The role of solvent interactions in protein conformation

On the origin of the enthalpy and entropy convergence temperatures in protein folding

Temperature dependence of the thermodynamics of folding/unfolding for cytochrome c has been determined as a function of moderate [0-10% (vol/vol)] concentrations of methanol. Heat capacity change (delta Cp) for unfolding decreases with increased concentrations of methanol, consistent with a higher solvent hydrophobicity. For a given transition temperature, this effect results in higher experimental enthalpy (delta H) and entropy (delta S) changes with increased methanol concentrations. When the enthalpy or entropy data sets obtained at different methanol concentrations are plotted as a function of temperature, they are seen to converge and assume common values around 100 degrees C for delta H and 112 degrees C for delta S. These convergence temperatures are similar to those obtained for different proteins in aqueous solution when delta H and delta S are normalized with respect to number of residues. It has been previously hypothesized that these convergence temperatures correspond to the temperatures at which the hydrophobic contributions to delta H and delta S are zero; the results presented here agree with this viewpoint.

The low-temperature heat capacity of solid proteins

Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low-frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T less than 30 K. The experimental b's of proteins are 1.6-1.8, and the theoretical, 1.1-1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100-200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.

The regulation and nature of the cyanide-resistant alternative oxidase of plant mitochondria

In addition to possessing multiple NAD(P)H dehydrogenases, most plant mitochondria contain a cyanide- and antimycin-insensitive alternative terminal oxidase. Although the general characteristics of this terminal oxidase have been known for a considerable number of years, the mechanism by which it is regulated is unclear and until recently there has been relatively little information on its exact nature. In the past 5 years, however, the application of molecular and novel voltametric techniques has advanced our understanding of this oxidase considerably. In this article, we review briefly current understanding on the structure and function of the multiple NADH dehydrogenases and consider, in detail, the nature and regulation of the alternative oxidase. We derive a kinetic model for electron transfer through the ubiquinone pool based on a proposed model for the reduction of the oxidase by quinol and show how this can account for deviations from Q-pool behaviour. We review information on the attempts to isolate and characterise the oxidase and finally consider the molecular aspects of the expression of the alternative oxidase.

Solvent-induced conformational changes of polypeptides probed by electrospray-ionization mass spectrometry

Electrospray-ionization (ESI) mass spectrometry is used to monitor higher order structural changes of polypeptides induced by alteration of the pH or organic solvent composition in the protein solution environment. A bimodal charge-state distribution is observed in the ESI mass spectrum of ubiquitin (relative molecular mass 8565) in solutions containing small amounts (less than 20%) of organic solvents. The distribution of peaks at high m/z (low-charge state) is found to represent the protein in its native, globular state; the higher-charge-state distribution is characteristic for a more extended conformation. Addition of methanol denaturant in excess of 40% v/v is needed to eliminate the low-charge-state distribution completely. Lesser amounts of acetonitrile, acetone, or isopropanol (approximately 20%) are required to denature the ubiquitin protein. Other proteins showing conformational effects in their ESI mass spectra are also illustrated. While the ESI spectra are related to solution phase structure, ESI-tandem mass spectrometry of multiply charged molecular ions of different conformation is suggested as a probe of gas-phase protein three-dimensional structure.

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.

Aggregation and thermo-inactivation of glutamine synthetase from an extreme thermophile, Bacillus caldolyticus

The extreme thermophile, Bacillus caldolyticus, contains two regulatory isoforms of glutamine synthetase (glutamate-ammonia ligase, EC 6.3.1.2), E-I and E-II, produced as separate gene products. Light scattering and electron microscopy data indicate that these thermophilic enzymes aggregate to higher molecular weight species in two stages: initial polymerization of native dodecamers, followed by 'melting' of the aggregated species to produce amorphous denatured protein. The initial stages of the aggregation occurred at temperatures below those for time-dependent denaturation, especially for E-II. In contrast, mesophilic (B. subtilis) enzyme showed no evidence of temperature-dependent aggregation. Thus, aggregation may be a stabilizing mechanism for the thermophilic systems. Bound metal ions and substrates caused dramatic increases in the temperatures at which aggregation and loss of activity occurred for thermophilic enzymes. Certain combinations of ligands (e.g., MnATP + L-glutamate) acted synergistically, so that these complexes denatured only above 90 degrees C. Various models were considered for heat-driven aggregation followed by denaturation, plus ligand stabilization. Taken together, the data are most consistent with unfolding of subunits within the dodecameric unit, rather than unfolding to monomers prior to aggregation.

