Factors affecting counteraction by methylamines of urea effects on aldose reductase

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Protecting thermodynamic stability of protein: The basic paradigm against stress and unfolded protein response by osmolytes

Organic osmolytes are known to play important role in stress protection by stabilizing macromolecules and suppressing harmful effects on functional activity. There is existence of several reports in the literature regarding their effects on structural, functional and thermodynamic aspects of many enzymes and the interaction parameters with proteins have been explored. Osmolytes are compatible with enzyme function and therefore, can be accumulated up to several millimolar concentrations. From the thermodynamic point of view, osmolyte raises mid-point of thermal denaturation (T_m) of proteins while having no significant effect on ΔG_D° (free energy change at physiological condition). Unfavorable interaction with the peptide backbone due to preferential hydration is the major driving force for folding of unfolded polypeptide in presence of osmolyte. However, the thermodynamic basis of stress protection and origin of compatibility paradigm has been a debatable issue. In the present manuscript, we attempt to elaborate the origin of stress protection and compatibility paradigm of osmolytes based on the effect on thermodynamic stability of proteins. We also infer that protective effects of osmolytes on ΔG_D° (of proteins) could also indicate its potential involvement in unfolded protein response and overall stress biology on macromolecular level.

Changing relations between proteins and osmolytes: a choice of nature

The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.

A current perspective on the compensatory effects of urea and methylamine on protein stability and function

Urea is a strong denaturant and inhibits many enzymes but is accumulated intracellularly at very high concentrations (up to 3-4 M) in mammalian kidney and in many marine fishes. It is known that the harmful effects of urea on the macromolecular structure and function is offset by the accumulation of an osmolytic agent called methylamine. Intracellular concentration of urea to methylamines falls in the ratio of 2:1 to 3:2 (molar ratio). At this ratio, the thermodynamic effects of urea and methylamines on protein stability and function are believed to be algebraically additive. The mechanism of urea-methylamine counteraction has been widely investigated on various approaches including, thermodynamic, structural and functional aspects. Recent advances have also revealed atomic level insights of counteraction and various molecular dynamic simulation studies have yielded significant molecular level informations on the interaction between urea and methylamines with proteins. It is worthwhile that urea-methylamine system not only plays pivotal role for the survival and functioning of the renal medullary cells but also is a key osmoregulatory component of the marine elasmobranchs, holocephalans and coelacanths. Therefore, it is important to combine all discoveries and discuss the developments in context to physiology of the mammalian kidney and adaptation of the marine organisms. In this article we have for the first time reviewed all major developments on urea-counteraction systems to date. We have also discussed about other additional urea-counteraction systems discovered so far including urea-NaCl, urea-myoinsoitol and urea-molecular chaperone systems. Insights for the possible future research have also been highlighted.

Purification and characterization of a urea sensitive lactate dehydrogenase from the liver of the African clawed frog, Xenopus laevis

The African clawed frog, Xenopus laevis, is able to withstand extremely arid conditions by estivating, in conjunction with dehydration tolerance and urea accumulation. Estivating X. laevis reduce their metabolic rate and recruit anaerobic glycolysis, driven by lactate dehydrogenase (LDH; E.C. 1.1.1.27) enzymes that reversibly convert pyruvate and NADH to lactate and NAD(+), to meet newly established ATP demands. The present study investigated purified LDH from the liver of dehydrated and control X. laevis. LDH from dehydrated liver showed a significantly higher K m for L-lactate (1.74 fold), NAD(+) (2.41 fold), and pyruvate (1.78 fold) in comparison to LDH from the liver of control frogs. In the presence of physiological levels of urea found in dehydrated animals, the K m values obtained for dehydrated LDH all returned to control LDH K m values. Dot blot analysis showed post-translational modifications may be responsible for the kinetic modification as the dehydrated form of LDH showed more phosphorylated serine residues (1.54 fold), less methylated lysine residues (0.43 fold), and a higher level of ubiquitination (1.90 fold) in comparison to control LDH. The physiological consequence of dehydration-induced LDH modification appears to adjust LDH function in conjunction with urea levels in dehydrated frogs. When urea levels are high during dehydration, LDH retains its normal function. Yet, as urea levels drop during rehydration, LDH function is reduced, possibly shunting pyruvate to the TCA cycle.

