Evaluation of selectivity changes in HIC systems using a preferential interaction based analysis

It is well established that salt enhances the interaction between solutes (e.g., proteins, displacers) and the weak hydrophobic ligands in hydrophobic interaction chromatography (HIC) and that various salts (e.g., kosmotropes, chaotropes, and neutral) have different effects on protein retention. In this article, the solute affinity in kosmotropic, chaotropic, and neutral mobile phases are compared and the selectivity of solutes in the presence of these salts is examined. Since solute binding in HIC systems is driven by the release of water molecules, the total number of released water molecules in the presence of various types of salts was calculated using the preferential interaction theory. Chromatographic retention times and selectivity reversals of both proteins and displacers were found to be consistent with the total number of released water molecules. Finally, the solute surface hydrophobicity was also found to have a significant effect on its retention in HIC systems.     

Effects of chaotropic and kosmotropic cosolvents on the pressure-induced unfolding and denaturation of proteins: an FT-IR study on staphylococcal nuclease

FT-IR spectroscopy was used to study the effects of various chaotropic and kosmotropic cosolvents (glycerol, sucrose, sorbitol, K(2)SO(4), CaCl(2), and urea) on the secondary structure and thermodynamic properties upon unfolding and denaturation of staphylococcal nuclease (Snase). The data show that the different cosolvents have a profound effect on the denaturation pressure and the Gibbs free energy (DeltaG(o)) and volume (DeltaV(o) change of unfolding. Moreover, by analysis of the amide I' infrared bands, conformational changes of the protein upon unfolding in the different cosolvents have been determined. An increase, a reduction, or an independence of the volume change of unfolding is observed, depending on the type of cosolvent, which can at least in part be attributed to the formation of a different unfolded state structure of the protein. The data are compared with the corresponding thermodynamic values of DeltaV(o) for the temperature-induced unfolding process of Snase as obtained by pressure perturbation calorimetry, and significant differences are observed and discussed.     

Changes in water structure induced by a hydrophobic solute probed by simulation of the water hydrogen bond angle and radial distribution functions.

In order to better characterize changes in water structure induced by a hydrophobic solute the oxygen-oxygen and hydrogen-hydrogen radial distribution functions (goo(r), ghh(r)) and the hydrogen bond angle distribution function p(theta) for water molecules in the first hydration shell of the tetramethyl ammonium (TMA) cation were computed using Monte Carlo simulations. goo(r) and ghh(r) were corrected for the effect of solute volume exclusion on the local solvent density so that intrinsic structural changes independent of local solvent density variations could be detected. Comparison of ghh(r) of TMA's first hydration shell water with ghh(r) for bulk water shows subtle but clear evidence of structure formation induced by the ion. These changes in ghh(r) are very similar to those seen experimentally for larger tetra-alkyl ammonium ions in previous neutron diffraction experiments. Larger changes in p(theta) in the first hydration shell of TMA were seen. Comparison of changes in p(theta) with changes in goo(r) and ghh(r) show that the angle distribution function provides the most sensitive way to analyze water structure changes associated with hydrophobic solvation.     

Effects of cryoprotectants on enzyme structure

The interaction between organic cosolvents and proteins is considered, especially from the point of view of effects on protein stability. It is concluded that each protein-cosolvent system constitutes a unique situation, making generalized predictions of expected effects difficult. Two classes of cosolvents are distinguished, based on the nature of their interactions with the protein surface. The thermodynamic instability to the system introduced by the presence of the cosolvent can be accommodated (i) by preferential exclusion of the cosolvent from the vicinity of the protein, (ii) by major structural changes of the protein, or (iii) by aggregation. Polyols tend to undergo preferential exclusion due to unfavorable interactions with nonpolar surface groups, whereas monohydric alcohols and other more hydrophobic cosolvents may undergo preferential exclusion due to adverse interactions with charged groups on the protein surface. Typical cosolvent effects on the structural and catalytic properties of enzymes are illustrated with data for ribonuclease and beta-lactamase with alcohol cosolvents. The relative hydrophobicity of the cosolvent is the major determinant of the effect of a cryosolvent on the enzyme stability and properties. Thus the position of the unfolding transition in cryosolvent will be decreased more by a more nonpolar cosolvent. Different cosolvents can have significantly different effects on the catalytic and structural properties of the same enzyme. Conversely the same cosolvent can have significantly different effects on similar proteins. The number and distribution of the nonpolar and charged groups on the protein's surface probably are the major determinants of the protein contribution to the solvent-protein interaction. The large temperature dependence of the rates of protein unfolding and refolding can be beneficially utilized in cryoprotectant studies of living cells.     

