Molecular mechanism for osmolyte protection of creatine kinase against guanidine denaturation

High efficiency of osmotically stable laccase for biotransformation and micro-detoxification of levofloxacin in the urea-containing solution: Catalytic performance and mechanism

Laccase-catalyzed oxidation was applied in the biotransformation of levofloxacin (a potentially environmental antibiotic contamination); however, the enzyme may denature in urea-containing wastewater and lead to the formation of an inactive form followed by decreasing the yield of the bio-removal. In this study, the osmolytes-stabilized laccase was used to eliminate levofloxacin in the urea-containing solution. Sorbitol and proline 100 mM appeared to be the two most efficient laccase protectants against the urea-induced denaturation. In a 1-M urea solution, the maximum velocity (V_max) of laccase was estimated to be 39.1 μmol min^-1 mg^-1. This value was improved to 101.7 and 51.8 μmol min^-1 mg^-1 in the presence of sorbitol and proline, respectively. In optimal conditions for the elimination of levofloxacin, sorbitol- and proline-treated laccase led to 82.9 % and 76.2 % bio-removal of the applied fluoroquinolone in 1 M urea solution, respectively. Biotransformation products of the parent antibiotic were spectroscopically analyzed that assigned to different reaction pathways including demethylation, defluorination, decarboxylation, deamination, and hydroxylation. A micro-toxicity study concerning the growth of some Gram⁺ and Gram^- bacteria exhibited decreasing in inhibition of laccase-treated levofloxacin after a 10-h incubation at 37 °C.

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.

Surface hydration and preferential interaction directs the charged amino acids-induced changes in protein stability

In the present study, we investigate the interaction of amino acid osmolytes, Arg, Lys, Asp and Glu, and a denaturant, guanidinium chloride (Gdm) with proteins. To achieve this, molecular dynamics (MD) simulation of RNase A and α-lactalbumin was performed in the presence of three charged amino acids Arg, Lys, and Asp and the molecular mechanism of amino acid-induced (de)stabilization of the proteins was examined by combining with our earlier report on Glu. As Arg has the side chain similar to that of Gdm and destabilizes the proteins, MD simulation was carried out in the presence of Gdm as well. Radial distribution function and hydration fraction around the protein surface reveals that preferential hydration increases upon the addition of any of the cosolvent; however, the extent of increase is more in the presence of stabilizing cosolvents (stAAs: Lys, Asp and Glu) compared to destabilizing cosolvents (Arg and Gdm). Moreover, the preferential interaction of Arg and Gdm with the proteins is higher than that of stAAs. Residue-level interaction analysis suggests that stAAs preferably interacts with charged amino acids of the proteins whereas Arg and Gdm interactions could be found on almost all the surface exposed residues which might provide higher preferential interaction for these residues. From the results, we propose that the net outcome of preferential hydration versus preferential interaction of the amino acids might determine their effect on the stability of proteins.

The effect of Zn(2+) on Pelodiscus sinensis creatine kinase: unfolding and aggregation studies

We studied the effects of Zn(2+) on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn(2+) inactivated the activity of PSCK (IC(50) = .079 ± .004 mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn(2+) induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn(2+) directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn(2+) bind to PSCK and one Zn(2+) is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn(2+) with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn(2+) on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.

Identification of an animal sucrose transporter

According to a classic tenet, sugar transport across animal membranes is restricted to monosaccharides. Here, we present the first report of an animal sucrose transporter, SCRT, which we detected in Drosophila melanogaster at each developmental stage. We localized the protein in apical membranes of the late embryonic hindgut as well as in vesicular membranes of ovarian follicle cells. The fact that knockdown of SCRT expression results in significantly increased lethality demonstrates an essential function for the protein. Experiments with Saccharomyces cerevisiae as a heterologous expression system revealed that sucrose is a transported substrate. Because the knockout of SLC45A2, a highly similar protein belonging to the mammalian solute carrier family 45 (SLC45) causes oculocutaneous albinism and because the vesicular structures in which SCRT is located appear to contain melanin, we propose that these organelles are melanosome-like structures and that the transporter is necessary for balancing the osmotic equilibrium during the polymerization process of melanin by the import of a compatible osmolyte. In the hindgut epithelial cells, sucrose might also serve as a compatible osmolyte, but we cannot exclude the possibility that transport of this disaccharide also serves nutritional adequacy.

