Hydration of nucleosides in dilute aqueous solutions. Ultrasonic velocity and density measurements

The values of the concentration increments of the ultrasound velocity and their temperature slopes, apparent molar volumes, apparent molar expansibilities, apparent molar adiabatic compressibilities and their temperature gradients for 12 nucleosides and their analogs, as well as for ribose and deoxyribose, have been obtained using precision measurements of ultrasound velocity and density. The following hydration parameters for the atomic groups of the nucleosides, reflecting the state of water in the hydration shells of these groups, have been analyzed: (1) the contribution of ribose to the values of the concentration increment of ultrasound velocity A, the apparent molar volumes phi v and apparent molar adiabatic compressibilities phi ks of nucleosides; (2) contributions of the CH3, NH2 and O = ... -H groups of nucleic bases to the A, phi v and phi ks values of nucleosides and free nucleic bases; (3) contributions of the 2'-OH group of ribose to the values of A, phi v and phi ks nucleosides; (4) changes in the A values of nucleosides and free nucleic bases upon their protonation and deprotonation. Data have been obtained on the mutual influence of the atomic groups of nucleosides on their hydration. It is shown that the GC pairs of free deoxynucleosides undergo hydration more vigorously than the AT pairs, which contrasts with the relation of the degree of hydration of the GC and AT pairs of the double helix.     

Some taste molecules and their solution properties.

The solution properties of a variety of different sapid substances from all four basic taste modalities, namely, sweet (n = 24), salty (n = 7), sour (n = 11) and bitter (n = 2), have been investigated. Some multisapophoric molecules, i.e. molecules exhibiting more than one taste, have also been included in the study in an attempt to define their properties in relation to the tastes they exhibit; eight sweet-bitter and three salty-bitter molecules were used. The density and sound velocity of their solutions in water have been measured and their apparent volumes, apparent compressibilities and compressibility hydration numbers calculated and compared. Apparent molar volumes (phi(v)) and apparent specific volumes (ASV) reflect the state of hydration of the molecules, and thus their extent of interaction with water structure. The range of ASVs reported are 0.13-0.49 cm3/g for salty molecules, 0.55-0.68 cm3/g for sweet molecules, 0.53-0.88 cm3/g for sweet-bitter molecules and a much wider range (0.16-0.85 cm3/g) for sour molecules. Isentropic apparent specific compressibilities range from -2.33 x 10(-5) to -8.06 x 10(-5) cm3/g x bar for salty molecules, -3.38 x 10(-7) to -2.34 x 10(-5) cm3/g x bar for sweet molecules, +6.35 x 10(-6) to -2.22 x 10(-5) cm3/g x bar for sweet-bitter molecules and +6.131 x 10(-6) to -2.99 x 10(-5) cm3/g x bar for sour molecules. Compressibility hydration numbers are also determinable from the measurements of isentropic compressibilities and these reflect the number of water molecules that are disturbed by the presence of the solutes in solution. This study also shows that it is possible to group isentropic apparent molar compressibility values by the taste quality exhibited by the molecules in the same order as for ASV.     

Experimental data and modelling of apparent molar volumes, isentropic compressibilities and refractive indices in aqueous solutions of glycine + NaCl

Experiments have been performed at 298.15 K to measure the density, sound velocity and refractive index of glycine in aqueous solutions of NaCl over a wide range of both glycine and NaCl concentrations. The values of apparent molar volume and isentropic compressibility of glycine were calculated from the measured data. The results show a positive transfer volume of glycine from an NaCl solution to a more concentrated NaCl solution. This indicates that the size of a glycine molecule is larger in a solution with higher NaCl concentration. The negative values of apparent isentropic compressibility imply that the water molecules around the glycine molecules are less compressible than the water molecules in the bulk solution. These effects are attributed to the doubly charged behaviour of glycine and to the formation of physically bonded ion-pairs between the charged groups of glycine and sodium and chloride ions. The formation of ion-pairs, whose extents of binding reactions depend on the concentrations of both NaCl and glycine, alter the hydration number of glycine. This also explains the reason for the increase in the size of glycine with an increase in the NaCl concentration. A model based on the Pitzer formalism has been developed to correlate the activity coefficient, apparent molar volume and isentropic compressibility of glycine in aqueous solutions of NaCl. The results show that the model can accurately correlate the interactions in aqueous solutions of glycine and NaCl.     

