Studies of interactions of carbonic anhydrase B with water and urea: II. Spin diffusion of associates of protein intermediate state at 4.2 M of urea

The formation of carbonic anhydrase B associates (pH 5.7, urea concentration 4.2 M, 297 K) was studied as a function of protein concentration and time by nuclear magnetic resonance spectroscopy (spin diffusion method). It was found that the association process proceeds in two steps. The first step is relatively fast and cannot be controlled by our methods. During this step, persistent units are built. These consist of protein molecules that are able to interact with solvent molecules and with each other when protein solution contains 4.2 M of urea. Persistent units are relatively small (two, three protein molecules), and their mobility matches one of a single protein. The second step is slower, and throughout this step large structures are formed from persistent units. The parameters G* and S*, which characterize spin diffusion in a protein and a solvent, respectively (when spin diffusion excitation happens away from NMR spectral signals) are related to the probable size distribution of protein-solvent associates and are determined by their collective properties.     

Carbonic Anhydrase B Interactions with Water and Urea

High-resolution NMR spectroscopy has been used to study native carbonic anhydrase B unfolding with urea at pH 5.75 and T = 298 K. The rigidity parameter reflecting the effectiveness of spin diffusion (SD) displays a sigma-like dependence on urea concentration, which is characteristic of denaturing processes. The ratio between the integral intensities of urea and protein signals measured in SD spectra and normal 1D spectra are the same. This suggests the absence of a predominant interaction between urea and protein molecules. The concentration of large protein-solvent complexes rapidly increases at urea concentrations of 4.2–6.2 M, which is apparently related to the transition of the protein into the molten globule state. If the urea concentration is increased to 6.6 M, these complexes dissociate, and the polypeptide chain of carbonic anhydrase B becomes completely unfolded.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 497–503.Original Russian Text Copyright © 2005 by Prokhorov, Kutyshenko, Khristoforov.     

Dynamics of oligomer formation by denatured carbonic anhydrase II

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. Many proteins unrelated to amyloidoses also fibrillate at the appropriate conditions. These proteins serve as a model for studying the processes of protein misfolding, oligomerization and fibril formation. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation. The urea-induced unfolding of bovine carbonic anhydrase II, BCA II, is characterized by a combination of high-resolution NMR, circular dichroism spectroscopy and small angle X-ray scattering. It is shown that the formation of associates of protein molecules in complex with solvent (water and urea), APS, takes place in the presence of 4-6 M urea. The subsequent increase in urea concentration to 8 M is accompanied by a disruption of APS and leads to a complete unfolding of a protein molecule. Analysis of BCA II self-association in the presence of 4.2 M urea revealed that APS are relatively large mostly beta-structural blocks with the averaged molecular mass of 190-220 kDa. This work also demonstrates some novel NMR-based methodological approaches that provide useful information on protein self-association.     

Carbonic anhydrase B interactions with water and urea

Carbonic anhydrase B unfolding with urea (pH 5.7, T = 298 K) was studied by high-resolution NMR spectroscopy. The effectiveness of spin-diffusion influencing compactness of the protein molecule can be described with the rigidity parameter G. Parameter G displays sigma-like characteristic behavior when concentration increases. The ratio between integral intensities of urea and protein signals in spin-diffusion and normal 1D spectra are the same. This suggests that there is no predominant urea-protein molecular interaction. The concentration of large protein-solvent associates increases rapidly at urea levels of 4.2-6.2 M implying that protein molecule shifts to a molten globule state. Protein-solvent associates are dissipating with urea concentration increase to above 6.6 M when carbonic anhydrase B polypeptide chain is completely unfolded.     

Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, ¹⁵N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested.     

