analysis of two-phase partitioned root membrane fractions and whole-mount immunolocalization in root hairs revealed the plasma membrane to be enriched in AtDUR3 protein. Expression of the AtDUR3 gene in nitrogen-deficient roots was repressed by ammonium and nitrate but induced after supply of urea. Higher accumulation of urea in roots of wild-type plants relative to atdur3-1 and atdur3-3 confirmed that urea was the substrate transported by AtDUR3. Influx of 15N-labeled urea in atdur3-1 and atdur3-3 showed a linear concentration dependency up to 200 μm external urea, whereas influx in wild-type roots followed saturation kinetics with an apparent Km of 4 μm. The results indicate that AtDUR3 is the major transporter for high-affinity urea uptake in Arabidopsis roots and suggest that the high substrate affinity of AtDUR3 reflects an adaptation to the low urea levels usually found in unfertilized soils.

Urea and Renal Function in the 21st Century: Insights from Knockout Mice

Abstract: Since the turn of the 21st century, gene knockout mice have been created for all major urea transporters that are expressed in the kidney: the collecting duct urea transporters UT-A1 and UT-A3, the descending thin limb isoform UT-A2, and the descending vasa recta isoform UT-B. This article discusses the new insights that the results from studies in these mice have produced in the understanding of the role of urea in the urinary concentrating mechanism and kidney function. Following is a summary of the major findings: (1) Urea accumulation in the inner medullary interstitium depends on rapid transport of urea from the inner medullary collecting duct (IMCD) lumen via UT-A1 and/or UT-A3; (2) as proposed by Robert Berliner and colleagues in the 1950s, the role of IMCD urea transporters in water conservation is to prevent a urea-induced osmotic diuresis; (3) the absence of IMCD urea transport does not prevent the concentration of NaCl in the inner medulla, contrary to what would be predicted from the passive countercurrent multiplier mechanism in the form proposed by Kokko and Rector and Stephenson; (4) deletion of UT-B (vasa recta isoform) has a much greater effect on urinary concentration than deletion of UT-A2 (descending limb isoform), suggesting that the recycling of urea between the vasa recta and the renal tubules quantitatively is less important than classic countercurrent exchange; and (5) urea reabsorption from the IMCD and the process of urea recycling are not important elements of the mechanism of protein-induced increases in GFR. In addition, the clinical relevance of these studies is discussed, and it is suggested that inhibitors that specifically target collecting duct urea transporters have the potential for clinical use as potassium-sparing diuretics that function by creation of urea-dependent osmotic diuresis.

Metabolic and immune responses in Chinese mitten-handed crab (Eriocheir sinensis) juveniles exposed to elevated ambient ammonia.

Abstract: The toxicity of ammonia to Eriocheir sinensis juveniles was determined. The 24 h-, 48 h-, 72 h-, 96 h-LC(50) values of total ammonia (TAN) were 251.68, 217.61, 156.05, and 119.67 mg L(-1), respectively. Following these results, crabs were then exposed for a 2-day period to 20, 40, 60 and 80 mg L(-1) TAN and sampled at 3, 6, 24 and 48 h for changes in metabolic parameters (including haemolymph ammonia concentration, glucose, lactate, urea, triacylglycerol, glutamine, and glutamate levels) and immunity indicators (the total of haemocyte count and superoxide dismutase activity). Results showed a distinct linear relationship between ambient ammonia and haemolymph ammonia and a notable increase in haemolymph ammonia content after ammonia exposure. Compared with the control group, lower concentration of triglycerides and significantly higher glucose, urea, and lactate level in haemolymph were observed when ambient ammonia increased. This suggested a reduced use of carbohydrates through anaerobic metabolism and an increase in the use of lipids to satisfy the metabolic demand. A significant surge of the ammonia metabolic product, glutamate, was observed after 3 h ammonia exposure, and the compensatory response to reduced glutamate was manifested by increased glutamine synthesis. During the same period, total haemocyte count decreased while ambient ammonia increased. Superoxide dismutase (SOD) activity in haemolymph was stimulated by lower ambient ammonia concentration after short time exposure and depressed by higher ammonia concentration. Therefore, haemolymph ammonia accumulation resulted in an increase in energy demand and a depression in immune capacity. The mechanism to detoxification of ammonia may be to transform ammonia to urea and glutamine.

Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies

Abstract: We performed molecular dynamics simulations of urea solutions at different concentrations with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodynamic solution properties. Our simulation results showed that hydrogen-bonding properties such as the average number of hydrogen bonds and their lifetime distributions were nearly constant at all concentrations between infinite dilution and the solubility limit. This implies that the characterization of urea−water solutions in the molarity concentration scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concentration does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. We found that the KBFF urea model in TIP3P water better reproduced the experimental density and diffusion constant data. Preferential solvation analysis showed that there were weak urea−urea an...

Liquid structure of the urea-water system studied by dielectric spectroscopy.

