Effects of hydrated water on protein unfolding

The conformational stability of a protein in aqueous solution is described in terms of the thermodynamic properties such as unfolding Gibbs free energy, which is the difference in the free energy (Gibbs function) between the native and random conformations in solution. The properties are composed of two contributions, one from enthalpy due to intramolecular interactions among constituent atoms and chain entropy of the backbone and side chains, and the other from the hydrated water around a protein molecule. The hydration free energy and enthalpy at a given temperature for a protein of known three-dimensional structure can be calculated from the accessible surface areas of constituent atoms according to a method developed recently. Since the hydration free energy and enthalpy for random conformations are computed from those for an extended conformation, the thermodynamic properties of unfolding are evaluated quantitatively. The evaluated hydration properties for proteins of known transition temperature (Tm) and unfolding enthalpy (delta Hm) show an approximately linear dependence on the number of constituent heavy atoms. Since the unfolding free energy is zero at Tm, the enthalpy originating from interatomic interactions of a polypeptide chain and the chain entropy are evaluated from an experimental value of delta Hm and computed properties due to the hydrated water around the molecule at Tm. The chain enthalpy and entropy thus estimated are largely compensated by the hydration enthalpy and entropy, respectively, making the unfolding free energy and enthalpy relatively small. The computed temperature dependences of the unfolding free energy and enthalpy for RNase A, T4 lysozyme, and myoglobin showed a good agreement with the experimental ones.(ABSTRACT TRUNCATED AT 250 WORDS)     

Modelling the microenvironment of a lipase immobilized in polyurethane foams

The effects of partition of substrates and product on the modelling of the microenvironment of an immobilized lipase were evaluated using Response Surface Methodology. The esterification of butyric acid with ethanol in n-hexane, catalyzed by Candida rugosa lipase immobilized in two biocompatible and relatively hydrophilic polyurethane foams (“Hypol FHP 2002™” and “Hypol FHP 5000™”) was used as the model system. For each set of initial conditions, the final concentration of substrates and ethyl butyrate in the microenvironment, at equilibrium, Cmicro, were estimated by mass balancing bulk and foams. The Cmicro values obtained were used to estimate the corresponding partition coefficients of ethanol (P_EtOH), butyric acid (P_BA) and ester (P_EB), between the foams (microenvironment) and the bulk medium. Foams containing previously inactivated lipase, as well as lipase-free foams were used. For both substrates, Cmicro values were, in the majority of the experiments, higher than their macroenvironmental counterparts. The lowest Cmicro values were observed with the less hydrophilic foam (“FHP 5000”). A decrease of Cmicro_EtOH in both foams and Cmicro_BA in “FHP 5000” foams, was obtained upon lipase immobilization. P_EB values were, in all cases, close to zero. This is beneficial in terms of the shift in reaction equilibrium, product recovery and alleviation of product inhibition effects.     

Association of the minor groove binding drug Hoechst 33258 with d(CGCGAATTCGCG)2: volumetric, calorimetric, and spectroscopic characterizations

We employed ultrasonic velocimetry, high-precision densimetry, circular dichroism and fluorescence spectroscopy, and isothermal titration calorimetry to characterize the binding of Hoechst 33258 to the d(CGCGAATTCGCG)(2) oligomeric duplex at 25 degrees C. We used this experimental combination to determine the full thermodynamic profile for the binding of Hoechst 33258 to the DNA. Specifically, we report changes in binding free energy, enthalpy, entropy, volume, and adiabatic compressibility accompanying the binding. We interpret our volumetric data in terms of hydration and evaluate the number of waters of hydration that become released to or taken up from the bulk. Our calorimetric data reveal that the drug-DNA binding event studied in this work is entropy-driven and proceeds with an unfavorable change in enthalpy. The favorable binding entropy predominantly results from hydration changes. In contrast to a large and positive change in hydrational entropy, the binding-induced change in configurational entropy is insignificant. The latter observation is consistent with the "lock-and-key" mode of minor groove binding.     