Modeling Hydration Water and its Role in Polymer Folding

The hydrophobic effect is the dominant force which drives a proteintowards its native state, but its physics has not been thoroughlyunderstood yet. We introduce an exactly solvable model of the solvation ofnon-polar molecules in water, which shows that the reduced number ofallowed configurations of water molecules when the solute is present isenough to give rise to hydrophobic behaviour. We apply our model to anon-polar homopolymer in aqueous solution, obtaining a clear evidence ofboth `cold' and `warm' collapse transitions that recall those of proteins.Finally we show how the model can be adapted to describe the solvation ofaromatic and polar molecules.     

Some ways of looking at compensatory kosmotropes and different water environments

Hydration of macromolecular structures determines biological activity. Stabilizing solutes are kosmotropic (increase order of water) rather than chaotropic (decrease order). Preferential hydration of surfaces is a thermodynamic consequence of the solution behavior of kosmotropic solutes, but inconsistencies imply interactions such as the hydration of specific sites within macromolecules. Thermodynamic measures require bulk pure solutes; here simpler measures of the effects on bulk water, water at surfaces and hydration water of probes have been applied to solutes including natural stabilizers, analogues and example chaotropes. Changes in the near-infrared spectra, water proton NMR chemical shifts and relaxation times measure changes in the bulk liquid; HPLC-column retention of solutes indicate interactions with hydration water at different surfaces, and fluorescence probes detect effects on functional group hydration water. Ab initio calculations and Monte-Carlo simulations of the solutes in water measure the energetics of the solute-water interactions, the dipole moments of these molecules, their charge distributions and the effect of the solute molecules on the structure of water. The rankings of the test solutes by these measures are not consistent. Thus, stabilizing solutes are not interchangeable in biological systems and the intracellular replacement of one by another could affect the integration of cell metabolism.     

Hydration and Hydrodynamic Interactions of Lysozyme: Effects of Chaotropic versus Kosmotropic Ions

Using static and dynamic light scattering we have investigated the effects of either strongly chaotropic, nearly neutral or strongly kosmotropic salt ions on the hydration shell and the mutual hydrodynamic interactions of the protein lysozyme under conditions supportive of protein crystallization. After accounting for the effects of protein interaction and for changes in solution viscosity on protein diffusivity, protein hydrodynamic radii were determined with ±0.25 Å resolution. No changes to the extent of lysozyme hydration were discernible for all salt-types, at any salt concentration and for temperatures between 15-40°C. Combining static with dynamic light scattering, we also investigated salt-induced changes to the hydrodynamic protein interactions. With increased salt concentration, hydrodynamic interactions changed from attractive to repulsive, i.e., in exact opposition to salt-induced changes in direct protein interactions. This anti-correlation was independent of solution temperature or salt identity. Although salt-specific effects on direct protein interactions were prominent, neither protein hydration nor solvent-mediated hydrodynamic interactions displayed any obvious salt-specific effects. We infer that the protein hydration shell is more resistant than bulk water to changes in its local structure by either chaotropic or kosmotropic ions.     

Thermodynamic stability of ribonuclease A in alkylurea solutions and preferential solvation changes accompanying its thermal denaturation: a calorimetric and spectroscopic study

The effect of methylurea, N,N'-dimethylurea, ethylurea, and butylurea as well as guanidine hydrochloride (GuHCl), urea and pH on the thermal stability, structural properties, and preferential solvation changes accompanying the thermal unfolding of ribonuclease A (RNase A) has been investigated by differential scanning calorimetry (DSC), UV, and circular dichroism (CD) spectroscopy. The results show that the thermal stability of RNase A decreases with increasing concentration of denaturants and the size of the hydrophobic group substituted on the urea molecule. From CD measurements in the near- and far-UV range, it has been observed that the tertiary structure of RNase A melts at about 3 degrees C lower temperature than its secondary structure, which means that the hierarchy in structural building blocks exists for RNase A even at conditions at which according to DSC and UV measurements the RNase A unfolding can be interpreted in terms of a two-state approximation. The far-UV CD spectra also show that the final denatured states of RNase A at high temperatures in the presence of different denaturants including 4.5 M GuHCl are similar to each other but different from the one obtained in 4.5 M GuHCl at 25 degrees C. The concentration dependence of the preferential solvation change delta r23, expressed as the number of cosolvent molecules entering or leaving the solvation shell of the protein upon denaturation and calculated from DSC data, shows the same relative denaturation efficiency of alkylureas as other methods.     

