Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: an analysis by solvent exchange model

Folded protein stabilization or destabilization induced by cosolvent in mixed aqueous solutions has been studied by differential scanning microcalorimetry and related to difference in preferential solvation of native and denatured states. In particular, the thermal denaturation of a model system formed by lysozyme dissolved in water in the presence of the stabilizing cosolvent glycerol has been considered. Transition temperatures and enthalpies, heat capacity, and standard free energy changes have been determined when applying a two-state denaturation model to microcalorimetric data. Thermodynamic parameters show an unexpected, not linear, trend as a function of solvent composition; in particular, the lysozyme thermodynamic stability shows a maximum centered at water molar fraction of about 0.6. Using a thermodynamic hydration model based on the exchange equilibrium between glycerol and water molecules from the protein solvation layer to the bulk, the contribution of protein-solvent interactions to the unfolding free energy and the changes of this contribution with solvent composition have been derived. The preferential solvation data indicate that lysozyme unfolding involves an increase in the solvation surface, with a small reduction of the protein-preferential hydration. Moreover, the derived changes in the excess solvation numbers at denaturation show that only few solvent molecules are responsible for the variation of lysozyme stability in relation to the solvent composition.     

A protein molecule in an aqueous mixed solvent: fluctuation theory outlook

In the present paper a procedure to calculate the properties of proteins in aqueous mixed solvents, particularly the excesses of the constituents of the mixed solvent near the protein molecule and the preferential binding parameters, is suggested. Expressions for the Kirkwood-Buff integrals in ternary mixtures and for the preferential binding parameter were derived and used to calculate various properties of infinitely dilute proteins in aqueous mixed solvents. The derived expressions and experimental information regarding the partial molar volumes and the preferential binding parameters were used to calculate the excesses (deficits) of water and cosolvent (in comparison with the bulk concentrations of protein-free mixed solvent) in the vicinity of ribonuclease A, ribonuclease T1, and lysozyme molecules. The calculations showed that water was in excess in the vicinity of ribonuclease A for water/glycerol and water/trehalose mixtures, and the cosolvent urea was in excess in the vicinity of ribonuclease T1 and lysozyme. The derivative of the activity coefficient of the protein with respect to the mole fraction of water was also calculated. This derivative was negative for the water/glycerol and water/trehalose mixed solvents and positive for the water/urea mixture. The mixture of lysozyme in the water/urea solvent is of particular interest, because the lysozyme at pH 7.0 is in its native state up to 9.3M urea, while at pH 2.0 it is denaturated between 2.5 and 5M and higher concentrations of urea. Our results demonstrated a striking similarity in the hydration of lysozyme at both pHs. It is worthwhile to note that the excesses of urea were only weakly composition dependent on both cases.     

Local composition in the vicinity of a protein molecule in an aqueous mixed solvent

This paper is focused on the composition of a cosolvent in the vicinity of a protein surface (local composition) and its dependence on various factors. First, the Kirkwood-Buff theory of solution is used to obtain analytical expressions that connect the excess or deficit number of cosolvent and water molecules in the vicinity of a protein surface with experimentally measurable quantities such as the bulk concentration of the mixed solvent, the preferential binding parameter, and the molar volumes of water and cosolvent. Using these expressions, relations between the preferential binding parameter (at a molal concentration scale) and the above excesses (or deficits) are established. In addition, the obtained expressions are used to examine the effect of the nonideality of the water + cosolvent mixtures and of the molar volume of the cosolvent on the excess (or deficit) number of cosolvent molecules in the vicinity of the protein surface. It is shown that at least for the mixed solvents considered (water + urea and water + glucose) the nonideality of the mixed solvent is not an important factor in the local compositions around a protein molecule and that the main contribution is provided by the nonidealities of the protein-water and protein-cosolvent mixtures. Special attention is paid to urea as cosolvent, because urea is one of only a few compounds with a concentration at the protein surface larger than its concentration in the bulk. The composition dependence of the excess of urea around a protein molecule is calculated for the water + lysozyme + urea mixture at pH = 7.0 and 2.0. At pH = 7.0, the excess of urea becomes almost composition independent at high urea concentrations. Such independence could be explained by assuming that urea totally replaces water in some areas of the protein surface, whereas on the remaining areas of the protein surface both water and urea are present with concentration comparable to those in the bulk. The Schellman exchange model was used to relate the preferential binding parameter in water + lysozyme + urea mixtures to the urea concentration.     