Thermodynamic changes in the binding of Ca2+ to a mutant human lysozyme (D86/92). Enthalpy-entropy compensation observed upon Ca2+ binding to proteins.

The thermodynamic change in the binding of Ca2+ to a mutant human lysozyme having an engineered Ca2+ binding site (Kuroki, R., Taniyama, Y., Seko, C., Nakamura, H., Kikuchi, M., and Ikehara, M. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 6903-6907) was analyzed by calorimetry and interpreted in terms of structural information obtained from x-ray crystallography. It was found that the enthalpic contribution for the Ca2+ binding reaction was small, driven primarily by entropy release (10 kcal/mol). This release of entropy was also observed in some organic chelators. Moreover, through the information of the tertiary structures of the apo- and holomutant lysozyme, it was confirmed that the entropy release (10 kcal/mol) upon the binding of Ca2+ arises primarily from the release of bound water molecules hydrating the free Ca2+. Previous studies of Ca2+ binding to proteins have involved significant changes in protein conformation. They can now be reevaluated to determine the contribution of conformational changes to Ca2+ binding. After removing the thermodynamic contribution of Ca2+ binding itself, it is found that upon the binding of Ca2+ the enthalpy change is negative but is almost compensated by the negative entropy change. The negative change in both enthalpy and entropy is characteristic of values seen in the thermodynamic change upon the folding of proteins.     

Arguments against the significance of the Fenton reaction contributing to signal pathways under in vivo conditions

One of the common explanations for oxidative stress in the physiological milieu is based on the Fenton reaction, i.e. the assumption that radical chain reactions are initiated by metal-catalyzed electron transfer to hydrogen peroxide yielding hydroxyl radicals. On the other hand — especially in the context of so-called “iron switches” — it is postulated that cellular signaling pathways originate from the interaction of reduced iron with hydrogen peroxide.

Using fluorescence detection and EPR for identification of radical intermediates, we determined the rate of iron complexation by physiological buffer together with the reaction rate of concomitant hydroxylations of aromatic compounds under aerobic and anaerobic conditions. With the obtained overall reaction rate of 1,700 M^-1s^-1 for the buffer-dependent reactions and the known rates for Fenton reactions, we derive estimates for the relative reaction probabilities of both processes.

As a consequence we suggest that under in vivo conditions initiation of chain reactions by hydroxyl radicals generated by the Fenton reaction is of minor importance and hence metal-dependent oxidative stress must be rather independent of the so-called “peroxide tone”. Furthermore, it is proposed that — in the low (subtoxic) concentration range — hydroxylated compounds derived from reactions of “non-free” (crypto) OH radicals are better candidates for iron-dependent sensing of redox-states and for explaining the origin of cellular signals than the generation of “free” hydroxyl radicals.     

A differential vapor-pressure equipment for investigations of biopolymer interactions

The design and performance of an equipment for the measurement of vapor pressures over liquid or solid samples is presented. The equilibrium pressure difference, ΔP, between a sample and a reference of known vapor pressure is recorded as a function of composition and/or temperature. Through the use of high-accuracy capacitance manometers and a leak-tight system of stainless steel pipes, below-sealed valves and metal-gasket fittings, ΔP can be measured with a resolution of about 0.5 μbar (0.05 Pa) in some applications. This sensitivity level, along with other features of the equipment, particularly a “gas-phase titration” routine for changing the cell composition, makes it effective for the investigations of several types of biopolymer interactions. These include isothermal studies of net affinities such as the adsorption of water to proteins or membranes, the preferential interaction of biopolymers with the components of a mixed solvent, the partitioning of solutes between a membrane and the aqueous bulk and the weak, specific binding of ligands to macromolecules. Furthermore, a temperature-scanning mode allows real-time elucidation of such interactions at thermally induced conformational changes in biopolymers. Selected examples of these applications are presented and discussed.     