Luciferase protection against proteolytic degradation: a key for improving signal in nano-system biology

Luciferase is most widely used bioluminescence protein in biotechnological processes, but the enzyme is susceptible to proteolytic degradation, thereby its intracellular half-life decreased. Osmolytes are known to enhance the stability of proteins and protect them in a native folded and functional state. The effects of osmolytes, including sucrose, glycine and DMSO on the stability of luciferase were investigated. To different extents, all osmolytes protected the luciferase towards proteolytic degradation in a concentration-dependent manner. The results showed that 1.5M sucrose, 1.5M glycine and 15% DMSO are the best. The ability of these osmolytes to protect luciferase against proteolysis decreased from sucrose, glycine, and finally DMSO. Enzymatic kinetic data showed that the luciferase activity is significantly kept in the presence of sucrose and glycine compared to DMSO, particularly at high temperatures. Bioluminescence intensity, circular dichroism (CD), intrinsic and ANS fluorescence experiments showed change in secondary and tertiary luciferase structure. These results suggest that osmolytes exert an important effect on stabilization of luciferase conformation; decreasing the unfolding rate, preventing adaptation and binding of luciferase at the active site of proteases, thereby the proteolytic digestion reduced and its active conformation was kept.

Genetic engineering for heat tolerance in plants

High temperature tolerance has been genetically engineered in plants mainly by over-expressing the heat shock protein genes or indirectly by altering levels of heat shock transcription factor proteins. Apart from heat shock proteins, thermotolerance has also been altered by elevating levels of osmolytes, increasing levels of cell detoxification enzymes and through altering membrane fluidity. It is suggested that Hsps may be directly implicated in thermotolerance as agents that minimize damage to cell proteins. The other three above approaches leading to thermotolerance in transgenic experiments though operate in their own specific ways but indirectly might be aiding in creation of more reductive and energy-rich cellular environment, thereby minimizing the accumulation of damaged proteins. Intervention in protein metabolism such that accumulation of damaged proteins is minimized thus appears to be the main target for genetically-engineering crops against high temperature stress.

Stability of collagen with polyols against guanidine denaturation

The effect of polyol osmolytes such as erythritol, xylitol and sorbitol on the protection of collagen against guanidine hydrochloride (GdmCl) was studied using circular dichroism and fluorescence spectroscopy. Collagen was denatured by various concentrations of GdmCl in the presence of polyols. The absorbance was high for GdmCl treated collagen than native and polyols treated analogue. Fluorescence emission properties were studied at the excitation wavelength of 235 nm. The emission wavelength is red shifted from 308 to 370 nm for GdmCl treated collagen with polyols. Increasing the concentration of GdmCl did not affect the peak position. CD studies proved that the aggregation of collagen in the presence of lower concentrations of GdmCl. At higher concentrations of GdmCl due to the loss of secondary structure no clear CD spectra were observed. This shows that the unfolding of collagen is closely related to GdmCl concentrations. The ability of the polyols to protect collagen against guanidine denaturation decreased in order from erythritol to xylitol to sorbitol. The presence of OH group in the solvent structure is important for stabilization of collagen due to the formation of additional stabilizing hydrogen bonds.

The protective effects of osmolytes on arginine kinase unfolding and aggregation

Osmolytes are a series of different kinds of small molecules that can maintain the correct conformation of protein by acting as molecular chaperons. In this study, the protective effects of four compatible osmolytes, i.e., proline, sucrose, DMSO and glycerol, were studied during arginine kinase (EC 2.7.3.3) unfolding and aggregation. The results showed that all the osmolytes applied in this study obviously prevented AK unfolding and inactivation that was due to a GdnHCl denaturant by reducing the inactivation rate constants (k(i)), increasing the transition free energy changes (DeltaDeltaG(i)) and increasing the value for the midpoint of denaturation (C(m)). Furthermore, the osmolytes remarkably prevented AK aggregation in a concentration-dependent manner during AK refolding. Our results strongly indicated that osmolytes were not only metabolism substrates, but they were also important compounds with significant physiological protective functions for proteins, especially in some extremely harsh environments.

Polyvinylpyrrolidone 40 Assists the Refolding of Bovine Carbonic Anhydrase B by Accelerating the Refolding of the First Molten Globule Intermediate

Protecting proteins from aggregation is one of the most important issues in both protein science and protein engineering. In this research, the mechanism of enhancing the refolding of guanidine hydrochloride-denatured carbonic anhydrase B by polyvinylpyrrolidone 40 (PVP40) was studied by both kinetic and equilibrium refolding experiments. The reactivation and refolding kinetics indicated that the rate constant of refolding the first refolding intermediate (I(1)) to the second one (I(2)) is promoted by the addition of PVP. Fluorescence quenching studies further indicated that PVP could bind to the aggregation-prone species I(1), resulting in the protection of the exposed hydrophobic surface, a minimization of the protein surface, and more importantly, an increase of the refolding rate of I(1). These properties were quite different from those of poly(ethylene glycol) (PEG), which has been shown to have a strong and stoichiometric binding to I(1) and does not interfere with the refolding pathway. Unlike PEG, the binding of PVP to I(1) does not block the aggregation pathway directly but decreases the energy barrier for I(1) to refold to I(2) and thus reduces the accumulation of I(1). These results suggested that PVP works by a quite different mechanism from those well established ones in chaperones and chemical promoters. PVP is more like a folding catalyst rather than a chemical chaperone. The distinct mechanism of enhancing protein aggregation by PVP is expected to facilitate the attempt to develop new chemical compounds as well as new strategies to protect proteins from aggregation.