Protein stabilization and counteraction of denaturing effect of urea by glycine betaine

The counteraction of the denaturing effect of urea by osmolytes has been one of the most studied problems of osmolyte action. However, the possibility of synergy in osmolyte mixtures has often been neglected. Here, we report synergy in the glycine betaine (GB)-urea mixture by using a model peptide. The results show that in the GB-urea mixture, GB acts as a stronger osmolyte and urea becomes a weaker denaturing agent. This is reflected by an increase in the exclusion of GB from the peptide surface and a decrease in interactions between the peptide and urea. The cause of this synergistic behaviour includes direct interactions between GB and urea through hydrogen bonding, van der Waals interactions between them and strengthening of hydrogen bonding network of water in the GB-urea mixture. The results obtained in this study provide insights into osmolyte induced counteraction of the denaturing effect of urea.

Insights into the in vivo regulation of glutamate dehydrogenase from the foot muscle of an estivating land snail

Land snails, Otala lactea, survive in seasonally hot and dry environments by entering a state of aerobic torpor called estivation. During estivation, snails must prevent excessive dehydration and reorganize metabolic fuel use so as to endure prolonged periods without food. Glutamate dehydrogenase (GDH) was hypothesized to play a key role during estivation as it shuttles amino acid carbon skeletons into the Krebs cycle for energy production and is very important to urea biosynthesis (a key molecule used for water retention). Analysis of purified foot muscle GDH from control and estivating conditions revealed that estivated GDH was approximately 3-fold more active in catalyzing glutamate deamination as compared to control. This kinetic difference appears to be regulated by reversible protein phosphorylation, as indicated by ProQ Diamond phosphoprotein staining and incubations that stimulate endogenous protein kinases and phosphatases. The increased activity of the high-phosphate form of GDH seen in the estivating land snail foot muscle correlates well with the increased use of amino acids for energy and increased synthesis of urea for water retention during prolonged estivation.

Relationship between functional activity and protein stability in the presence of all classes of stabilizing osmolytes

We report the effects of stabilizing osmolytes (low molecular mass organic compounds that raise the midpoint of thermal denaturation) on the stability and function of RNase-A under physiological conditions (pH 6.0 and 25 degrees C). Measurements of Gibbs free energy change at 25 degrees C (DeltaG(D) degrees ) and kinetic parameters, Michaelis constant (K(m)) and catalytic constant (k(cat)) of the enzyme mediated hydrolysis of cytidine monophosphate, enabled us to classify stabilizing osmolytes into three different classes based on their effects on kinetic parameters and protein stability. (a) Polyhydric alcohols and amino acids and their derivatives do not have significant effects on DeltaG(D) degrees and functional activity (K(m) and k(cat)). (b) Methylamines increase DeltaG(D) degrees and k(cat), but decrease K(m). (c) Sugars increase DeltaG(D) degrees , but decrease both K(m) and k(cat). These findings suggest that, among the stabilizing osmolytes, (a) polyols, amino acids and amino acid derivatives are compatible solutes in terms of both stability and function, (b) methylamines are the best refolders (stabilizers), and (c) sugar osmolytes stabilize the protein, but they apparently do not yield functionally active folded molecules.

Osmolyte counteracts urea-induced denaturation of alpha-chymotrypsin

The stability of proteins is reduced by urea, which is methylamine and nonprotecting osmolyte; eventually urea destabilizes the activity and function and alters the structure of proteins, whereas the stability of proteins is raised by the osmolytes, which are not interfering with the functional activity of proteins. The deleterious effect of urea on proteins has been counteracted by methylamines (osmolytes), such as trimethylamine N-oxide (TMAO), betaine, and sarcosine. To distinctly enunciate the comparison of the counteracting effects between these methylamines on urea-induced denaturation of alpha-chymotrypsin (CT), we measured the hydrodynamic diameter (d(H)) and the thermodynamic properties (T(m), DeltaH, DeltaG(U), and DeltaC(p)) with dynamic light scattering (DLS) and differential scanning calorimeter (DSC), respectively. The present investigation compares the compatibility and counteracting hypothesis by determining the effects of methylamines and urea, as individual components and in combination at a concentration ratio of 1:2 (methylamine:urea) as well as various urea concentrations (0.5-5 M) in the presence of 1 M methylamine. The experimental results revealed that the naturally occurring osmolytes TMAO, betaine, and sarcosine strongly counteracted the urea actions on alpha-chymotrypsin. The results also indicated that TMAO counteracting the urea effects on CT was much stronger than betaine or sarcosine.

