Probing protein-sugar interactions

We have investigated the partial specific volumes (2) (ml/g), hydration, and cosolvent interactions of rabbit muscle aldolase by equilibrium sedimentation in the analytical ultracentrifuge and by direct density increment (partial differential/partial differentialc(2))(mu) measurements over a range of sugar concentrations and temperature. In a series of sugars increasing in size, glucose, sucrose, raffinose, and alpha-cyclodextrin, (partial differential/ partial differentialc(2))(mu) decreases linearly with the solvent density rho(0). These sugar cosolvents do not interact with the protein; however, the interaction parameter B(1) (g water/g protein) mildly increases with increasing sugar size. The experimental B(1) values are smaller than values calculated by excluded volume (rolling ball) considerations. B(1) relates to hydration in this and in other instances studied. It decreases with increasing temperature, leading to an increase in (2) due to reduced water of hydration electrostriction. The density increments (partial differential/ partial differentialc(2))(mu), however, decrease in concave up form in the case of glycerol and in concave down form for trehalose, leading to more complex behavior in the case of carbohydrates playing a biological role as osmolytes and antifreeze agents. A critical discussion, based on the thermodynamics of multicomponent solutions, is presented.     

Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models

The structural stability and preference of a protein are highly sensitive to the environment accommodating it. In this work, the solvation effect on the structure and folding dynamics of a small peptide, NS4B H2, was studied by computer simulation. The native structure of NS4B H2 was solved previously in 50 % v/v water/2,2,2-trifluoroethanol (TFE) mixed solvent. In this work, both pure water and water/TFE cosolvent were utilized. The force field parameters for water were taken from the TIP3P water model, and those for TFE were generated following the routine of the general AMBER force field (GAFF). The simulated structure of NS4B H2 in the mixed solvent is quite in line with experimental data, while in pure water it undergoes a large structural deformation. The generalized Born (GB) model was also investigated by tuning the dielectric constant to match experimental measurements. However, the results show that its performance was less satisfactory. Two independent direct folding simulations of NS4B H2 in explicit water/TFE cosolvent were carried out, both of which resulted in successful folding. Investigation of the distribution of solvent molecules around the peptide indicates that folding is triggered by the aggregation of TFE on the peptide surface.     

Solvent modulation in hydrophobic interaction chromatography

Solvents play a critical role in hydrophobic interaction chromatography (HIC), since the separation of proteins by HIC is based on the hydrophobicity of the proteins presented to the solvents. This review first describes the solvent properties which determine the effect of cosolvents on the binding and elution of proteins in HIC; i.e., the protein solvent interactions and the surface tension of water/cosolvent mixture. Second are presented the various cosolvents which have been tested as facilitating binding or elution of the proteins. Last, some examples of solvent manipulation which resolved complex mixtures of proteins by HIC are reviewed.     

Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro

To interpret or to predict the responses of biopolymer processes in vivo and in vitro to changes in solute concentration and to coupled changes in water activity (osmotic stress), a quantitative understanding of the thermodynamic consequences of interactions of solutes and water with biopolymer surfaces is required. To this end, we report isoosmolal preferential interaction coefficients (Gamma(mu1) determined by vapor pressure osmometry (VPO) over a wide range of concentrations for interactions between native bovine serum albumin (BSA) and six small solutes. These include Escherichia coli cytoplasmic osmolytes [potassium glutamate (K(+)Glu(-)), trehalose], E. coli osmoprotectants (proline, glycine betaine), and also glycerol and trimethylamine N-oxide (TMAO). For all six solutes, Gamma(mu1) and the corresponding dialysis preferential interaction coefficient Gamma(mu1),(mu3) (both calculated from the VPO data) are negative; Gamma(mu1), (mu3) is proportional to bulk solute molality (m(bulk)3) at least up to 1 m (molal). Negative values of Gamma(mu1),(mu3) indicate preferential exclusion of these solutes from a BSA solution at dialysis equilibrium and correspond to local concentrations of these solutes in the vicinity of BSA which are lower than their bulk concentrations. Of the solutes investigated, betaine is the most excluded (Gamma(mu1),(mu3)/m(bulk)3 = -49 +/- 1 m(-1)); glycerol is the least excluded (Gamma(mu1),(mu3)/m(bulk)3 = -10 +/- 1 m(-1)). Between these extremes, the magnitude of Gamma(mu1),(mu3)/m(bulk)3 decreases in the order glycine betaine > proline >TMAO > trehalose approximately K(+)Glu(-) > glycerol. The order of exclusion of E. coli osmolytes from BSA surface correlates with their effectiveness as osmoprotectants, which increase the growth rate of E. coli at high external osmolality. For the most excluded solute (betaine), Gamma(mu1),(mu3) provides a minimum estimate of the hydration of native BSA of approximately 2.8 x 10(3) H(2)O/BSA, which corresponds to slightly less than a monolayer (estimated to be approximately 3.2 x 10(3) H(2)O). Consequently, of the solutes investigated here, only betaine might be suitable for use in osmotic stress experiments in vitro as a direct probe to quantify changes in hydration of protein surface in biopolymer processes. More generally, however, our results and analysis lead to the proposal that any of these solutes can be used to quantify changes in water-accessible surface area (ASA) in biopolymer processes once preferential interactions of the solute with biopolymer surface are properly taken into account.     

Analytical ultracentrifugation in a Gibbsian perspective

The analytical ultracentrifuge has come into new intensive use following complete instrumental redesign and the use of advanced computer technologies for the analysis and interpretation of experimental results. Major attention is now devoted to the evaluation of interactions between similar and dissimilar biological macromolecules in dilute and concentrated systems. Electrostatically charged biological solute systems additionally comprise low molecular weight charged and non-charged cosolvents. Solvent/cosolvent interactions, insufficiently considered in most current analytical ultracentrifugation analyses, may quantitatively affect solute/solute interactions. For comprehensive analysis the Svedberg derivation considering a buoyant molar mass (1 - rho0 partial specific volume)M2 and valid at vanishing solute concentration for strictly two component systems only, should be replaced, following classical thermodynamic analysis, by the ratio (delta rho/delta c2)(mu)/d pi/dc2 of the density increment at constant chemical potential of diffusible cosolvents, to the derivative of the osmotic pressure with solute concentration. Disregard of the solvent/cosolvent and solute/cosolvent interactions should be avoided.     

Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin

Understanding the mechanisms of protein folding requires knowledge of both the energy landscape and the structural dynamics of a protein. We report a neutron-scattering study of the nanosecond and picosecond dynamics of native and the denatured alpha-lactalbumin. The quasielastic scattering intensity shows that there are alpha-helical structure and tertiary-like side-chain interactions fluctuating on sub-nanosecond time-scales under extremely denaturing conditions and even in the absence of disulfide bonds. Based on the length-scale dependence of the decay rate of the measured correlation functions, the nanosecond dynamics of the native and the variously denatured proteins have three dynamic regimes. When 0.051.0 A(-1) is a regime that displays the local dynamic behavior of individual residues, Gamma proportional to Q(1.8+/-0.3). The picosecond time-scale dynamics shows that the potential barrier to side-chain proton jump motion is reduced in the molten globule and in the denatured proteins when compared to that of the native protein. Our results provide a dynamic view of the native-like topology established in the early stages of protein folding.     

A theoretical investigation of the interactions between hydroxyl-functionalized ionic liquid and water/methanol/dimethyl sulfoxide

Density functional calculations have been used to investigate the interactions of 1-(2-hydroxyethyl)-3-methylimidazolium ([C₂OHmim]⁺)-based ionic liquids (hydroxyl ILs) with water (H₂O), methanol (CH₃OH), and dimethyl sulfoxide (DMSO). It was found that the cosolvent molecules interact with the anion and cation of each ionic liquid through different atoms, i.e., H and O atoms, respectively. The interactions between the cosolvent molecules and 1-ethyl-3-methylimizolium ([C₂mim]⁺)-based ionic liquids (nonhydroxyl ILs) were also studied for comparison. In the cosolvent–[nonhydroxyl ILs] systems, a furcated H-bond was formed between the O atom of the cosolvent molecule and the C2-H and C6-H, while there were always H-bonds involving the OH group of the cation in the cosolvent–[hydroxyl ILs] systems. Introducing an OH group on the ethyl side of the imidazolium ring may change the order of solubility of the molecular liquids.     