Detectability and criterion measures in temporal generalization

Computer simulation of performance on “normal” and “episodic” temporal generalization tasks was used to examine the relations between the theoretical parameters of models which fit temporal generalization data (“timing sensitivity” and “threshold”), and the d′ (detectability) and beta (decision criterion) measures of signal-detection theory. In general, changes in timing sensitivity altered d′, whereas threshold changes affected beta, supporting the assertion that the two sorts of variables (“sensitivity/detectability” and “threshold/criterion”) were psychologically equivalent. Cases where temporal generalization gradients were apparently contaminated by “random responding” could be treated by changes in beta, but cases in which temporal generalization gradients were not peaked at the standard posed severe problems for a simple signal-detection account, although existing models of temporal generalization performance could deal with them.     

Molecular Dynamics Free Energy Calculations to Assess the Possibility of Water Existence in Protein Nonpolar Cavities

Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1β, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of four protein nonpolar cavities by means of the molecular dynamics thermodynamic integration method. In addition to the IL-1β cavity (69 ų), we selected the three largest nonpolar cavities of AvrPphB (81 ų), Trp repressor (87 ų), and hemoglobin (108 ų) from the structural database, in view of the simulation result from another study that showed larger nonpolar cavities are more likely to be hydrated. The calculations were performed with flexible and rigid protein models. The calculated free energy changes were all positive; hydration of the nonpolar cavities was energetically unfavorable for all four cases. Because hydration of smaller cavities should happen more rarely, we conclude that existing protein nonpolar cavities are not likely to be hydrated. Although a possibility remains for much larger nonpolar cavities, such cases are not found experimentally. We present a hypothesis to explain this: hydrated nonpolar cavities are quite unstable and the conformation could not be maintained.     

Thermodynamic properties of globular proteins and the principle of stabilization of their native structure

A semi-empirical method has been used to estimate the thermodynamic parameters of hydration of buried surface areas of ribonuclease S, lysozyme and myoglobin from the model of complete unfolding according to Ooi et al. ((1987) Proc. Natl. Acad. Sci. USA 84, 3086-3090). The buried surface area of proteins is considered as the difference between the accessible surface area of native protein and the completely extended polypeptide chain according to Lee and Richards ((1971) J. Mol. Biol. 55, 379-400). The contributions of nonpolar and polar protein groups to the general value of Gibbs energy, enthalpy, entropy and heat capacity of hydration have been determined. The obtained results on the thermodynamic behavior of proteins in the process of complete unfolding are in good agreement with the results of microcalorimetric studies of thermal denaturation.     

Energetics of interactions of aromatic hydrocarbons with water

The thermodynamics of transfer of aromatic (benzene, toluene) and aliphatic (ethane, propane, butane) hydrocarbons from the gas phase into water in the temperature range 5–125°C have been analyzed in order to determine the net hydration effect of these compounds. In the case of the aromatic hydrocarbons the enthalpic contribution predominates over the entropic contribution to the Gibbs energy of hydration. This results in a negative value of the hydration Gibbs energy of aromatic hydrocarbons, in contrast to the positive Gibbs energy of hydration of aliphatic hydrocarbons. The different sign of the hydration Gibbs energies indicates that the mechanism causing hydrophobicity of aromatic hydrocarbons has different nature than that causing the hydrophobicity of aliphatic hydrocarbons. The comparison of hydration of aliphatic and aromatic hydrocarbons leads to the following thermodynamic parameters for these additional interactions between the benzene ring and water at 25°C: enthalpy −5.4 kJ/mol, entropy 26.8 J/K mol and Gibbs energy −13.4 kJ/mol. The large enthalpic contribution to the Gibbs energy of hydration of aromatic hydrocarbons probably comes from the ability of the aromatic ring to accept hydrogens from water, forming hydrogen bonds.     