Optimization and quality assessment of the post-digestion O labeling based on urea for protein denaturation by HPLC/ESI-TOF mass spectrometry

The post-digestion ¹⁸O labeling method decouples protein digestion and peptide labeling. This method allows labeling conditions to be optimized separately and increases labeling efficiency. A common method for protein denaturation in proteomics is the use of urea. Though some previous studies have used urea-based protein denaturation before post-digestion ¹⁸O labeling, the optimal ¹⁸O labeling conditions in this case have not been yet reported. Present study investigated the effects of urea concentration and pH on the labeling efficiency and obtained an optimized protocol. It was demonstrated that urea inhibited ¹⁸O incorporation depending on concentration. However, a urea concentration between 1 and 2 M had minimal effects on labeling. It was also demonstrated that the use of FA to quench the digestion reaction severely affected the labeling efficiency. This study revealed the reason why previous studies gave different optimal pH for labeling. They neglect the effects of different digestion conditions on the labeling conditions. Excellent labeling quality was obtained at the optimized conditions using urea 1–2 M and pH 4.5, 98.4 ± 1.9% for a standard protein mixture and 97.2 ± 6.2% for a complex biological sample. For a 1:1 mixture analysis of the ¹⁶O- and ¹⁸O-labeled peptides from the same protein sample, the average abundance ratios reached 1.05 ± 0.31, demonstrating a good quantitation quality at the optimized conditions. This work will benefit other researchers who pair urea-based protein denaturation with a post-digestion ¹⁸O labeling method.     

Effects of low urea concentrations on protein-water interactions

Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran–PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of the phases in the ATPSs were quantified by analysis of partitioning of the homologous series of sodium salts of dinitrophenylated amino acids with aliphatic alkyl side chains. Furthermore, partitioning of eleven different proteins in the ATPSs was studied. The analysis of protein partition behavior in a set of ATPSs with protective osmolytes (sorbitol, sucrose, trehalose, and TMAO) at the concentration of .5 M, in osmolyte-free ATPS, and in ATPSs with .5 or 2.0 M urea in terms of the solvent properties of the phases was performed. The results show unambiguously that even at the urea concentration of .5 M, this denaturant affects partitioning of all proteins (except concanavalin A) through direct urea–protein interactions and via its effect on the solvent properties of the media. The direct urea–protein interactions seem to prevail over the urea effects on the solvent properties of water at the concentration of .5 M urea and appear to be completely dominant at 2.0 M urea concentration.     

Absorption of molecular urea by rice under flooded and non-flooded soil conditions

A pot experiment was conducted with rice to study the relative absorption of urea in molecular form compared to the other forms of N produced in soil from the applied urea. A method involving application of ¹⁴C-labelled urea and ¹⁵N-labelled urea alternately in two splits was used to quantify the absorption of molecular urea and other forms of N formed from it. Biomass production and N uptake were greater in plants grown under flooded soil conditions than in plants grown under non-flooded (upland) conditions. Absorption of N by rice increased with increasing rate of urea application up to 250 mg pot⁻¹ and declined thereafter. The absorption of urea from the flooded soil constituted 9.4% of total N uptake from applied N compared to only 0.2% from the non-flooded. Under submerged conditions, absorption of urea from topdressing was about twice that from basal application at planting. High water solubility of the fertilizer and better developed rice root system might have enhanced the absorption of molecular urea by flooded rice, especially from topdressing. Thus, in the flooded rice system, the direct absorption of molecular urea from topdressing accounted for 6.3% of the total N uptake from added urea. Under upland condition, it was 0.12%. This revised version was published online in June 2006 with corrections to the Cover Date.     

Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea

Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. HspA has been shown to be important for the protection of Photosystem II and the Phycobilisome antenna complex at elevated temperatures. Heterologously expressed HspA requires the presence of 1–2 M urea to maintain its solubility at concentrations required for most characterization methods. Spectroscopic studies reveal the presence of the β-sheet structure and intactness of the tertiary fold in HspA. In vitro assays show that the HspA maintains chaperone-like activity in protecting soluble proteins from thermal aggregation. Chromatography and electron microscopy show that the HspA exists as a mixture of oligomeric forms in the presence of 2 M urea. HspA was successfully crystallized only in the presence of 2 M urea. The crystal structure of HspA shows urea-induced loss of about 30% of the secondary structure without major alteration in the tertiary structure of the protein. The electron density maps reveal changes in the hydrogen bonding network which we attribute to the presence of urea. The crystal structure of HspA demonstrates a mixture of both direct interactions between urea and protein functionalities and interactions between urea and the surrounding solvent that indirectly affect the protein, which are in accordance with previously published studies.     

