Hydrogen exchange kinetics of RNase A and the urea:TMAO paradigm

A key paradigm in the biology of adaptation holds that urea affects protein function by increasing the fluctuations of the native state, while trimethylamine N-oxide (TMAO) affects function in the opposite direction by decreasing the normal fluctuations of the native ensemble. Using urea and TMAO separately and together, hydrogen exchange (HX) studies on RNase A at pH* 6.35 were used to investigate the basic tenets of the urea:TMAO paradigm. TMAO (1 M) alone decreases HX rate constants of a select number of sites exchanging from the native ensemble, and low urea alone increases the rate constants of some of the same sites. Addition of TMAO to urea solutions containing RNase A also suppresses HX rate constants. The data show that urea and TMAO independently or in combination affect the dynamics of the native ensemble in opposing ways. The results provide evidence in support of the counteraction aspect of the urea:TMAO paradigm linking structural dynamics with protein function in urea-rich organs and organisms. RNase A is so resistant to urea denaturation at pH* 6.35 that even in the presence of 4.8 M urea, the native ensemble accounts for >99.5% of the protein. An essential test, devised to determine the HX mechanism of exchangeable protons, shows that over the 0-4.8 M urea concentration range nearly 80% of all observed sites convert from EX2 to EX1. The slow exchange sites are all EX1; they do not exhibit global exchange even at urea concentrations (5.8 M) well into the denaturation transition zone, and their energetically distinct activated complexes leading to exchange gives evidence of residual structure. Under these experimental conditions, the use of DeltaG(HX) as a basis for HX analysis of RNase A urea denaturation is invalid.     

Effects of urea and trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in solution

The effect of two physiological cosolutes (urea and trimethylamine-N-oxide) and of KCl on the intermolecular interactions in concentrated lysozyme solutions were studied by synchrotron radiation small angle x-ray scattering. The evolution of the structure factors as a function of cosolute and/or salt concentration was modeled using pair potentials following an approach recently described in the literature. It was found that the structure factors for salt and/or cosolute concentration series at a fixed protein concentration can best be described using a variable depth attractive potential and a constant effective charge rather than a constant attractive potential and a variable effective charge as done in previous work.     

Investigation of radical-based damage of RNase A in aqueous solution and lipid vesicles

The gamma-irradiation of bovine pancreatic ribonuclease A (RNase A) in aqueous solution were investigated at different doses by vibrational spectroscopy as well as enzymatic assay, electrophoresis, and HPLC analysis. Both functional and structural changes of the protein were caused by attack of H(*) atoms and (*)OH radicals. In particular, Raman spectroscopy was shown to be a useful tool in identifying conformational changes of the protein structure and amino acidic residues that are preferential sites of the radical attack (i.e., tyrosine and methionine). After partial structural changes by the initial radical attack, the internal sulfur-containing amino acid residues were rendered susceptible to transformation. By using the biomimetic model of dioleoyl phosphatidyl choline vesicle suspensions containing RNase A, the damage to methione residues could be connected to a parallel alteration of membrane unsaturated lipids. In fact, thiyl radical species formed from protein degradation can diffuse into the lipid bilayer and cause isomerization of the naturally occurring cis double bonds. As a consequence, trans unsaturated fatty acids are formed in vesicles and can be considered to be markers of this protein damage.     

A glycine betaine transport system in Aphanothece halophytica and other glycine betaine-synthesising cyanobacteria