Partial molar volumes and adiabatic compressibilities of unfolded protein states

We determined the partial molar volumes, V degrees , and adiabatic compressibilities, K degrees (S), of N-acetyl amino acids with neutralized carboxyl termini, N-acetyl amino acid amides, and N-acetyl amino acid methylamides between 18 and 55 degrees C. The individual compounds in the three classes have been selected so as to collectively cover the 20 naturally occurring amino acid side chains. We interpret our experimental results in terms of the volumetric contributions and hydration properties of individual amino acid side chains and their constituent atomic groups. We also conducted pH-dependent densimetric and acoustic measurements to determine changes in volume and compressibility accompanying protonation of the aspartic acid, glutamic acid, histidine, lysine, and arginine side chains. We use our resulting data to develop an additive scheme for calculating the partial molar (specific) volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We discuss the differences and similarities between our proposed scheme and the reported additive approaches. We compare our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in water (for apocytochrome c) or acidic pH (for apomyoglobin). At these respective experimental conditions, the two proteins are unfolded. However, the comparison between the calculated and experimental volumetric characteristics suggests that neither apocytochrome c nor apomyoglobin are fully unfolded and retain a sizeable core of solvent-inaccessible groups.     

Changes in the contractibility of the cytochrome c globule during redox transition

Changes of the volume and compressibility of cytochrome c molecule in solution during red-ox transition were investigated using differential measurements of density and ultrasound velocity. Small changes were obtained: intrinsic compressibility of the globule increases by (2.5 +/- 1)% and intrinsic volume increases by not more than 0.2%. The results are in contradiction with the recently reported data of Eden et al. claiming that oxidation of the protein is accompanied by a large, of about 40%, increase of compressibility. The validity of our results is verified by three different methods; by comparison of independently measured absolute values of apparent volumes and compressibilities of the oxidized and reduced protein (i); by differential densimetric and ultrasound velocimetric titrations of oxidized cytochrome with ascorbate (ii) and of reduced cytochrome with ferricyanide (iii). The obtained data lead to the conclusion that oxidation-induced-changes of the root mean square amplitude for intramolecular motion of atoms of cytochrome c globule is really 50-fold less than that estimated from X-ray data.     

Effect of cation and anion of an electrolyte on apparent molar volume, isentropic compressibility and refractive index of glycine in aqueous solutions

Experiments at 298.15 K have been performed to measure the density, velocity of sound and refractive index in three water+glycine+electrolyte systems. The electrolytes studied were KCl, KNO3 and NaNO3. The values of apparent molar volume and isentropic compressibility of glycine in aqueous electrolyte solutions were calculated from the measured data. The results obtained in this study and those reported previously for water+glycine+NaCl system have been comparatively studied. The results show that the nature of both the cation and the anion of an electrolyte influence the behaviour of glycine in aqueous solutions. For all four electrolytes studied, the comparison shows a positive volume transfer for glycine from an electrolyte solution to a more concentrated solution of the same electrolyte. The results also show a negative apparent isentropic compressibility for glycine in the presence of the electrolytes studied. These effects indicate that the volume of a glycine molecule is larger in solutions with higher electrolyte concentration and the water molecules around the glycine molecules are less compressible than the water molecules in the bulk solution. These effects were attributed to the doubly charged behaviour of glycine and to the formation of physically bonded ion-pairs between the charged groups of glycine and the cation and the anion of the electrolyte.     

Cholesterol-induced variations in the volume and enthalpy fluctuations of lipid bilayers.