Non-polar solutes in water and in aqueous solutions of protein denaturants. Modeling of solution and transfer processes

A simple molecular model for the thermodynamic behavior of non-polar solutes in water and in aqueous solutions of protein denaturants is presented. Three contributions are considered: (i) combinatorial arising from the mixing process, (ii) interactional characterizing the molecular interactions occurring in the mixture and (iii) a contribution originating from the structural changes occurring in the first shell of water molecules around the solute. The latter is modeled assuming that water molecules in contact with the solute are involved in a chemical equilibrium between two states. The model describes well the temperature and denaturant concentration dependences of the Gibbs energies of solution and transfer for benzene, toluene and alkanes in water and aqueous solutions of urea and guanidine hydrochloride. Model parameters are physically meaningful, allowing a discussion of the molecular interactions involved. A preferential solvation of the solute by the denaturant is found. However, the non-polar solute-denaturant interaction is not specific, i.e. leading to a distinct chemical entity. Urea and guanidine hydrochloride are non-polar solubilizing agents because their interactions with the solute are less unfavorable than those between water and the solute.     

Solvational tuning of the unfolding, aggregation and amyloidogenesis of insulin

Solvational perturbations, accomplished by the addition of the three model cosolvents glycerol, ethanol and trifluoroethanol, exert pronounced and diversified effects on the unfolding, non-native assembly and fibril formation of the amyloidogenic protein insulin. Fluorescence, CD and UV-spectroscopic methods as well as atomic force microscopy imaging have been employed to reveal distinct structural and kinetic features upon the aggregation of insulin under different solvational perturbations, which ultimately manifest in morphological variations of mature aggregates and fibrils. In particular, fluorescence anisotropy studies proved to be very valuable in characterizing the corresponding aggregation nuclei. Glycerol stabilizes, through enhanced hydration, native oligomerization and retards fibrillar aggregation at all concentrations studied (up to 40% (w/w)). In contrast, both monoalcohols facilitate the formation of aggregation-prone intermediates by destabilization of the native assembly. The reversal from a kosmotropic to a merely chaotropic solvational behaviour can explain the accelerating effect on ordered fibrillation of low concentrations and the inhibitory nature of high concentrations of ethanol and trifluoroethanol, ultimately leading to amorphous aggregate structures. Mechanistically, dimer dissociation under stabilizing and nucleation under destabilizing conditions have been identified to be the rate-limiting steps that account for the non-monotonic concentration effects of the monoalcohols on the aggregation kinetics. A rationale as to how solvational constraints can tune the stability of the species on the native self-assembly and non-native aggregation pathway, and the energetic barriers that need to be overcome for the required structural interconversions has been put forward. We may propose that the concept of perturbed solvation is generally applicable to phenomena that are related to pathogenic amyloidogenesis of proteins and, in general, solvational effects, besides other aspects of the cellular environment, may play a significant role in a reshaping of the folding/aggregation funnel of proteins.     

Solvent viscosity effects on protein dynamics studied by ultrasonic absorption

Solvent viscosity is known to play an important role in the kinetics of biochemical reactions, and has been suggested to modulate the dynamic structure of proteins. The effect of viscous cosolvents, of various molecular sizes, on the apparent ultrasonic absorption of bovine serum albumin in solution, at 37 degrees, has been measured in attempt to investigate the following phenomena: 1) The predicted modulating effect of viscous cosolvents on the "internal friction" of proteins, and 2) Possible differences between the microscopic and macroscopic pictures of the solvent viscosity concerning the proposed effect. We have found that A) The absorption of ultrasound (3-17 MHz) by the protein increases with increasing the cosolvent concentration. B) That increase correlates with the solvent viscosity for small cosolvent molecules, but not with macromolecular cosolvents, and C) Dextran solutions with the same concentration by weight, reveal similar ultrasonic absorption, in spite of large differences in their viscosity. A possible explanation is discussed.     

Effect of ions and other compatible solutes on enzyme activity, and its implication for biocatalysis using ionic liquids

The effect of ions on enzyme activity and stability usually follows the Hofmeister series (or the kosmotropicity order): kosmotropic anions and chaotropic cations stabilize enzymes while chaotropic anions and kosmotropic cations destabilize them. The effect of ionic liquids (ILs) on the enzyme activity/stability/enantioselectivity is complicated especially when there is no or little water presence in the IL media. However, when aqueous solutions of hydrophilic ILs are employed as reaction media, the enzyme seems to follow the Hofmeister series since ILs dissociate into individual ions in water.     