Uptake of exogenous ¹⁴C-glycine betaine has been followed in the cyanobacterium Aphanothece halophytica and other species able to synthesise glycine betaine in response to osmotic stress. At 1 mmol dm^–3 uptake was rapid (flux rate=29.50 nmol m^–2 s^–1), equilibrating at an internal concentration of 120 mmol dm^–3 within 30 min. This rapid uptake, coupled with high internal accumulation, was characteristic of glycine betaine-synthesising cyanobacteria only. The ¹⁴C-glycine betaine transported was not catabolised. Kinetic studies indicated a Michaelis-Menten type relationship (K _m=2.0 mol dm^–3, V _max=45 nmol min^–1 mm^–3 cell volume), with a pH optimum of 8.0–8.5. Darkness dramatically decreased the flux rate. Higher ¹⁴C-glycine betaine levels occurred in cells growth in medium of elevated osmotic strength, and glycine betaine uptake was sensitive to changes in external salinity. A relationship between Na⁺ availability and glycine betaine uptake was observed, with >80 mmol dm^–3 Na⁺ required for optimal stimulation of uptake in seawater-grown cells. Severe hyperosmotic stress (1000 mmol dm^–3 NaCl) reduced the rate of glycine betaine uptake but increased internal glycine betaine concentration at equilibrium. Hypo-osmotic stress caused a decline in the internal glycine betaine concentration due to an increased rate of loss, indicating that the efflux system was also sensitive to ambient salinity changes. It is envisaged that this active transport system may be an adaptive mechanism in halophilic glycine betaine-synthesising cyanobacteria.     

Overaccumulation of glycine betaine alleviates the negative effects of salt stress in wheat

To investigate the physiological mechanisms of glycinebetaine (GB) involved in the improvement of salt tolerance of wheat, three transgenic wheat (Triticum aestivum L.) lines-T1, T4, and T6-and the wild-type (WT) line Shi4185 were used. The transgenic lines were generated by introducing the BADH gene encoding betaine aldehyde dehydrogenase, which was cloned from Atriplex hortensis L. The BADH gene induced overexpression of GB in transgenic lines. Salt stress was induced by adding 200 mM NaCl, and the osmotic adjustment (OA), ion homeostasis, and antioxidant characteristics of wheat plants were observed. Under salt stress, the OA in the transgenic wheat lines was significantly higher than that in WT; this may be attributed to GB itself and/or the GB-induced overaccumulation of other osmolytes, such as free proline, soluble protein, and soluble sugar. Moreover, the transgenic lines could maintain the lower Na⁺ and Cl⁻ concentrations in their leaves by accumulating these ions in the sheaths in order to protect the leaves from ion toxicity; however, these lines maintained a higher K⁺ concentration in the leaves since K⁺ functions as an osmolyte and maintains ion homeostasis in the leaf cells. Furthermore, the in vivo overaccumulated GB could enhance or stabilize the activity of antioxidant enzymes that can scavenge reactive oxygen species (ROS) and mitigate oxidative damage of biomembranes. The experimental results suggest that GB overexpression can enhance the salt tolerance of transgenic plants by regulating ion homeostasis, enhancing OA, and scavenging ROS. Published in Russian in Fiziologiya Rastenii, 2009, vol. 56, No. 3, pp. 410–417. This text was submitted by the authors in English.     

Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability

Interactions of the solutes glycine betaine (GB) and urea with mononucleosomal calf thymus DNA in aqueous salt solutions are characterized by vapor pressure osmometry (VPO). Analysis of osmolality as a function of solute and DNA concentration yields the effect of the solute on the chemical potential, mu(2), of the DNA. Although both GB and urea generally are nucleic acid denaturants and therefore must interact favorably with the nucleic acid surface exposed upon melting, VPO demonstrates that neither interacts favorably with duplex DNA. Addition of GB greatly increases mu(2) of DNA, indicating that the average local concentration of GB in the vicinity of the double helix is much less than its bulk concentration. By contrast, addition of urea has almost no effect on mu(2) of duplex DNA, indicating that the average local concentration of urea in the vicinity of duplex DNA is almost the same as in bulk solution. Qualitatively, we conclude that the nonuniform distribution of GB occurs primarily because duplex DNA and GB prefer to interact with water rather than with each other. Comparison with thermodynamic data for the interaction of GB with various protein surfaces (Felitsky et al., Biochemistry, 43, 14732-14743) shows that GB is excluded primarily from anionic DNA surface and that the hydration of anionic DNA phosphate oxygen surface (>or approximately 17 H(2)O per nucleotide or >or approximately 0.22 H(2)O A(-)(2)) involves at least two layers of water. From analysis of literature data for effects of urea and of GB on DNA melting, we propose that urea is an effective nonspecific nucleic acid denaturant because of its favorable interactions with the polar amide-like surface of G, C, and especially T or U bases exposed in denaturation, whereas GB is a specific GC denaturant because of its favorable interaction with G and/or C surface in the single-stranded state.     

