Solvation Of Urea Research Articles

Synergistic behavior of glycine betaine-urea mixture: A molecular dynamics study

Glycine betaine (GB) is one of the most important osmolyte which is known to stabilize proteins as well as counteract the denaturing effect of urea. There have been many studies indicating protein stabilization and counteraction of the effect of urea by GB. However, the exact mechanism of counteraction is still debated and is of important research interest. In this study, distribution functions, hydrogen bonds, and energetics were analysed to understand different interactions between GB and urea, and their solvation properties in presence of each other. The results show that in the GB-urea mixture, GB acted as a stronger osmolyte and urea became a weaker denaturing agent than its individual counterparts. The increase in the solvation of urea and GB in GB-urea mixture and their mutual interactions through hydrogen bonding and coulombic energy resulted in more involvement of GB and urea with solvent as well as with themselves. This might result in the increase of the exclusion of GB from protein surface and decrease in the protein-urea interactions in the mixture. This synergistic behavior might be the prime reason for the counteraction of denaturing effect of urea by GB.

Effect of Urea on the β-Hairpin Conformational Ensemble and Protein Denaturation Mechanism

Despite the daily use of urea to influence protein folding and stability, the molecular mechanism with which urea acts is still not well understood. Here the use of combined parallel tempering and metadynamics simulation allows us to study the free-energy landscape associated with the folding/unfolding of β-hairpin GB1 equilibrium in 8 M urea and pure water. The nature of the unfolded state in both solutions has been analyzed: in urea solution the addition of denaturants acts to expand the denatured state, while in pure water solution the unfolded state is noticeably more compact. For what concerns the mechanism by which urea acts as a denaturant, a preferential direct interaction between urea molecules and protein backbone has been found. However, the bias toward urea solvation is largest at intermediate values of the gyration radius.

Using the New Developed Equation to Reproduce the Enthalpies of Transfer of Urea from Water to Aqueous Ethanol, Propan-1-ol and Acetonitrile at 298 K

The enthalpies of transfer, <TEX>$\Delta H_t^\theta$</TEX>, of urea from water to aqueous ethanol, EtOH, propan-1-ol, PrOH, and acetonitrile, MeCN, are reported and analysed in terms of the new solvation theory. The analyses show that the solvation of urea is random in the considered solvent mixtures. It is also found that urea interact more strongly with EtOH or PrOH than water.

Enthalpies of solution of urea in water-methanol mixtures at 298.15 K

The standard enthalpies of solution of urea in water-methanol mixtures were determined over the entire range of solvent compositions at 298.15 K. A comparison of the results obtained with the published data on mixtures of water with ethanol and n-propanol revealed a differentiating effect of the alcohol concentration on the enthalpy of solution of urea. Only for water-methanol solutions, an increase in the alkanol content in the mixture (0.6 mole fractions < x2 < 1.0 mole fractions) caused an increase in the degree of solvation of urea.

Importance of Excluded Volume on the Solvation of Urea in Water

We have used molecular dynamics simulations to probe the concentration-dependent solvation of urea in water. Two models of urea are considered: one is the OPLS potential, and the other is the recently introduced KBFF model whose parameters were obtained to reproduce the experimental values of the Kirkwood-Buff integrals. Although the partial charges on the urea atoms in the models are dramatically different, the concentration-dependent structural characteristics of water are similar. The largest difference between the two models is in the prediction of the tendency of urea to self-associate. The OPLS model leads to stronger urea-urea association than the KBFF model. Surprisingly, this difference is traced to the variations in the Lennard-Jones parameters rather than the charge distributions. These results suggest that solvation of urea depends not only on its ability to form hydrogen bonds with water but also its excluded volume. More generally, we propose that the denaturation efficiency of polar nonelectrolytes, such as urea, is determined by the ability of the cosolute to form hydrogen bonds with the polypeptide chain which, in turn, depends on its size.

Effector-induced dissociation of glyceraldehyde-3-phosphate dehydrogenase discriminated by urea solvation.

The dissociation of glyceraldehyde-3-phosphate dehydrogenase (GAPD) from pig muscle in water solutions (0.1 M phosphate, pH 7) at increased urea concentrations was studied by means of frontal-gel chromatography, intrinsic (TRP) fluorescence, differential absorption spectroscopy and selective chemical modification at TRP0193. The results are in agreement with a consecutive two-step model of dissociation of the tetramer and the dimer (C*T = 0.42 M urea < C*D = 1.39 M urea). The binding effector(s) destabilizes the oligomeric structures (delta GT changes from -1.00 to -0.54 kcal/mol; delta GD from -2.30 to -1.22 kcal/mol). The introduction of the bulky Koshland-reagent group to TRP-193 at the subunit-subunit interface leads to a decrease of the stability with delta delta G approximate to 1 kcal/mol, owing to TRP-193...TYR-39...TYR-92 cluster destruction. By using lobster GAPD atomic coordinates (PDB file 1GPD) and pig muscle GAPD amino-acid sequence, a tentative molecular model was constructed and the subunit contacts in terms of the Lee-Richard static accessibilities were described. A detailed analysis of the dissociation as a transfer of the buried residues from the molecular interface to the urea solutions was performed.

Solvation and association of urea in aqueous solutions and mixtures of water with 1‐propanol

AbstractSelf‐diffusion coefficients of urea have been measured at 25.0 °C in aqueous solutions and in mixtures of water with 1‐propanol, as a function of the urea concentration and of the mixed solvent composition. The hydrodynamic radius of urea has been calculated. It has been found that both in aqueous solutions as well as in 1‐propanol‐water mixtures dimers of urea, if they exist, do not play any role in the diffusion processes. Diffusion is, however, a collective process and motions of urea depend on the numbers of neighbours, therefore they are very sensitive on the structure of the solvent. The results have also confirmed the previous supposition that urea does not affect the water structure, but it does fit the water structure quite well. It has been also found that the solvation of urea is determined by the structure of the mixed solvent.

Solvation of urea and methyl-substituted ureas by water and DMF

The hydrogen bond enthalpies of urea and methyl-substituted ureas with water and DMF have been determined by the pure-base calorimetric method. Transfer enthalpies between water and DMF have been calculated for dilute solutions of the ureas according to a previously developed model. The first solvation sphere of urea in water consists of five water molecules. Solvation spheres are given for other methyl-substituted ureas in water and DMF.