The sound velocity and density of suspensions of large unilamellar liposomes from dimyristoylphosphatidylcholine with admixed cholesterol have been measured as a function of temperature around the chain melting temperature of the phospholipid. The cholesterol-to-phospholipid molar ratio xc has been varied over a wide range (0 </= xc </= 0.5). The temperature dependence of the sound velocity number, of the apparent specific partial volume of the phospholipid, and of the apparent specific adiabatic compressibility have been derived from the measured data. These data are particularly discussed with respect to the volume fluctuations within the samples. A theoretical relation between the compressibility and the excess heat capacity of the bilayer system has been derived. Comparison of the compressibilities (and sound velocity numbers) with heat capacity traces display the close correlation between these quantities for bilayer systems. This correlation appears to be very useful as it allows some of the mechanical properties of membrane systems to be calculated from the specific heat capacity data and vice versa.     

Partial molar volumes,expansibilities, and compressibilities of oligoglycines in aqueous solutions at 18–55°C

We have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of glycine, diglycine, triglycine, tetraglycine, and pentaglycine over the temperature range 18–55°C. These data were analyzed and interpreted in terms of the hydration of these short oligoglycines and their constituent groups. From our results, we have estimated the contributions of the peptide group to the partial molar volume and the partial molar adiabatic compressibility of these oligoglycines. Based on these data, we propose that each of the polar atomic groups of the peptide bond forms approximately two hydrogen bonds with adjacent water molecules. Furthermore, the temperature dependence of the partial molar volume suggests that water that solvates the polar groups of a peptide linkage behaves more like a “normal” liquid than does bulk water, which exhibits its well-known anomalous liquid properties. © 1994 John Wiley & Sons, Inc.     

Volumetric characterization of the hydration properties of heterocyclic bases and nucleosides

We have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of six heterocyclic nucleic acid bases, five ribonucleosides, and six 2'-deoxyribonucleosides within the temperature range 18-55 degrees C. We interpret the resulting data in terms of the hydration of the component hydrophobic and polar atomic groups. From our temperature-dependent volumetric studies, we found that the total contraction of water caused by polar groups of each individual heterocyclic base and nucleoside depends on the proximity and chemical nature of other functional groups of the solute. In addition, the compressibility contributions of polar groups vary greatly in sign and magnitude depending on the surrounding functional groups. In agreement with previous studies, our results are suggestive of little or no interaction between the sugar and base moieties of a nucleoside. In general, our data shed light into the hydration properties of individual heterocyclic bases and nucleosides, which may have significant implications for the sequence-dependent hydration of nucleic acids. We discuss the potential importance of our results for developing an understanding of the role that solvent plays in the stabilization/destabilization of nucleic acid structures.     

Hydration of diglycyl tripeptides with non-polar side chains: a volumetric study

We have determined the apparent molar volumes and the apparent molar adiabatic compressibilities at 25 degrees C of 10 X-Gly-Gly and Gly-Gly-X tripeptides in which X represents a residue with a non-polar side chain. We also have determined the changes in volume and compressibility which accompany neutralization of the amino and carboxyl termini in these tripeptides. The mutual influence of the non-polar side chain of the X residue and the terminal amino and carboxyl groups on the hydration of each other depends on the chemical nature of the side chain and the state of ionization of the termini. We interpret our data in terms of the hydration of the component aliphatic, aromatic, and charged atomic groups, as well as the mutual interactions between these groups.     

Hydrational and intrinsic compressibilities of globular proteins

Partial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 ± 3) × 10^?6 bar ^?1 for the isothermal compressibility coefficient of the protein interior at 25°C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x-ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 × 10^?6 bar ^?1, which is 20% less than that of pure water. © 1993 John Wiley & Sons, Inc.     