A contribution to the theory of preferential interaction coefficients

A simple and complete derivation of the relation between concentration-based preferential interaction coefficients and integrals over the relevant pair correlation functions is presented for the first time. Certain omissions from the original treatment of pair correlation functions in multicomponent thermodynamics are also addressed. Connections between these concentration-based quantities and the more common molality-based preferential interaction coefficients are also derived. The pair correlation functions and preferential interaction coefficients of both solvent (water) and cosolvent (osmolyte) in the neighborhood of a macromolecule contain contributions from short-range repulsions and generic long-range attractions originating from the macromolecule, as well as from osmolyte-solvent exchange reactions beyond the macromolecular surface. These contributions are evaluated via a heuristic analysis that leads to simple insightful expressions for the preferential interaction coefficients in terms of the volumes excluded to the centers of the water and osmolyte molecules and a sum over the contributions of exchanging sites in the surrounding solution. The preferential interaction coefficients are predicted to exhibit the experimentally observed dependence on osmolyte concentration. Molality-based preferential interaction coefficients that were reported for seven different osmolytes interacting with bovine serum albumin are analyzed using the this formulation together with geometrical parameters reckoned from the crystal structure of human serum albumin. In all cases, the excluded volume contribution, which is the volume excluded to osmolyte centers minus that excluded to water centers in units of V1, exceeds in magnitude the contribution of the exchange reactions. Under the assumption that the exchange contribution is dominated by sites in the first surface-contiguous layer, the ratio of the average exchange constant to its neutral random value is determined for each osmolyte. These ratios all lie in the range 1.0 +/- 0.15, which indicates rather slight deviations from random occupation near the macromolecular surface. Finally, a mechanism is proposed whereby the chemical identity of an osmolyte might be concealed from partially ordered multilayers of water in clefts, grooves, and pits, and its consequences are noted.     

Bioreduction of a carbon–nitrogen double bond using immobilized baker's yeast’a first report

Immobilized baker's yeast entrapped in calcium alginate beads efficiently reduces N-benzylidinemethylamine to N-methylbenzylamine in hexane at 37°C and tetrahydrofuran (THF) at 30°C in the presence of 18-crown-6, while in the presence of water as cosolvent and glucose as an additive N-benzylidinemethylamine undergoes decomposition. Benzaldoxime in a hexane–water (1:9) solvent system containing glucose as an additive is reduced to N-benzylhydroxylamine. On using an ethanol–water (1:1) solvent system, benzaldoxime is converted to benzyl alcohol and in hexane, benzene, THF, hexane–water (1:1) or acetonitrile–water (1:1) solvent systems, or using dried baker's yeast in different solvent systems, transformation of benzaldoxime does not occur.     

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 cosolvents on the adsorption of peptides at the solid-liquid interface

The adsorption of a peptide at solid surfaces is the result of a complex interplay of interactions between the peptide, solvent, and surface. In this work, Monte Carlo simulations were performed to evaluate the effect of the solvent hydrogen bonding ability on the adsorption of the peptide ASP(1)-ASP(2)-ILE(3)-ILE(4)-ASP(5)-ASP(6)-ILE(7)-ILE(8) at a charged surface consisting of CH(2) atoms with a fixed lattice arrangement. Various water-alcohol mixtures were used as solvent because alcohols are known to alter the dielectric constant, hydrophobicity, and hydrogen bonding capacity of water. Solvent-solvent, solvent-surface, solvent-peptide, and peptide-surface interactions were studied independently and correlated with the observed peptide behavior at the solvent-surface interface. We concluded that the behavior (and orientation) of the peptide at the surface is directly related to changes in water-water hydrogen bonding properties in water-alcohol mixtures. In the presence of increasing concentrations of methanol, the strength of solvent-peptide and solvent-surface interactions was reduced, and as a result, a stronger interaction between the peptide and the surface was observed. Stronger solvent-peptide and solvent-surface interactions were responsible for a weaker interaction of the peptide with the surface in the presence of increasing concentrations of glycerol. These results suggest that by changing solvent conditions it is possible to finely tune the orientation of a macromolecule at solid/liquid interfaces.     