Evidence for carrier-mediated,energy-dependent uptake of urea in some bacteria

Evidence for the existence of an energy-dependent urea permease was found for Alcaligenes eutrophus H16 and Klebsiella pneumoniae M5a1 by studying uptake of ¹⁴C-urea. Since intracellular urea was metabolized immediately, uptake did not result in formation of an urea pool. Evidence is based on observations that the in vivo urea uptake and in vitro urease activity differ significantly with respect to kinetic parameters, temperature optimum, pH optimum, response towards inhibitors and regulation. The K _m for urea uptake was 15–20 times lower (38 M and 13 M urea for A. eutrophus and K. pneumoniae, respectively) than the K _m of urease for urea (650 M and 280 M urea), the activity optimum for A. eutrophus was at pH 6.0 and 35°C for the uptake and pH 9.0 and 65°C for urease. Uptake but not urease activity in both organisms strongly decreased upon addition of inhibitors of energy metabolism, while in K. pneumoniae, potent inhibitors of urease (thiourea and hydroxyurea) did not affect the uptake process. Significant differences in the uptake rates were observed during growth with different nitrogen sources (ammonia, nitrate, urea) or in the absence of a nitrogen source; this suggested that a carrier is involved which is subject to nitrogen control. Some evidence for the presence of an energy-dependent uptake of urea was also obtained in Pseudomonas aeruginosa DSM 50071 and Providencia rettgeri DSM 1131, but not in Proteus vulgaris DSM 30118 and Bacillus pasteurii DSM 33.Non-standard abbreviations CCCP Carbonylcyanide-m-chlorphenylhydrazone - DCCD dicyclohexylcarbodiimide - DNP 2,4-dinitrophenole     

Studies of slow conformational equilibria in macromolecules by exchange of heteronuclear longitudinal 2-spin-order in a 2D difference correlation experiment

Summary Observation of the exchange of heteronuclear longitudinal 2-spin-order in a 2D difference correlation experiment enables studies of slow dynamic processes in biological macromolecules with minimal interference from background signals. The experiment is used to establish relations between corresponding¹⁵N–¹H groups in the native globular form and an unfolded form of the protein 434 repressor (1–69) present in aqueous solution containing 4.2 M urea.     

Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains

Chemical denaturants are frequently used to unfold proteins and to characterize mechanisms and transition states of protein folding reactions. The molecular basis of the effect of urea and guanidinium chloride (GdmCl) on polypeptide chains is still not well understood. Models for denaturant--protein interaction include both direct binding and indirect changes in solvent properties. Here we report studies on the effect of urea and GdmCl on the rate constants (k(c)) of end-to-end diffusion in unstructured poly(glycine-serine) chains of different length. Urea and GdmCl both lead to a linear decrease of lnk(c) with denaturant concentration, as observed for the rate constants for protein folding. This suggests that the effect of denaturants on chain dynamics significantly contributes to the denaturant-dependence of folding rate constants for small proteins. We show that this linear dependency is the result of two additive non-linear effects, namely increased solvent viscosity and denaturant binding. The contribution from denaturant binding can be quantitatively described by Schellman's weak binding model with binding constants (K) of 0.62(+/-0.01)M(-1) for GdmCl and 0.26(+/-0.01)M(-1) for urea. In our model peptides the number of binding sites and the effect of a bound denaturant molecule on chain dynamics is identical for urea and GdmCl. The results further identify the polypeptide backbone as the major denaturant binding site and give an upper limit of a few nanoseconds for residence times of denaturant molecules on the polypeptide chain.     

Capillary isoelectric focusing of a difficult-to-denature tetrameric enzyme using alkylurea–urea mixtures

Capillary isoelectric focusing (cIEF) is normally run under denaturing conditions using urea to expose any buried protein residues that may contribute to the overall charge. However, urea does not completely denature some proteins, such as the tetrameric enzyme Erwinia chrysanthemil-asparaginase (ErA), in which case electrophoresis-compatible alternative denaturants are required. Here, we show that alkylureas such as N-ethylurea provide increased denaturation during cIEF. The cIEF analysis of ErA in 8 M urea alone resulted in a cluster of ill-resolved peaks with isoelectric points (pI values) in the range 7.4 to 8.5. A combination of 2.0 to 2.2 M N-ethylurea and 8 M urea provided sufficient denaturation of ErA, resulting in a main peak with a pI of 7.35 and an acidic species minor peak at 7.0, both comparing well with predicted pI values based on the sum of protein residue pK_a values. Recombinant deamidated ErA mutants were also demonstrated to migrate to pI values consistent with predictions (pI 7.0 for one deamidation). The quantitation of ErA acidic species in samples from full-scale manufacturing (1.0–3.5% of total peak area) was found to be reproducible and linear. Use of alkylureas as denaturing agents in capillary electrophoresis and cIEF should be considered during biopharmaceutical assay development.     