The evolution from asparagine or threonine to cysteine in position 146 contributes to generation of a more efficient and stable form of muscle creatine kinase in higher vertebrates

Creatine kinase, a key enzyme in vertebrate excitable tissues that require large energy fluxes, catalyzes the reversible transfer of phosphate between adenosine triphosphate and creatine. Sequence alignment indicated that the 146th amino acid is cysteine in the muscle creatine kinase of higher vertebrates including Amphibia, Reptilia, Aves and Mammalia. In fishes, it is cysteine in Agnatha and Chondrichthyes, and asparagine or threonine in Osteichthyes, which is the ancestor of Amphibia, Reptilia, Aves and Mammalia. To explore the structural and functional role of this special residue, a series of site-directed mutants of rabbit muscle creatine kinase were constructed, including C146S, C146N, C146T, C146G, C146A, C146D and C146R. A detailed comparison was made between wild-type creatine kinase and the mutants in catalytic activity, physico-chemical properties and structural stability against thermal inactivation and guanidine hydrochloride denaturation. It was found that except for C146S, the mutants had relatively lower catalytic activity and structural stability than Wt-CK. Wt-CK and C146S were the most stable ones, followed by C146N and C146T, and then C146G and C146A, and C146D and C146R were the least stable mutants. These results suggested that the 146th residue plays a crucial role in maintaining the structural stability of creatine kinase, and that the evolution in this amino acid from asparagine or threonine to cysteine contributes to the generation of a more efficient and more stable form of creatine kinase in higher vertebrates.

Trehalose and 6-aminohexanoic acid stabilize and renature glucose-6-phosphate dehydrogenase inactivated by glycation and by guanidinium hydrochloride

A number of naturally occurring small organic molecules, primarily involved in maintaining osmotic pressure in the cell, display chaperone-like activity, stabilizing the native conformation of proteins and protecting them from various kinds of stress. Most of them are sugars, polyols, amino acids or methylamines. In addition to their intrinsic protein-stabilizing activity, these small organic stress molecules regulate the activity of some molecular chaperones, and may stabilize the folded state of proteins involved in unfolding or in misfolding diseases, such as Alzheimer's and Parkinson's diseases, or alpha1-antitrypsin deficiency and cystic fibrosis, respectively. Similar to molecular chaperones, most of these compounds have no substrate specificity, but some specifically stabilize certain proteins, e.g., 6-aminohexanoic acid (AHA) stabilizes apolipoprotein A. In the present work, the capacity of 6-aminohexanoic acid to stabilize non-specifically other proteins is demonstrated. Both trehalose and AHA significantly protect glucose-6-phosphate dehydrogenase (G6PD) against glycation-induced inactivation, and renatured enzyme already inactivated by glycation and by guanidinium hydrochloride (GuHCl). To the best of our knowledge, there are no data on the effect of these compounds on protein glycation. The correlation between the recovery of enzyme activity and structural changes indicated by fluorescence spectroscopy and Western blotting contribute to better understanding of the protein stabilization mechanism.

Influence of Osmolytes on Inactivation and Aggregation of Muscle Glycogen Phosphorylase b by Guanidine Hydrochloride. Stimulation of Protein Aggregation under Crowding Conditions

The effects of the osmolytes trimethylamine-N-oxide (TMAO), betaine, proline, and glycine on the kinetics of inactivation and aggregation of rabbit skeletal muscle glycogen phosphorylase b by guanidine hydrochloride (GuHCl) have been studied. It is shown that the osmolytes TMAO and betaine exhibit the highest protective efficacy against phosphorylase b inactivation. A test system for studying the effects of macromolecular crowding induced by osmolytes on aggregation of proteins is proposed. TMAO and glycine increase the rate of phosphorylase b aggregation induced by GuHCl.

Refolding of the full-length non-structural protein 3 of hepatitis C virus

An easy and reproducible procedure for purification and refolding of the full-length non-structural protein 3 (NS3) from hepatitis C virus has been developed. Refolding was achieved by simply diluting the protein into a suitable buffer. Low protein concentration, high pH, highly reducing conditions, the presence of detergent, and low viscosity were important parameters for high refolding efficiency. Refolding was insignificantly affected by the presence of Zn(2+) in the refolding buffer, while the addition of NS4A cofactor inhibited refolding. A comparison of the kinetic parameters showed that the refolded enzyme is not as catalytically competent as the native enzyme. Nevertheless, the activity of the refolded NS3 protease was dependent on the specific NS4A-peptide cofactor and was inhibited by the specific substrate-based NS3 protease inhibitor, which indicates that the refolded NS3 can be appropriate for inhibitor screening. The yield of pure protein from the insoluble fraction of cell lysate was 6 mg/L of bacterial culture, which is 18 times higher than obtained from the soluble fraction. Improvement of the refolding conditions has resulted in a 50-fold higher activity of the protease as compared to refolding in buffer with neutral pH and no additives.

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.