The partial molar volumes of anesthetics in lipid bilayers

The excess volumes of mixing of benzyl alcohol, halothane, and methoxyflurane in water and in suspensions of several lipid bilayers have been determined at 25 degrees C using a novel excess volume dilatometer. The excess volumes of mixing in water were all found to be negative, whereas in lipid suspensions they were all more positive than those in water alone. From known partition coefficients the partial molar volumes of these three solutes in the lipid bilayers were calculated. These values were all close to the molar volumes of the pure anesthetics, as was a value determined for halothane in olive oil. Halothane was studied in dipalmitoylphosphatidylcholine below its phase transition, and was found to exhibit a much larger excess volume than in any other system we studied. The potency of these three anesthetics was determined in tadpoles. It was calculated that at equi-anesthetic doses these three agents caused an expansion in egg lecithin/cholesterol (2:1) bilayers of 0.21 +/- 0.015%. This result is consistent with the hypothesis that general anesthetics act by expanding membranes.     

Relaxational contributions to protein compressibility from ultrasonic data

The ultrasonic absorption spectra of proteins in solution generally show relaxational behaviour. There will be a corresponding dispersion of sound velocities accompanying each relaxation. The compressibility of the protein as measured by sound velocity techniques will therefore include a relaxational contribution. We have evaluated this contribution for a number of proteins and found that in some cases the relaxational contribution is a significant fraction of the total compressibility. The relaxational contribution will be large only if the molecule has a large number of degrees of freedom with low force constants. However, such motions are likely to be those involved in the biological functioning of the molecule. Care is needed in interpreting the relaxation spectrum since proton transfer processes give large apparent relaxational compressibilities.     

Partial molar volumes of some alpha-amino acids in aqueous sodium acetate solutions at 308.15 K

The apparent molar volumes V(2,phi) have been determined for glycine, DL-alpha-alanine, DL-alpha-amino-n-butyric acid, DL-valine and DL-leucine in aqueous solutions of 0.5, 1.0, 1.5 and 2.0 mol kg(-1) sodium acetate by density measurements at 308.15 K. These data have been used to derive the infinite dilution apparent molar volumes V(0)(2,phi) for the amino acids in aqueous sodium acetate solutions and the standard volumes of transfer, Delta(t)V(0), of the amino acids from water to aqueous sodium acetate solutions. It has been observed that both V(0)(2,phi) and Delta(t)V(0) vary linearly with increasing number of carbon atoms in the alkyl chain of the amino acids. These linear correlations have been utilized to estimate the contributions of the charged end groups (NH(3)(+), COO(-)), CH(2) group and other alkyl chains of the amino acids to V(0)(2,phi) and Delta(t)V(0). The results show that V(0)(2,phi) values for (NH(3)(+), COO(-)) groups increase with sodium acetate concentration, and those for CH(2) are almost constant over the studied sodium acetate concentration range. The transfer volume increases and the hydration number of the amino acids decreases with increasing electrolyte concentrations. These facts indicate that strong interactions occur between the ions of sodium acetate and the charged centers of the amino acids. The volumetric interaction parameters of the amino acids with sodium acetate were calculated in water. The pair interaction parameters are found to be positive and decreased with increasing alkyl chain length of the amino acids, suggesting that sodium acetate has a stronger dehydration effect on amino acids which have longer hydrophobic alkyl chains. These phenomena are discussed by means of the co-sphere overlap model.     

Changes in the adiabatic compressibility of mono- and polyclonal antibodies during interaction with antigens

The values of apparent adiabatic compressibility of free and antigen-bound antibodies were determined by means of precise density and ultrasound velocity measurements. It was shown that during the formation of soluble immune complexes (insulin--monoclonal antibodies to insulin and alpha-amylase--monovalent Fab-fragments of antibodies to alpha-amylase), the apparent compressibility of antibodies decreased by (0.3 divided by 0.9).10(-6) cm3/g.bar. During the formation of large insoluble aggregates (alpha-amylase--polyclonal antibodies to alpha-amylase), the apparent compressibility decreased by (5.5 +/- 0.7).10(-6) cm3/g.bar. It is suggested that the decrease in the magnitude of thermal fluctuations of the molecular volume of antibodies during antigen binding, manifesting itself by the decrease in their compressibility and strengthened several-fold by precipitate formation, may favour the activation of the effectory functions of antibodies.     