Fluorescence characteristics of lyophilized maize chloroplasts suspended in buffer

Fluorescence transients were measured in lyophilized maize chloroplasts (suspended in Tris-maleate buffer (pH 6.6)) after extraction with heptane. (The fluorescence characteristics before extraction were qualitatively similar to those in the fresh chloroplasts.) The initial fluorescence level (m) in the (dry) heptane-extracted sample remained the same as in the unextracted material, but the variable fluorescence (Δm) was drastically diminished. A portion of variable fluorescence, however, could be restored by adding Na₂S₂O₄. If the heptane extraction was made in the presence of water (wet), the m level was almost as high as (or higher than) the final level (M) of the unextracted sample, and Δm was reduced. The “jet” of O₂ (that measures the pool size of the intersystem intermediate A) and the “microjet” (that measures the pool size of the reaction center complex E), present in the unextracted samples, were absent in both types of extracted samples. Some of the above data may be interpreted in a hypothesis in which two quenchers (Q₁ and Q₂) control the fluorescence (O → P) of chloroplasts — the reduction of Q₁ being responsible for the rapid and that of Q₂ for the slow fluorescence rise.     

Characterisation of sorbed water molecules on neutral and ionic polysaccharides

Ionic and neutral polysaccharides with well-defined structures were chosen to investigate the mechanism of water sorption at different relative humidities. From an experimental point of view, the freezing water was determined by DSC when the total sorbed water was obtained from thermogravimetry. The isotherms of sorption and enthalpies of interaction were determined using the combination of a microbalance and a microcalorimeter. It is shown that freezing water appears for P/P₀ > 0.85 especially with the neutral polymers. The differential molar enthalpy of interaction is higher for P/P₀ < 0.85 corresponding to the fixation of two water molecules forming double H-bonds; this result is confirmed by molecular modelling; saturation is obtained experimentally for 4 water molecules interacting per glucose unit. On ionic polymers, the water retention increases especially over P/P₀ 0.8 and the enthalpy of interaction is higher for the first water molecules sorbed. For P/P₀ 0.8, the numbers of bound water molecules found are 2 per glucopyranosyl unit for neutral polysaccharides, 5 for glucuronan and 9–10 for carboxymethylcellulose (CMC) of D = 2 and hyaluronan (HA)     

Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description

A strain of Cochliopodium isolated from grassland soil at Sourhope Research Station (Scotland, UK) was found to be identical to the strain “Cochliopodium sp.2” studied by Bark in 1973. We name it Cochliopodium barki. It belongs to a group of species (comprising also C. minus and Cochliopodium sp. “NYS strain”) with very similar scale pattern.     

Thermodynamic functions of biopolymer hydration. II. Enthalpy–entropy compensation in hydrophilic hydration processes

The thermodynamic functions of biopolymer hydration were investigated by multitemperature vapor pressure studies. Desorption measurements were performed that allowed determination of reversible isotherms in the hydration range of 0.1 to 0.3–0.5 g H₂O/g dry polymer. These isotherms are accessible to thermodynamic interpretation and are relevant to the interaction of water with biopolymers in their solution conformation. The results obtained on a series of different biopolymers (lysozyme, α-chymotrypsin, apo-lactoferrin, and desoxyribonucleic acid), show the following common features of interest: (1) The differential excess enthalpies (ΔH^e ) and entropies (ΔS^e ) are negative, and exhibit pronounced anomalies in a well-defined low-humidity range (approx. 0.1 g H₂O/g dry polymer). These initial extrema are interpretable by structural changes, induced in the native biopolymer structures by water removal below a critical degree of hydration. (2) The ΔH^e and ΔS^e terms exhibit statistically significant linear enthalpy–entropy compensation effects in all biopolymer–water systems investigated. The compensation temperatures \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta = \overline {\Delta H} ^e /\overline {\Delta S} ^e $\end{document} are approximately identical for all biopolymers, ranging from 360 to 500 K. The compensation effects are attributable to phase transitions of water molecules between the bulk liquid and the inner-sphere hydration shell of native biopolymers. (3) The negative excess free energies (ΔG^e ) decrease monotonically with increasing water content and are close to zero at 0.3 to 0.5 g H₂O/g polymer. This result indicates that only transitions between the bulk liquid and the inner-sphere hydration shell are associated with significant net free energy effects. The outer-sphere hydration water is thermodynamically comparable to bulk water. The importance of the proportionality factor \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta $\end{document} in the control of the free energy term is discussed.     