Cosolvent effects on gel-entrapped oxidoreductase: the glucose oxidase model

An intrinsic problem often involved in biotransformations carried out by immobilized cells is the poor solubility of substrate and product in water. Increase in hydrophobic substrate availability to such gel-entrapped cells may be attained by the replacement of a fraction of the aqueous medium by water-miscible solvents (cosolvents). The introduction of cosolvents results in increased solubility, but may simultaneously affect enzymic activity and stability. Recently, criteria and guidelines for cosolvent selection on the basis of its effect on intracellular enzyme stability were reported (Freeman, A., and Lilly, M.D. (1987) Appl. Microbiol. Biotechnol. 25, 495-501). In order to understand the impact of the preferable or unsuitable cosolvents on enzyme kinetics and stability, the effects of 1-5 M concentrations of a series of cosolvents (e.g., ethylene glycol, dimethylsulfoxide, N,N-dimethylformamide, ethanol) on a well-characterized, highly specific enzyme model (glucose oxidase) were investigated. The presence of 1-5 M of the cosolvents studied imposed 10-50% reduction in Vmax of the enzyme, but Km was only mildly affected (+/- 25%). This inhibition was attributed to cosolvent effect on small, reversible, conformational changes in the enzyme native structure. Determination of the rate constant of thermal inactivation (at 55 degrees C) of glucose oxidase, in the presence of cosolvents, was employed for the quantitative evaluation of cosolvent effect on enzyme stability. A clear pattern of cosolvent preference in respect to its denaturing effect was obtained, which was identical to the pattern previously observed in a study of oxidoreductases operating from within a whole cell. In both cases diols (e.g., ethylene glycol) were found to be the preferable group of cosolvents. Our results indicate that a soluble enzyme and an intracellular enzyme operating from a whole cell are affected by cosolvents via the same mechanism.     

Preferential interactions of proteins with solvent components in aqueous amino acid solutions

The preferential interactions of proteins with solvent components in concentrated amino acid solutions were measured by high-precision densimetry. Bovine serum albumin and lysozyme were preferentially hydrated in all of the amino acids examined, glycine, α- and β-alanine, and betaine i.e., addition of these amino acids resulted in an unfavorable free energy change. It was shown that, for the former three amino acids, known to have a positive surface tension increment, their perturbation of the surface free energy of water is consistent with their preferential exclusion from the protein surface. In the case of betaine, which does not increase the surface tension of water, preferential exclusion from protein surface must reflect the chemical structure of this cosolvent, which is considerably more hydrophobic than that of the other three amino acids.     

Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein

Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO₄ and NaF salts to the solution. The process is separated into two parts. In the first, ‘promotion’ phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, ‘rearrangement’ phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins’s rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.     

Formation of α-synuclein aggregates in aqueous ethylammonium nitrate solutions

The effect of adding ethylammonium nitrate (EAN), which is an ionic liquid (IL), on the aggregate formation of α-synuclein (α-Syn) in aqueous solution has been investigated. FTIR and Raman spectroscopy were used to investigate changes in the secondary structure of α-Syn and in the states of water molecules and EAN. The results presented here show that the addition of EAN to α-Syn causes the formation of an intermolecular β-sheet structure in the following manner: native disordered state → polyproline II (PPII)-helix → intermolecular β-sheet (α-Syn amyloid-like aggregates: α-SynA). Although cations and anions of EAN play roles in masking the charged side chains and PPII-helix-forming ability involved in the formation of α-SynA, water molecules are not directly related to its formation. We conclude that EAN-induced α-Syn amyloid-like aggregates form at hydrophobic associations in the middle of the molecules after masking the charged side chains at the N- and C-terminals of α-Syn.     

Simulation of peptide folding with explicit water--a mean solvation method

A new approach to efficiently calculate solvent effect in computer simulation of macromolecular systems has been developed. Explicit solvent molecules are included in the simulation to provide a mean solvation force for the solute conformational search. Simulations of an alanine dipeptide in aqueous solution showed that the new approach is significantly more efficient than conventional molecular dynamics method in conformational search, mainly because the mean solvation force reduced the solvent damping effect. This approach allows the solute and solvent to be simulated separately with different methods. For the macromolecule, the rigid fragment constraint dynamics method we developed previously allows large time-steps. For the solvent, a combination of a modified force-bias Monte Carlo method and a preferential sampling can efficiently sample the conformational space. A folding simulation of a 16-residue peptide in water showed high efficiency of the new approach.     

Effective interactions between chaotropic agents and proteins

Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. In this work, we represent the chaotropic agent as a factor that reduces the amount of order in the structures formed by water molecules, both in the bulk and the hydration shells around hydrophobic amino acids. In this framework we show that low chaotrope concentrations lead to a destabilization of the native state of proteins, and that high concentrations induce complete denaturation. We also find that the reduction of the number of bulk ordered states of water molecules can give origin to an effective interaction between chaotropic molecules and proteins.