Nitrogen-15 balances for urea and neem coated urea applied to lowland rice following two cowpea cropping systems

Little is known about whether the high N losses from inorganic N fertilizers applied to lowland rice (Oryza sativa L.) are affected by the combined use of either legume green manure or residue with N fertilizers. Field experiments were conducted in 1986 and 1987 on an Andaqueptic Haplaquoll in the Philippines to determine the effect of cowpea [Vigna unguiculata (L.) Walp.] cropping systems before rice on the fate and use efficiency of¹⁵N-labeled, urea and neem cake (Azadirachta indica Juss.) coated urea (NCU) applied to the subsequent transplanted lowland rice crop. The pre-rice cropping systems were fallow, cowpea incorporated at the flowering stage as a green manure, and cowpea grown to maturity with subsequent incorporation of residue remaining after grain and pod removal. The incorporated green manure contained 70 and 67 kg N ha⁻¹ in 1986 and 1987, respectively. The incorporated residue contained 54 and 49 kg N ha⁻¹ in 1986 and 1987, respectively. The unrecovered¹⁵N in the¹⁵N balances for 58 kg N ha⁻¹ applied as urea or NCU ranged from 23 to 34% but was not affected by pre-rice cropping system. The partial pressure of ammoniapNH₃, and floodwater (nitrate + nitrite)-N following application of 29 kg N ha⁻¹ as urea or NCU to 0.05-m-deep floodwater at 14 days after transplanting was not affected by pre-rice cropping system. In plots not fertilized with urea or NCU, green manure contributed an extra 12 and 26 kg N ha⁻¹, to mature rice plants in 1986 and 1987, respectively. The corresponding contributions from residue were 19 and 23 kg N ha⁻¹, respectively. Coating urea with 0.2g neem cake per g urea had no effect on loss of urea-N in either year; however, it significantly increased grain yield (0.4 Mg ha⁻¹) and total plant N (11 kg ha⁻¹) in 1987 but not in 1986.     

Reversibility of nucleosome conformation perturbed by urea

Monomer nucleosomes (ν₁) from chicken erythrocyte nuclei were diluted into 9 M urea plus 0.2 mM EDTA (pH 7.0), and urea was removed by dialysis. The ν₁ thus obtained were fractionated by sucrose gradient ultracentrifugation. Each fraction was examined in 0.2 mM EDTA for reversibility of ν₁ structure perturbed by urea. At least 30% of the initial amount of ν₁ exposed to urea was restored to the original structure, as shown by sedimentation velocity, electron microscopy, circular dichroism, thermal melting, and fluorescence of ν₁ labeled with $\text{N}$-(3-pyrene) maleimide on thiol groups of H3 histone.     

Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue

Molecular dynamics simulations of the S-peptide analogue AETAAAKFLREHMDS in water at 278 and 358 K, and in 8 M urea at 278 K were performed. The results show agreement with experiments. The helix is stable at low temperature (278 K), while at 358 K, unfolding is observed. The effects of urea on protein stability have been studied. The data support a model in which urea denatures proteins by: (1) diminishing the hydrophobic effect by displacing water molecules from the solvent shell around nonpolar groups; and (2) binding directly to amide units (NH and CO groups) via hydrogen bonds. The results of cluster analysis and essential dynamics analysis suggest that the mechanism of urea and thermal-induced denaturation may not be the same.     