New insights into urea action on proteins: a SANS study of the lysozyme case

We present a study on lysozyme dissolved in mixtures of water and urea, which is ubiquitously used as a protein denaturant. Despite the wide use of urea, the basic molecular mechanisms inducing protein unfolding are not still clarified. Small-angle neutron scattering (SANS) experiments have been performed using little amounts of denaturant in solutions in order to investigate the urea effect on lysozyme preceding the unfolding process. A global fit strategy, applied to analyze SANS experiments, provides an estimation of the average composition of the solvent in the close vicinity of the protein surface and the change of the protein-protein interactions due to the presence of urea. In particular, the thermodynamic equilibrium constant responsible for cosolvent balancing between the bulk and solvation layer has been determined. It turns out that urea is preferentially driven to the protein surface, confirming literature results at infinite dilute conditions. SANS data also reveal a possible variation of the protein net charge as a function of urea concentration, opening new perspectives and questions about the protein surface architecture at the first stages of unfolding processes.     

Estimation of excess solvation numbers of water and cosolvents from preferential interaction and volumetric experiments

To elucidate, at a molecular level, how cosolvents influence protein stability, it is indispensable to understand the distribution of water and cosolvent molecules around proteins. Calculation of excess solvation numbers of water and cosolvents serves this purpose, and I show that they can be extracted from preferential interaction parameter and volumeric data via the Kirkwood-Buff theory. This scheme was applied to trehalose and glycerol (stabilizers) and urea (denaturant). Important insights from the application include stabilizer-induced enhancement of protein hydration, which, together with the stabilizer's exclusion from protein surfaces, may contribute to protein stabilization at high osmolyte concentrations.     

The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein

A single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local values of diffusion coefficients (translational and rotational) of water adjacent to specific patches on the protein surface seem not to be correlated to the orientational ordering of hydration water, but instead they depend on spatial roughness and degree of exposure of the patch to the solvent. Finally, a relationship between the mobility of various surface atoms of the protein and the mean values of the diffusion coefficient of the adjacent water molecules has been observed. The latter finding suggests a close relationship between the dynamics of the inner kinesin movements and the behavior of solvation water which is in turn determined by the topography of the contact surface between the protein and the surrounding water molecules.     

Solubility of phenobarbital in aqueous cosolvent mixtures revisited: IKBI preferential solvation analysis

The preferential solvation parameters of phenobarbital in aqueous binary mixtures of 1,4-dioxane, t-butanol, n-propanol, ethanol, propylene glycol and glycerol were derived from solution thermodynamic properties by using the IKBI method. This drug is sensitive to preferential solvation effects in all these mixtures. The preferential solvation parameter by the cosolvent (δx_1,3) is negative in almost all the water-rich mixtures but positive in mixtures with similar proportions of solvents and cosolvent-rich mixtures, except in 1-propanol + water mixtures, where negative values are also found in mixtures with x₁ ≥ 0.70. Hydrophobic hydration around the non-polar ethyl and phenyl groups of this drug in water-rich mixtures could play a relevant role in drug solvation. Otherwise, in mixtures of similar solvent compositions and in cosolvent-rich mixtures the preferential solvation by cosolvent could be due to the acidic behaviour of the drug.     

How do trehalose, maltose, and sucrose influence some structural and dynamical properties of lysozyme? Insight from molecular dynamics simulations

The influence of three well-known disaccharides, namely, trehalose, maltose, and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found to be relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars, and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.     