Effects of osmolytes on hexokinase kinetics combined with macromolecular crowding

We investigated the effect of compatible and non-compatible osmolytes in combination with macromolecular crowding on the kinetics of yeast hexokinase. This was motivated by the fact that almost all studies concerning the osmolyte effects on enzyme activity have been performed in diluted buffer systems, which are far from the physiological conditions within cells, where the cytosol contains several hundred mg protein ml(-1). Four organic (glycerol, betaine, TMAO and urea) and one inorganic (NaCl) osmolyte were tested. It was concluded that the effect of compatible osmolytes (glycerol, betaine and TMAO) on V(max) and K(M) was practically equivalent in pure buffer and in 200-250 mg BSA ml(-1) supporting the view that these small organic osmolytes do minimal perturbance on enzyme function in physiological solutions. The effect of urea on enzyme kinetics was not independent of protein concentration, since the presence of 250 mg BSA ml(-1) partly compensated the perturbing effect of urea. Even though the organic osmolytes glycerol, betaine and TMAO are generally considered compatible with enzyme function, especially glycerol did have a significant effect on hexokinase kinetics, decreasing both k(cat), K(M) and k(cat)/K(M). The osmolytes decreased k(cat)/K(M) in the order: NaCl>Urea>TMAO/glycerol>betaine. For the organic osmolytes this order correlates with the degree of exclusion from protein-water interfaces. Thus, the stronger the exclusion the weaker the perturbing effects on k(cat)/K(M).

Trimethylamine N-oxide counteracts the denaturing effects of urea or GdnHCl on protein denatured state

To understand trimethylamine N-oxide (TMAO) attenuation of the denaturating effects of urea or guanidine hydrochloride (GdnHCl), we have determined the apparent transfer free energies (DeltaG(tr)(')) of cyclic dipeptides (CDs) from water to TMAO, urea or GdnHCl, and also the blends of TMAO and denaturants (urea or GdnHCl) at a 1:2 ratio as well as various denaturant concentrations in the presence of 1M TMAO, through the solubility measurements, at 25 degrees C. The CDs investigated in the present study included cyclo(Gly-Gly), cyclo(Ala-Ala) and cyclo(Val-Val). The observed DeltaG(tr)(') values indicate that TMAO can stabilize the CDs while urea or GdnHCl can destabilize the CDs. Furthermore, the DeltaG(tr)(') values of the blends of TMAO with urea or GdnHCl revealed that TMAO strongly counteracted the denaturating effects of urea on CDs in all instances, however, TMAO partially counteracted the perturbing effects of GdnHCl on CDs. TMAO counteraction ability of the deleterious effects of denaturants depended on the denaturant-CDs pair. The experimental results were further used to estimate the transfer free energies (Deltag(tr)(')) of the various functional group contributions from water to TMAO, urea or GdnHCl individually and to the combinations of TMAO and the denaturants in various ratios.

Cellular Response to Hyperosmotic Stresses

Cells in the renal inner medulla are normally exposed to extraordinarily high levels of NaCl and urea. The osmotic stress causes numerous perturbations because of the hypertonic effect of high NaCl and the direct denaturation of cellular macromolecules by high urea. High NaCl and urea elevate reactive oxygen species, cause cytoskeletal rearrangement, inhibit DNA replication and transcription, inhibit translation, depolarize mitochondria, and damage DNA and proteins. Nevertheless, cells can accommodate by changes that include accumulation of organic osmolytes and increased expression of heat shock proteins. Failure to accommodate results in cell death by apoptosis. Although the adapted cells survive and function, many of the original perturbations persist, and even contribute to signaling the adaptive responses. This review addresses both the perturbing effects of high NaCl and urea and the adaptive responses. We speculate on the sensors of osmolality and document the multiple pathways that signal activation of the transcription factor TonEBP/OREBP, which directs many aspects of adaptation. The facts that numerous cellular functions are altered by hyperosmolality and remain so, even after adaptation, indicate that both the effects of hyperosmolality and adaptation to it involve profound alterations of the state of the cells.