Effect of physiological concentration of urea on the conformation of human serum albumin

We report that the presence of very low concentrations (<0.1 M) of urea, a widely used chemical denaturant, induces structure formation in the water-soluble globular protein human serum albumin (HSA) at pH 7. We have presented results suggesting an almost 8% and 5% increase in alpha-helix in the presence of 10 mM urea (U) and 20 mM monomethylurea (MMU), respectively. Far and near-UV circular dichroism studies along with tryptophan fluorescence and 1-anilino-8-naphthalenesulphonicacid (ANS) binding support our view. We hypothesize that both U and MMU, at such low concentrations, modify the solvent structure, increase the dielectric constant and consequently increase hydrophobic forces resulting in enhanced alpha-helical content. The implications of these results of the lower urea regime are significant because the physiological blood urea ranges from 2.5 to 7.5 mM.     

Cytokinin activity of N-phenyl-N′-(4-pyridyl)urea derivatives

We have synthesized 35 N-phenyl-N′-(4-pyridyl)urea derivatives and tested their cytokinin activity in the tobacco callus bioassay. Among them, N-phenyl-N′- (2-chloro-4-pyridyl)urea is highly active, the optimum concentration of which is lower than 4 × 10^?9 M (0.001 ppm), 3 compounds, i.e. N-(2-methylphenyl)-N′-(2-chloro-4-pyridyl)urea, N-(3-methylphenyl)-N′-(2-chloro-4-pyridyl)urea and N-(3-chlorophenyl)-N′-(2-chloro-4-pyridyl) urea are as active as N⁶-benzyladenine (concentration for optimum yield: 4.4 × 10^?8 M or 0.01 ppm), and N-phenyl-N′-(2-methyl-4-pyridyl)urea and N-(2-chlorophenyl)-N′-(2-chloro-4-pyridyl)urea are as active as N-phenyl-N′-(4-pyridyl)urea (concentration for optimum yield: 4.7 × 10^?7 M or 0.1 ppm), while the activity of the other 29 compounds are not so remarkable and 11 of them are almost or completely inactive.     

Effects of urea and guanidine hydrochloride on the sliding movement of actin filaments with ATP hydrolysis by myosin molecules

To evaluate the role of the hydration layer on the protein surface of actomyosin, we compared the effects of urea and guanidine-HCl on the sliding velocities and ATPase activities of the actin-heavy meromyosin (HMM) system. Both chemicals denature proteins, but only urea perturbs the hydration layer. Both the sliding velocity of actin filaments and actin-activated ATPase activity decreased with increasing urea concentrations. The sliding movement was completely inhibited at 1.0 M urea, while actin filaments were bound to HMM molecules fixed on the glass surface. Guanidine-HCl (0-0.05 M) drastically decreased both the sliding velocity and ATPase activation of acto-HMM complexes. Under this condition, actin filaments almost detached from HMM molecules. In contrast, the ATPase activity of HMM without actin filaments was almost independent of urea concentrations <1.0 M and guanidine-HCl concentrations <0.05 M. An increase in urea concentrations up to 2.0 M partly induced changes in the ternary structure of HMM molecules, while the actin filaments were stable in this concentration range. Hydration changes around such actomyosin complexes may alter both the stability of part of the myosin molecules, and the affinity for force transmission between actin filaments and myosin heads.     

A kinetic study of beta-lactoglobulin amyloid fibril formation promoted by urea

The formation of fibrillar aggregates by beta-lactoglobulin in the presence of urea has been monitored by using thioflavin T fluorescence and transmission electron microscopy (TEM). Large quantities of aggregated protein were formed by incubating beta-lactoglobulin in 3-5 M urea at 37 degrees C and pH 7.0 for 10-30 days. The TEM images of the aggregates in 3-5 M urea show the presence of fibrils with diameters of 8-10 nm, and increases in thioflavin T fluorescence are indicative of the formation of amyloid structures. The kinetics of spontaneous fibrillogenesis detected by thioflavin T fluorescence show sigmoidal behavior involving a clear lag phase. Moreover, addition of preformed fibrils into protein solutions containing urea shows that fibril formation can be accelerated by seeding processes that remove the lag phase. Both of these findings are indicative of nucleation-dependent fibril formation. The urea concentration where fibril formation is most rapid, both for seeded and unseeded solutions, is approximately 5.0 M, close to the concentration of urea corresponding to the midpoint of unfolding (5.3 M). This result indicates that efficient fibril formation involves a balance between the requirement of a significant population of unfolded or partially unfolded molecules and the need to avoid conditions that strongly destabilize intermolecular interactions.