Levels of glycine betaine in growing cells and spores of Bacillus species and lack of effect of glycine betaine on dormant spore resistance

Bacteria of various Bacillus species are able to grow in media with very high osmotic strength in part due to the accumulation of low-molecular-weight osmolytes such as glycine betaine (GB). Cells of Bacillus species grown in rich and minimal media contained low levels of GB, but GB levels were 4- to 60-fold higher in cells grown in media with high salt. GB levels in Bacillus subtilis cells grown in minimal medium were increased approximately 7-fold by GB in the medium and 60-fold by GB plus high salt. GB was present in spores of Bacillus species prepared in media with or without high salt but at lower levels than in comparable growing cells. With spores prepared in media with high salt, GB levels were highest in B. subtilis spores and > or =20-fold lower in B. cereus and B. megaterium spores. Although GB levels in B. subtilis spores were elevated 15- to 30-fold by GB plus high salt in sporulation media, GB levels did not affect spore resistance. GB levels were similar in wild-type B. subtilis spores and spores that lacked major small, acid-soluble spore proteins but were much lower in spores that lacked dipicolinic acid.     

Solubility and property of chitin in NaOH/urea aqueous solution

NaOH/urea aqueous solution has been used as a solvent for chitin for the first time. Effects of this solvent composition and temperature on the solubility and stability of chitin solution were studied with an optical microscope, from which 8 wt% NaOH/4 wt% urea concentrations were deduced as suitable and −20 °C as the appropriate temperature. The original and regenerated chitin were characterized by viscosity, elemental analysis, FI-IR and X-RD analysis, and the effect of solvent composition and temperature on chitin structure was investigated. It was inferred that 8 wt% NaOH/4 wt% urea solvent under low temperature adventitiously has little effect on chitin structure and the urea is of benefit to the stability of chitin solution. In addition, the rheological properties suggested that chitin aqueous solution in high concentration is a pseudoplastic fluid and that chitin aqueous solution in low concentrations is a Newtonian fluid. This chitin aqueous solution is sensitive to temperature and will transform it to a gel when temperature increases.     

Oligo-glycine synthesis in an aqueous solution of glycine under oxidative conditions

Di-and tri-glycine were synthesized in 1M aqueous solution of glycine by bubbling for 90 hr with oxygen discharged in the path from an oxygen cylinder. The peptides were also produced by an incubation at 37°C of 2M glycine solution prepared with 75% hydrogen peroxide, and the yields were traced for 200 days. The final yields were about 0.25% and 0.01% for di-and tri-glycine, respectively. The solution at 166 days of incubation was applied to a Sephadex G 10 column, and the fractions around the top of the chromatogram were found to increase the intensity of ninhydrin color about 45 times after hydrolysis, indicating an existence of oligo-glycine. The solutions of 1M glycine and 0.5M diglycine prepared with 30% hydrogen peroxide were incubated at 37°C for 38 days, and di-and tetra-glycine were detected in the yields of 0.12% and 0.33%, respectively.     

Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding

Thermodynamic analysis of urea-biopolymer interactions and effects of urea on folding of proteins and alpha-helical peptides shows that urea interacts primarily with polar amide surface. Urea is therefore predicted to be a quantitative probe of coupled folding, remodeling, and other large-scale changes in the amount of water-accessible polar amide surface in protein processes. A parallel analysis indicates that glycine betaine [N,N,N-trimethylglycine (GB)] can be used to detect burial or exposure of anionic (carboxylate, phosphate) biopolymer surface. To test these predictions, we have investigated the effects of these solutes (0-3 m) on the formation of 1:1 complexes between lac repressor (LacI) and its symmetric operator site (SymL) at a constant KCl molality. Urea reduces the binding constant K(TO) [initial slope dlnK(TO)/dm(urea) = -1.7 +/- 0.2], and GB increases K(TO) [initial slope dlnK(TO)/dm(GB) = 2.1 +/- 0.2]. For both solutes, this derivative decreases with an increase in solute concentration. Analysis of these initial slopes predicts that (1.5 +/- 0.3) x 10(3) A2 of polar amide surface and (4.5 +/- 1.0) x 10(2) A2 of anionic surface are buried in the association process. Analysis of published structural data, together with modeling of unfolded regions of free LacI as extended chains, indicates that 1.5 x 10(3) A2 of polar amide surface and 6.3 x 10(2) A2 of anionic surface are buried in complexation. Quantitative agreement between structural and thermodynamic results is obtained for amide surface (urea); for anionic surface (GB), the experimental value is approximately 70% of the structural value. For LacI-SymL binding, two-thirds of the structurally predicted change in amide surface (1.0 x 10(3) A2) occurs outside the protein-DNA interface in protein-protein interfaces formed by folding of the hinge helices and interactions of the DNA binding domain (DBD) with the core of the repressor. Since urea interacts principally with amide surface, it is particularly well-suited to detect and quantify the extent of coupled folding and other large-scale remodeling events in the steps of protein-nucleic acid interactions and other protein associations.     

Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution

The biophysical characterization of nonfunctional protein aggregates at physiologically relevant temperatures is much needed to gain deeper insights into the kinetic and thermodynamic relationships between protein folding and misfolding. Dynamic and static laser light scattering have been employed for the detection and detailed characterization of apomyoglobin (apoMb) soluble aggregates populated at room temperature upon dissolving the purified protein in buffer at pH 6.0, both in the presence and absence of high concentrations of urea. Unlike the beta-sheet self-associated aggregates previously reported for this protein at high temperatures, the soluble aggregates detected here have either alpha-helical or random coil secondary structure, depending on solvent and solution conditions. Hydrodynamic diameters range from 80 to 130 nm, with semiflexible chain-like morphology. The combined use of low pH and high urea concentration leads to structural unfolding and complete elimination of the large aggregates. Even upon starting from this virtually monomeric unfolded state, however, protein refolding leads to the formation of severely self-associated species with native-like secondary structure. Under these conditions, kinetic apoMb refolding proceeds via two parallel routes: one leading to native monomer, and the other leading to a misfolded and heavily self-associated state bearing native-like secondary structure.     

Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface

Two thermodynamic models have been developed to interpret the preferential accumulation or exclusion of solutes in the vicinity of biopolymer surface and the effects of these solutes on protein processes. The local-bulk partitioning model treats solute (and water) as partitioning between the region at/or near the protein surface (the local domain) and the bulk solution. The solvent exchange model analyzes a 1:1 competition between water and solute molecules for independent surface sites. Here we apply each of these models to interpret thermodynamic data for the interactions of urea and the osmoprotectant glycine betaine (N,N,N-trimethylglycine; GB) with the surface exposed in unfolding the marginally stable lacI HTH DNA binding domain. The partition coefficient K(P) quantifying accumulation of urea at this protein surface (K(P) approximately equal 1.1) is only weakly dependent on urea concentration up to 6 M urea. However, K(P) quantifying exclusion of GB from the vicinity of this protein surface increases from 0.83 (extrapolated to 0 M GB) to 1.0 (indicating that local and bulk GB concentrations are equal) at 4 M GB (activity > 40 M). We interpret the significant concentration dependence of K(P) for GB, predicted to be general for excluded, nonideal solutes such as GB, as a modest (8%) attenuation of the GB concentration dependence of solute nonideality in the local domain relative to that in the bulk solution. Above 4 M, K(P) for the interaction of GB with the surface exposed in protein unfolding is predicted to exceed unity, which explains the maximum in thermal stability observed for RNase and lysozyme at 4 M GB (Santoro, M. M., Liu, Y. F., Khan, S. M. A., Hou, L. X., and Bolen, D. W. (1992) Biochemistry 31, 5278-5283). Both thermodynamic models provide good two-parameter fits to GB and urea data for lacI HTH unfolding over a wide concentration range. The solute partitioning model allows for a full spectrum of attenuation effects in the local domain, encompasses the cases treated by the competitive binding model, and provides a somewhat better two-parameter fit of effects of high GB concentration on lacI HTH stability. Parameters of this fit should be applicable to isothermal and thermal unfolding data for all proteins with similar compositions of surface exposed in unfolding.     