The Hydrophobic Effect: A New Insight from Cold Denaturation and a Two-State Water Structure

Herein we provide a new insight into the hydrophobic effect in protein folding. Our proposition explains the molecular basis of cold denaturation, and of intermediate states in heat and their absence in cold denaturation. The exposure of non-polar surface reduces the entropy and enthalpy of the system, at low and at high temperatures. At low temperatures the favorable reduction in enthalpy overcomes the unfavorable reduction in entropy, leading to cold denaturation. At high temperatures, folding/unfolding is a two-step process: in the first, the entropy gain leads to hydrophobic collapse, in the second, the reduction in enthalpy due to protein-protein interactions leads to the native state. The different entropy and enthalpy contributions to the Gibbs energy change at each step at high, and at low, temperatures can be conveniently explained by a two-state model of the water structure. The model provides a clear view of the dominant factors in protein folding and stability. Consequently, it appears to provide a microscopic view of the hydrophobic effect and is consistently linked to macroscopic thermodynamic parameters.     

Stabilization of antibody VH-domains by proteolytic selection

Single variable domains of antibodies represent the smallest antigen binding fragments but are less stable than when associated with their cognate variable domains. Here we have attempted to improve the thermodynamic stability of a model heavy chain variable domain (V_H) by “proteolytic selection” a method whereby the protease-resistance of the displayed protein is coupled to the infectivity of a filamentous bacteriophage. The gene encoding the heavy chain variable domain was taken from the anti-lysozyme antibody HyHEL-10, mutated at random by error-prone PCR, and displayed on filamentous bacteriophage by fusion between the domains of the phage p3 protein. As the entire p3 protein is required for phage infectivity, treatment of the phage library with trypsin at an elevated temperature (which leads to cleavage of p3 fusions with unfolded variable domains) selects for infectious phages bearing the more stable variable domains. After several rounds of selection, a mutant (S65G/T70S/D99N) was obtained with improved stability (T_m=58.5 °C and ΔG_25°C=6.3 kcal/mol compared to 51.6 °C and 4.2 kcal/mol for the parent domain). These mutations are conservative and the mutant domain retains the ability to pair with its cognate light chain variable domain in an Fv fragment and to mediate binding to lysozyme. Our results show that the thermodynamic stability of antibody single domains can be improved by “proteolytic selection” and this may represent a step towards making useful antibody single domains for biotechnological application.     

Relations between pigments and proteins in the photosynthetic membranes of Rhodopseudomonas spheroides

We have isolated from Rhodopseudomonas spheroides a pigment-protein complex of apparent weight 9 kdaltons that bears more than 60% of the light harvesting bacteriochlorophyll. The isolation procedure involved exposure to 1% lauryl dimethyl amine oxide (LDAO). The purified 9-kdalton fraction showed the light harvesting bacteriochlorophyll components B800 and B850, plus carotenoids. The ratio of bacteriochlorophyll to protein was 17%. This protein is probably the same as the “band 15” protein of Fraker and Kaplan. It may exist in vivo as characteristic aggregates of higher molecular weight. LDAO added to Rps. spheroides chromatophores converted the bacteriochlorophyll component B870 to a form absorbing at 770 nm but had little effect on the “B800 + B850” system, causing only a reversible shift of the 850-nm band to 845 nm. Anti-reaction center serum, added to subcellular fractions from Rps. spheroides with 1% LDAO, precipitated reaction center chromoprotein unaccompanied by light harvesting bacteriocholorophyll. Other antisera precipitated light harvesting components and left the reaction center chromophores in solution. A major protein of apparent weight 45 kdaltons was found in relatively nonpigmented fractions from Rps. spheroides, associated with cell wall fragments. The 45-kdalton protein showed considerable interstrain variability, whereas the 9-kdalton and reaction center proteins appeared constant.