Abstract: Dielectric spectroscopy measurements for aqueous urea solutions were performed at 298 K through a concentration range from 0.5 to 9.0 M with frequencies between 200 MHz and 40 GHz. Observed dielectric spectra were well represented by the superposition of two Debye type relaxation processes attributable to the bulk-water clusters and the urea-water coclusters. Our quantitative analysis of the spectra shows that the number of hydration water molecules is approximately two per urea molecule for the lower concentration region below 5.0 M, while the previous molecular dynamics studies predicted approximately six water molecules. It was also indicated by those studies, however, that there are two types of hydration water molecule in urea solution, which are strongly and weakly associated to the urea molecule, respectively. Only the strongly associated water was distinguishable in our analysis, while the weakly associated water exhibited the same dynamic feature as bulk water. This implies that urea retains the weakly associated water in the tetrahedral structure and, thus, is not a strong structure breaker of water. We also verified the model of liquid water where water consists of two states: the icelike-ordered and dense-disordered phases. Our dielectric data did not agree with the theoretical prediction based on the two-phase model. The present work supports the argument that urea molecules can easily replace near-neighbor water in the hydrogen-bonding network and do not require the presence of the disordered phase of water to dissolve into water.

Urea orientation at protein surfaces.

Abstract: We have exploited the unique ability of vibrational sum frequency spectroscopy (VSFS) to investigate interfacial urea molecules at protein surfaces. Experiments were carried out at the bovine serum albumin/water interface. The absolute orientation of interfacial urea could be followed directly by VSFS. It was found that urea orients with its NH groups pointing toward the protein at high pH, where the protein is negatively charged. The orientation flips at low pH, where the protein is positively charged. This behavior resembles that of interfacial water. The direct interactions between urea and proteins should be electrostatic in nature and, therefore, very sensitive to the charge state of the protein. Urea denaturation of proteins, however, is not sensitive to charge, which is inconsistent with a direct interaction mechanism.

Synthesis, in vitro degradation, and mechanical properties of two-component poly(ester urethane)urea scaffolds: effects of water and polyol composition.

Abstract: The development of minimally invasive therapeutics for orthopedic clinical conditions has substantial benefits, especially for osteoporotic fragility fractures and vertebral compression fractures. Poly(ester urethane)urea (PEUUR) foams are potentially useful for addressing these conditions because they cure in situ upon injection to form porous scaffolds. In this study, the effects of water concentration and polyester triol composition on the physicochemical, mechanical, and biological properties of PEUUR foams were investigated. A liquid resin (lysine diisocyanate) and hardener (poly(epsilon-caprolactone-co-glycolide-co-DL-lactide) triol, tertiary amine catalyst, anionic stabilizer, and fatty acid-derived pore opener) were mixed, and the resulting reactive liquid mixture was injected into a mold to harden. By varying the water content over the range of 0.5 to 2.75 parts per hundred parts polyol, materials with porosities ranging from 89.1 to 95.8 vol-% were prepared. Cells permeated the PEUUR foams after 21 days post-seeding, implying that the pores are open and interconnected. In vitro, the materials yielded non-cytotoxic decomposition products, and differences in the half-life of the polyester triol component translated to differences in the PEUUR foam degradation rates. We anticipate that PEUUR foams will present compelling opportunities for the design of new tissue-engineered scaffolds and delivery systems because of their favorable biological and physical properties.

Ammonia Volatilization and Nitrogen Uptake for Conventional and Conservation Tilled Dry-Seeded, Delayed-Flood Rice

Abstract: In the southern U.S. dry-seeded, delayed-flood rice (Oryza sativa L.) culture system, there are two practices that can aggravate NH 3 volatilization losses of urea applied preflood: untimely application of the permanent flood and conservation tillage. The objectives of this study were to determine the influence of tillage practice, N source, and application time on NH 3 volatilization, N uptake, and grain yield of delayed flood rice grown on a clay and silt loam soil. Multisite field studies were conducted in 2000 and 2001 using both stale-seedbed and conventional tillage practices with urea and (NH 4 ) 2 SO 4 applied 14 d preflood and urea 1 d preflood at four N rates. Ammonia volatilization was measured and plant samples were collected for N uptake and grain yield. Ammonia volatilization was the highest (14-32%) and N uptake and grain yield of rice the lowest when urea was applied 14 d preflood. Ammonium sulfate applied 14 d preflood lost little N (1.5-7%) via NH 3 volatilization and resulted in N uptake and grain yields of rice similar to urea applied 1 d preflood. The stale seedbed had no effect on NH 3 volatilization of (NH 4 ) 2 SO 4 and only affected urea in 1 yr on the silt loam soil when weedy residue was greater and the two tillage systems still produced rice with similar N uptakes and grain yields. Ammonia volatilization was more rapid and greater when urea was applied to the silt loam than to the clay. Ammonia volatilization loss of urea was impacted the most from delaying the flood and not from conservation tillage.