Unique gelation behavior of cellulose in NaOH/urea aqueous solution

A transparent cellulose solution was prepared by mixing 7 wt % NaOH with 12 wt % urea aqueous solution which was precooled to below -10 degrees C and which was able to rapidly dissolve cellulose at ambient temperature. The rheological properties and behavior of the gel-formed cellulose solution were investigated by using dynamic viscoelastic measurement. The effects of temperature, time, cellulose molecular weight, and concentrations on both the shear storage modulus (G') and the loss modulus (G") were analyzed. The cellulose solution having a viscosity-average molecular weight (M(eta)) of 11.4 x 10(4) had its sol-gel transition temperature decreased from 60.3 to 30.5 degrees C with an increase of its concentration from 3 to 5 wt %. The gelation temperature of a 4 wt % cellulose solution dropped from 59.4 to 30.5 degrees C as the M(eta) value was increased from 4.5 x 10(4) to 11.4 x 10(4). Interestingly, at either higher temperature (above 30 degrees C), or lower temperature (below -3 degrees C), or for longer gelation time, gels could form in the cellulose solutions. However, the cellulose solution remains a liquid state for a long time at the temperature range from 0 to 5 degrees C. For the first time, we revealed an irreversible gelation in the cellulose solution system. The gel having been formed did not dissolve even when cooled to the temperature of -10 degrees C, at which it was dissolved previously. Therefore, this indicates that either heating or cooling treatment could not break such stable gels. A high apparent activation energy (E(a)) of the cellulose solution below 0 degrees C was obtained and was used to explain the gel formation under the cooling process.     

The unusually strong stabilizing effects of glycine betaine on the structure and function of the oxygen-evolving Photosystem II complex

Natural osmoregulatory substances (osmolytes) allow a wide variety of organisms to adjust to environments with high salt and/or low water content. In addition to their role in osmoregulation, some osmolytes protect proteins from denaturation and deactivation by, for example, elevated temperature and chaotropic compounds. A ubiquitous protein-stabilizing osmolyte is glycine betaine (N-trimethyl glycine). Its presence has been reported in bacteria, in particular cyanobacteria, in animals and in plants from higher plants to algae. In the present review we describe the experimental evidence related to the ability of glycine betaine to enhance and stabilize the oxygen-evolving activity of the Photosystem II protein complexes of higher plants and cyanobacteria. The osmolyte protects the Photosystem II complex against dissociation of the regulatory extrinsic proteins (the 18 kD, 23 kD and 33 kD proteins of higher plants and the 9 kD protein of cyanobacteria) from the intrinsic components of the Photosystem II complex, and it also stabilizes the coordination of the Mn cluster to the protein cleft. By contrast, glycine betaine has no stabilizing effect on partial photosynthetic processes that do not involve the oxygen-evolving site of the Photosystem II complex. It is suggested that glycine betaine might act, in part, as a solute that is excluded from charged surface domains of proteins and also as a contact solute at hydrophobic surface domains.     

Homogeneous synthesis and characterization of quaternized chitin in NaOH/urea aqueous solution

Water-soluble and white quaternized chitin (QC) was homogeneously synthesized by stirring transparent chitin solution (2%) in 8 wt%NaOH/4 wt% urea aqueous solution containing 2,3-Epoxypropyltrimethylammonium Chloride (EPTMAC) at 10 °C for 24 h. The structure and properties of quaternized chitin were characterized by FT-IR, XRD, ¹H NMR, GPC, element analysis and ζ-potential. The results indicate that quaternary groups were successfully incorporated onto chitin backbones and the degree of substitution (DS) of quaternary groups can be easily adjusted by changing the molar ratio of chitin unit to EPTMAC. Additionally, quaternized chitin shows better antibacterial activity against Escherichia coli and Staphylococcus aureus as compared with chitosan. Thus, this work provides a simply and “green” method to functionalize chitin and the resulting quaternized chitin may have potential applications in environmental, food and biomedical fields.