Bioreduction of a carbon–nitrogen double bond using immobilized baker''s yeast’a first report

Immobilized baker's yeast entrapped in calcium alginate beads efficiently reduces N-benzylidinemethylamine to N-methylbenzylamine in hexane at 37°C and tetrahydrofuran (THF) at 30°C in the presence of 18-crown-6, while in the presence of water as cosolvent and glucose as an additive N-benzylidinemethylamine undergoes decomposition. Benzaldoxime in a hexane–water (1:9) solvent system containing glucose as an additive is reduced to N-benzylhydroxylamine. On using an ethanol–water (1:1) solvent system, benzaldoxime is converted to benzyl alcohol and in hexane, benzene, THF, hexane–water (1:1) or acetonitrile–water (1:1) solvent systems, or using dried baker's yeast in different solvent systems, transformation of benzaldoxime does not occur.     

Apoptosis supercedes necrosis in mitochondrial DNA-depleted Jurkat cells by cleavage of receptor-interacting protein and inhibition of lysosomal cathepsin

In the present study, we used mitochondrial DNA-depleted Jurkat subclones (rho0 cells) to demonstrate that Fas agonistic Ab (CH-11), at the concentrations that evoke apoptotic death of the parental Jurkat cells, induced necrosis mainly through generation of excess reactive oxygen species, lysosomal rupture, and sequential activation of cathepsins B and D, and in minor part through activation of receptor-interacting protein (RIP). In the rho0 cells treated with CH-11, ATP supplementation converted necrosis into apoptosis by the formation of the apoptosome and subsequent activation of procaspase-3. In these ATP-supplemented rho0 cells (ATP-rho0), generation of excess ROS and lysosomal rupture were still seen, yet cathepsins B and D were inactivated and RIP was degraded. The conversion of necrosis to apoptosis, RIP degradation, and cathepsin inactivation in ATP- rho0 cells were blocked by caspase-3 inhibitors. Activities of cathepsins B and D in the lysate of necrotic rho0 cells were inhibited by the addition of apoptotic parental Jurkat cell lysate. Thus, apoptosis may supercede necrosis.     

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.     

Microenvironmental control of enantiodifferentiating photocyclization of 5-hydroxy-1,1-diphenylpentene through selective solvation

For mechanistic elucidation of the photosensitized cyclization of 5-hydroxy-1,1-diphenylpentene (1), its methyl ether (4) was synthesized as an unreactive "dummy" substrate and used as a quencher of the sensitizer fluorescence to reveal the intervention of an exciplex intermediate that was unable to detect when reactive substrate 1 was used as a quencher/reactant In the enantiodifferentiating photocyclization of 1 to 2-(diphenylmethyl)tetrahydrofuran (2) sensitized by a chiral saccharide ester of 1,4-naphthalenedicarboxylate (3), the enantiomeric excess (ee) of chiral product 2 obtained in methylcyclohexane (MCH) at 25 °C was significantly enhanced from 20% to 35% upon 10-fold dilution of the sample solution by MCH, for which the reduced solvent polarity, discouraging dissociation of the intervening radical ionic exciplex, is likely to be responsible. Further attempts to microenvironmentally control the photochirogenic reaction and enhance the product's ee through selective solvation of polar cosolvent to the diastereomeric exciplex pair in nonpolar solvent were not successful probably due to the inherently high local polarity around the exciplex of saccharide-appended 3 with alcoholic substrate 1.