UV-visible spectroscopic study of solvation in ternary solvent mixtures: ketocyanine dye in methanol + acetone + water and methanol + acetone + benzene

Solvation characteristics of a ketocyanine dye have been studied in completely miscible ternary solvent mixtures, namely, methanol + acetone + water and methanol + acetone + benzene, by monitoring the solvatochromic absorption band of the dye. The maximum energy of absorption (E) of the solute in a ternary solvent mixture differs significantly from the mole fraction average of the E values in the component solvents. Results in the corresponding binary solvent mixtures also show a deviation of the E value from the mole fraction averaged E values. The results have been explained in terms of preferential solvation using a two phase model of solvation. The excess or deficit over the bulk composition of a solvent component in the vicinity of the solute molecule in a ternary solvent mixture has been estimated using the knowledge of solvation in the corresponding binary mixtures.     

The importance of preferential solvation of the CN ligands in electron- and proton-transfers observed for cis-[Ru(CN)2(bpy)2] under ion bombardment

Liquid secondary ion mass spectrometry (LSIMS) mass spectra of cis-[Ru(CN)2(bpy)2] with a strong hydrogen-bonding-induced solvatochromism were measured using 3-nitrobenzyl alcohol (NBA) (oxidizing agent) and glycerol (reducing agent), and mixtures of these solvents. The formation of M+ (oxidized molecule) correlated closely to the extent of preferential solvation by NBA (preferential solvation-shell) around the cyanide ligands as observed from changes in the energy of the maximum metal-to-ligand charge transfer absorption. (M + H)+ is caused mainly by the preferential orientation of OH groups with protons in the NBA molecules toward the cyanide ligands in the disrupted region of the solvent structure as observed from the variation in the peak position of the stretching vibration of (OH) in the solvents. Large decreases in (M + 2H)+ and (M + 3H)+ (reduced molecules) resulted from the large decrease in the interaction between the cyanide ligands and glycerol owing to the preferential solvation by NBA. The LSIMS mass spectra clearly showed the electron- and proton-transfer processes along with the change in the hydrogen-bonding interaction between the acceptor (NBA and glycerol) and donor (the cyanide ligands), and in the solvent structure of the preferential solvation-shell. These results indicate that the composition of solvent molecules around the cyanide ligands at the surface of the solvents in LSIMS still holds the composition in the preferential solvation around the ligands in the primary solvation-shell.     

Study on Preferential Solvation of Water by Electrochemical Method

The preferential solvation of water plays an important role in ferrocene research which is a subject of current interest. Voltammetric investigations were carried out for Au electrode in acetonitrile/water, showing preferential solvation of water. In our work, the preferential solvation of water in acetonitrile/water was studied by electrochemical methods including cyclic volitammetry, electrochemical impedance spectra and double‐step chronoamperometry. Ferrocenemethanol (FcCH₂OH) molecules as a solute spontaneously adsorb on the electrode surface in anhydrous acetonitrile, resulting from acetonitrile molecules tend to form an acetonitrile solvent layer on the surface of the electrode and acetonitrile solvent layer has a lower energy barrier than the aqueous solvent layer, which has been obtained by modeling solvation. The solvent strongly influences electrochemical behavior of solute. Once there is an amount of water in acetonitrile solvent, FcCH₂OH that adsorbed on the electrode surface desorb. This is because water preferentially solvate with FcCH₂OH in term of intermolecular forces between solvent and solute. Moreover, hydrogen bond between water molecules and FcCH₂OH molecules is stronger than dipole‐dipole interaction between acetonitrile molecules and FcCH₂OH molecules in solvation effect. Through electrochemical behavior of FcCH₂OH changing, preferential solvation of water is analyzed by electrochemical methods.     

Polar solvation dynamics of lysozyme from molecular dynamics studies

The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.     

Solvation of lithium chloride in aqueous and mixed solutions of an aprotic solvent

The dynamic hydration and solvation numbers of lithium chloride are estimated on the basis of experimental data on the limiting electrodialysis concentration of an electrolyte from aqueous and aqueousorganic solutions containing aprotic solvent N,N-dimethylacetamide. It is established that the dependence of the hydration numbers of the salt on the volume fraction of the aprotic solvent is of an extreme character, and its solvation number on N,N-dimethylacetamide does not depend on the composition of the mixed solution.     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

Hydration of alcohol clusters in 1-propanol-water mixture studied by quasielastic neutron scattering and an interpretation of anomalous excess partial molar volume