Effects of sucrose on the internal dynamics of azurin

Sucrose is a natural osmolyte accumulated in cells of organisms as they adapt to environmental stresses. In vitro, sucrose increases protein stability and forces partially unfolded structures to refold. Its effects on the native fold structure and dynamics are not fully established. This study, utilizing Trp phosphorescence spectroscopy, examined the influence of molar concentrations of sucrose on the flexibility of metal-free azurin from Pseudomonas aeruginosa. In addition, by means of specific mutants of the test protein, namely I7S, F110S, and C3A/C26A, that altered its thermodynamic stability, its intrinsic flexibility, and the extent of internal hydration, this investigation sought to identify possible correlations between these features of protein structure and the influence of the osmolyte on protein dynamics. Alterations of structural fluctuations were assessed by both the intrinsic phosphorescence lifetime (tau), which reports on local structure about the triplet probe, and the acrylamide bimolecular quenching rate constant (k(q)) that is a measure of the average acrylamide diffusion coefficient through the macromolecule. From the modulation of tau and k(q) across a wide temperature range and up to a concentration of 2M sucrose, it is concluded that sucrose attenuates structural fluctuations principally when macromolecules are internally hydrated and thermally expanded. Preliminary tests with trehalose and xylitol suggest that the effects of sucrose are general of the polyol class of osmolytes.

CELL SURVIVAL IN THE HOSTILE ENVIRONMENT OF THE RENAL MEDULLA

The countercurrent system in the medulla of the mammalian kidney provides the basis for the production of urine of widely varying osmolalities, but necessarily entails extreme conditions for medullary cells, i.e., high concentrations of solutes (mainly NaCl and urea) in antidiuresis, massive changes in extracellular solute concentrations during the transitions from antidiuresis to diuresis and vice versa, and low oxygen tension. The strategies used by medullary cells to survive in this hostile milieu include accumulation of organic osmolytes and heat shock proteins, the extensive use of the glycolysis for energy production, and a well-orchestrated network of signaling pathways coordinating medullary circulation and tubular work.

Low water-soluble uremic toxins

The uremic syndrome is the result of the retention of solutes, which under normal conditions are cleared by the healthy kidneys. Uremic retention products are arbitrarily subdivided according to their molecular weight. Low-molecular-weight molecules are characterized by a molecular weight below 500 D. The purpose of the present publication is to review the main water soluble, nonprotein bound uremic retention solutes, together with their main toxic effects. We will consecutively discuss creatinine, glomerulopressin, the guanidines, the methylamines, myo-inositol, oxalate, phenylacetyl-glutamine, phosphate, the polyamines, pseudouridine, the purines, the trihalomethanes, and urea per se.

Glutamate counteracts the denaturing effect of urea through its effect on the denatured state

The urea induced equilibrium denaturation behavior of glutaminyl-tRNA synthetase from Escherichia coli (GlnRS) in 0.25 m potassium l-glutamate, a naturally occurring osmolyte in E. coli, has been studied. Both the native to molten globule and molten globule to unfolded state transitions are shifted significantly toward higher urea concentrations in the presence of l-glutamate, suggesting that l-glutamate has the ability to counteract the denaturing effect of urea. d-Glutamate has a similar effect on the equilibrium denaturation of glutaminyl-tRNA synthetase, indicating that the effect of l-glutamate may not be due to substrate-like binding to the native state. The activation energy of unfolding is not significantly affected in the presence of 0.25 m potassium l-glutamate, indicating that the native state is not preferentially stabilized by the osmolyte. Dramatic increase of coefficient of urea concentration dependence (m) values of both the transitions in the presence of glutamate suggests destabilization and increased solvent exposure of the denatured states. Four other osmolytes, sorbitol, trimethylamine oxide, inositol, and triethylene glycol, show either a modest effect or no effect on native to molten globule transition of glutaminyl-tRNA synthetase. However, glycine betaine significantly shifts the transition to higher urea concentrations. The effect of these osmolytes on other proteins is mixed. For example, glycine betaine counteracts urea denaturation of tubulin but promotes denaturation of S228N lambda-repressor and carbonic anhydrase. Osmolyte counteraction of urea denaturation depends on osmolyte-protein pair.

Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins

Osmolytes increase the thermodynamic conformational stability of proteins, shifting the equilibrium between native and denatured states to favor the native state. However, their effects on conformational equilibria within native-state ensembles of proteins remain controversial. We investigated the effects of sucrose, a model osmolyte, on conformational equilibria and fluctuations within the native-state ensembles of bovine pancreatic ribonuclease A and S and horse heart cytochrome c. In the presence of sucrose, the far- and near-UV circular dichroism spectra of all three native proteins were slightly altered and indicated that the sugar shifted the native-state ensemble toward species with more ordered, compact conformations, without detectable changes in secondary structural contents. Thermodynamic stability of the proteins, as measured by guanidine HCl-induced unfolding, increased in proportion to sucrose concentration. Native-state hydrogen exchange (HX) studies monitored by infrared spectroscopy showed that addition of 1 M sucrose reduced average HX rate constants at all degrees of exchange of the proteins, for which comparison could be made in the presence and absence of sucrose. Sucrose also increased the exchange-resistant core regions of the proteins. A coupling factor analysis relating the free energy of HX to the free energy of unfolding showed that sucrose had greater effects on large-scale than on small-scale fluctuations. These results indicate that the presence of sucrose shifts the conformational equilibria toward the most compact protein species within native-state ensembles, which can be explained by preferential exclusion of sucrose from the protein surface.

Counteracting effects of urea and methylamines in function and structure of skeletal muscle myosin

Myosin is an asymmetric protein that comprises two globular heads (S1) and a double-stranded alpha-helical rod. We have investigated the effects of urea and the methylamines trimethylamine oxide (TMA-O) and glycine betaine (betaine) on activity and structure of skeletal muscle myosin. K(+) EDTA ATPase activity of myosin was almost completely inhibited by urea (2M); TMA-O stimulated myosin activity, whereas betaine had no effect. When combined with urea (0-2M), TMA-O or betaine (1 M) effectively protected the ATPase activity of myosin against inhibition. Intrinsic fluorescence measurements showed that in urea or TMA-O (0-2M), there were no shifts in the center of mass of the fluorescence spectrum of myosin, despite a decrease in fluorescence intensity. However, these osmolytes at concentrations above 2M produced a red shift in the emission spectrum. Betaine alone did not alter the center of mass at any concentration tested up to 5.2M. Thus, modifications in ATPase activity induced by low concentrations of solutes (<2M) are not directly correlated with the modifications in myosin structure detected by fluorescence. Both methylamines (>or=1M) were also able to protect myosin structure against urea-induced effects (2-8M). Protection was not observed for S1, supporting the hypothesis that these osmolytes have a biphasic effect on myosin: at lower concentrations there is an effect on the globular portion (S1), and at higher concentrations there is an effect on the coiled-coil (rod) portion of myosin.

Urea increases tolerance of yeast inorganic pyrophosphatase activity to ethanol: the other side of urea interaction with proteins

Ethanol is the major product of yeast sugar fermentation and yet, at certain concentrations, it is very toxic to yeast cells. The major targets for ethanol's toxicity are the plasma membrane and the cytosolic enzymes: ethanol alters membrane organization and permeability and inactivates and unfolds globular cytosolic enzymes. The effects of ethanol on the plasma membrane are attenuated by the presence of trehalose, a disaccharide of glucose that is accumulated simultaneously with urea. The data presented in this paper show that trehalose is not effective at protecting yeast cytosolic inorganic pyrophosphatase against the inactivation of its catalytic activity promoted by alcohols. In contrast, 1 M trehalose increased the toxicity of alcohols against pyrophosphatase by at least 34%. On the other hand, 1.5 M urea attenuated the inactivation of pyrophosphatase promoted by alcohols by approximately 50%. Here we propose that, in the presence of alcohols, urea functions as a molecular filter, enriching the vicinity of the protein with water and excluding alcohol molecules. Conversely, trehalose tends to increase the interaction of alcohols with protein molecules, by withdrawing water, leading to a stronger inactivation promoted for a given concentration of alcohol in the bulk solution on pyrophosphatase activity.