Specific volume and compressibility of human serum albumin-polyanion complexes

The ultrasound velocimetry, densitometry, and differential scanning calorimetry have been used to study the formation of the complexes between human serum albumin (HSA) and polyanions heparin (HEP) and/or dextran sulfate (DS). The values of the ultrasound velocity and specific volume allowed us to determine the specific adiabatic compressibility, phi(K)/beta(0), which reflects the degree of volume compressibility of the complexes. We showed that in the presence of HEP and DS the adiabatic compressibility of HSA decreases with increasing concentration of polyanions. HEP more strongly interacts with HSA than DS. pH of electrolyte in the range 4.7-8.5 weakly affects the adiabatic compressibility. Changes of compressibility of HSA can be caused by increase of the hydration due to the formation of the HSA-polyanion complexes and due to partial unfolding of HSA. The HSA-polyanion interaction resulted in decrease of phase transition temperature of the protein. This evidences about protein destabilization in the presence of polyanions.     

Partial molar volumes of proteins: amino acid side-chain contributions derived from the partial molar volumes of some tripeptides over the temperature range 10-90 degrees C

The partial molar volumes of tripeptides of sequence glycyl-X-glycine, where X is one of the amino acids alanine, leucine, threonine, glutamine, phenylalanine, histidine, cysteine, proline, glutamic acid, and arginine, have been determined in aqueous solution over the temperature range 10-90 degrees C using differential scanning densitometry . These data, together with those reported previously, have been used to derive the partial molar volumes of the side-chains of all 20 amino acids. The side-chain volumes are critically compared with literature values derived using partial molar volumes for alternative model compounds. The new amino acid side-chain volumes, along with that for the backbone glycyl group, were used to calculate the partial specific volumes of several proteins in aqueous solution. The results obtained are compared with those observed experimentally. The new side-chain volumes have also been used to re-determine residue volume changes upon protein folding.     

Thermodynamics of water-induced precipitation of cholesterol and its acetate, benzoate and stearate derivatives dissolved in 1,4-dioxane and 2-propanol

The energetics of the precipitation process depended on the solute-solvent combination and the enthalpy and entropy of precipitation compensated each other. The partial molal volumes of the lipids in both the solvents were greater than the anhydrous molar volumes, except for cholesterol in 1,4-dioxane and cholesteryl acetate in 2-propanol where the order was reverse. While the partial molal compressibilities of all the solutes studied were negative in 1,4-dioxane, those of cholesterol and cholesteryl acetate in 2-propanol were, respectively, negative and positive. The negative values were supported by considerable solvation of the solutes, particularly in 1,4-dioxane.     

Apparent molar volumes of sugars and their significance in sweet taste chemoreception

The apparent molar volumes (V) of selected sugars in 10–50%aqueous solutions have been determined at temperatures rangingfrom 20 to 40°C. The V values obtained accord well withmolecular weight of solute, but vary with molarity, particularlyat the higher temperatures studied. These changes may be ascribableto solute/solute and solute/solvent interactions which may inturn influence the sweet properties of the sugars. Althoughthe apparent molar volumes determined show no obvious relationshipto published sweetness values, their conversion to parachorsemphasises the manner in which attractive interations betweensugar motecules might mediate taste chemoreception.     

Changes of compressibility of low density lipoproteins following copper mediated oxidation

The methods of measuring the ultrasound velocity and density were used for study the adiabatic compressibility of low density lipoproteins (LDL) during their oxidation. We showed, that copper-mediated oxidation of LDL resulted in a decrease of apparent specific compressibility, phi(k)/beta0, of lipoproteins. The changes of ultrasound velocity and phi(k)/beta0 value started much earlier than the beginning of propagation phase corresponding to the fast increase in concentration of conjugated dienes, measured by absorption at 230 nm. It was assumed that the changes of compressibility could be in particularly due to increase in ordering of the phospholipids during reductive activation of Cu2+.