Quasielastic neutron scattering measurements have been made for 1-propanol-water mixtures in a range of alcohol concentration from 0.0 to 0.167 in mole fraction at 25 degrees C. Fraction alpha of water molecules hydrated to fractal surface of alcohol clusters in 1-propanol-water mixture was obtained as a function of alcohol concentration. Average hydration number N(ws) of 1-propanol molecule is derived from the value of alpha as a function of alcohol concentration. By extrapolating N(ws) to infinite dilution, we obtain values of 12-13 as hydration number of isolated 1-propanol molecule. A simple interpretation of structural origin of anomalous excess partial molar volume of water is proposed and as a result a simple equation for the excess partial molar volume is deduced in terms of alpha. Calculated values of the excess partial molar volumes of water and 1-propanol and the excess molar volume of the mixture are in good agreement with experimental values.     

Influence de la solvatation preferentielle sur les dimensions des polymeres en solution dans des melanges de solvants

We have studied the dependence of the intrinsic viscosity number of polymers on the composition of binary solvents. The systems studied are: polystyrene in CCl₄/CH₃OH, C₆H₆/CH₃OH and C₆H₆/heptane and poly-2-vinylpyridine in CHCl₃/CH₃CH₂OH. We have also studied, for the same systems, preferential solvation of the polymers, using light scattering.We have observed that, near the θ point, short polystyrene chains exhibit a higher expansion than long chains. This was explained in terms of the dependence of preferential solvation on molecular weight.For the system poly-2-vinylpyridine/CH₃CH₂OH/CHCl₃, we have established the viscosity increment dependence on solvent composition. The curve describing this increment differs markedly from the theoretical curve based on G^E values (excess free energy) of the solvent mixture. However, taking into consideration the process of preferential solvation, the experimental curve can be corrected and becomes very similar in shape to the theoretical curve but there still remains a quantitative difference between the two curves.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

Preferential solvation of etoricoxib in some aqueous binary cosolvent mixtures at 298.15 K

Preferential solvation parameters of etoricoxib in several aqueous cosolvent mixtures were calculated from solubilities and other thermodynamic properties by using the IKBI method. Cosolvents studied were as follows: 1,4-dioxane, N,N-dimethylacetamide, 1,4-butanediol, N,N-dimethylformamide, ethanol and dimethyl sulfoxide. Etoricoxib exhibits solvation effects, being the preferential solvation parameter δx_1,3, negative in water-rich and cosolvent-rich mixtures but positive in mixtures with similar proportions of both solvents. It is conjecturable that the hydrophobic hydration in water-rich mixtures plays a relevant role in drug solvation. In mixtures of similar solvent proportions where etoricoxib is preferentially solvated by the cosolvents, the drug could be acting as Lewis acid with the more basic cosolvents. Finally, in cosolvent-rich mixtures the preferential solvation by water could be due to the more acidic behaviour of water. Nevertheless, the specific solute–solvent interactions in the different binary systems remain unclear because no relation between preferential solvation magnitude and cosolvent polarities has been observed.     

Preferential solvation of methocarbamol in aqueous binary co-solvent mixtures at 298.15 K

The preferential solvation parameters of methocarbamol in dioxane + water, ethanol + water, methanol + water and propylene glycol + water mixtures are derived from their thermodynamic properties by using the inverse Kirkwood–Buff integrals (IKBI) method. This drug is sensitive to solvation effects, being the preferential solvation parameter δx_1,3, negative in water-rich and co-solvent-rich mixtures, but positive in mixtures with similar proportions of solvents, except in methanol + water mixtures, where positive values are found in all the methanol-rich mixtures. It is conjecturable that the hydrophobic hydration around the non-polar groups in water-rich mixtures plays a relevant role. Otherwise, in mixtures of similar solvent compositions, the drug is mainly solvated by co-solvent, probably due to the basic behaviour of the co-solvents; whereas, in co-solvent-rich mixtures, the preferential solvation by water could be due to the acidic behaviour of water. Nevertheless, the specific solute–solvent interactions present in the different binary systems remain unclear.