Alcohol-induced conformational changes of ubiquitin

Ubiquitin has been found to be soluble in ethylene glycol and alcohols as the perchlorate or hydrochloride salt. When the effect of alcohol on the structure of ubiquitin is examined, two reversible conformational transitions are observed. Upon lowering the dielectric constant of aqueous alcohol solutions of ubiquitin from 80 to 45, the native structure of ubiquitin is converted to a form consistent with 50% helical structure. This conformational change results in a change in exposure to solvent of the single methionine and the single tyrosine residues of ubiquitin. In agreement with crystallographic results, these residues are buried in the native conformation but become fully exposed to solvent upon undergoing this transition. Further lowering of the dielectric constant to 20 results in the accumulation of a conformation with almost complete helical structure. Thus, hydrophobic interactions cause facile conformational changes in the ubiquitin structure. These results are discussed in terms of a preferential solvation model. It is shown that the results obtained with different alcohols can be normalized by the use of a dielectric constant scale. This normalization corrects for the different molar volumes of different alcohols, allows comparison of results obtained with different alcohols, and should be useful in studying this phenomenon with different proteins.

Effects of acute and chronic ethanol exposure on the response of rat aorta to a thromboxane mimic, U46619

The spasmogenic properties of a stable thromboxane mimic, U46619, were determined in the isolated rat aorta after 1, 4, 8, or 12 hr of acute ethanol exposure in vitro or after 12 days of chronic exposure by inhalation. Acute ethanol exposure (87-822 mM) increased the baseline tension of aortic rings in a concentration-dependent manner. Moderate concentrations of ethanol (11 and 43 mM) decreased the maximum tensile response of rat aortic rings to U46619 after 8 and 4 hr of exposure, respectively. In contrast, higher ethanol concentrations (87 and 411 mM) did not significantly effect the maximum tensile response to U46619. Ethanol at 822 mM completely inhibited the response to U46619 and this inhibition could be 85% reversed after removal of ethanol. The inhibitory effect of 1.64 M ethanol was irreversible. Sensitivity to U46619 was inversely related to the ethanol concentration (greater than or equal to 43 mM) and incubation time. Similarly, chronic exposure to moderate blood ethanol levels (92-198 mg/100 ml) for 12 days decreased the maximum tensile response whereas high levels did not effect aortic contractility in vitro. Sensitivity of aorta from rats with mean blood ethanol levels greater than or equal to 92 mg/100 ml decreased at least one order of magnitude. The results suggest that the effect of physiologically tolerable ethanol concentrations on the amplitude of the tensile response to U46619 is biphasic both during acute exposure in vitro or following a chronic exposure period in vivo and the inhibitory effect on sensitivity for U46619 is both concentration- and time-dependent in the rat aorta preparation.

An evaluation of the hydration of lysozyme by an NMR titration method

In this study a new titration method is proposed to study the motional properties of water molecules in conjunction with globular proteins using proton NMR relaxation measurements. The method was applied to the study of the interaction of water with lysozyme and allowed identification of four water fractions-superbound water, polar-bound water, structured water and bulk water - in exchanged equilibrium. The titration demonstrated that 193 water molecules are hydrogen bonded directly to the lysozyme molecule. The combination of structured and bound water extends to 1.4 g H2O per g lysozyme and approx. two to three layers from the surface of the macromolecule. It is proposed that this structured water is related to non-isotropic water rotation in conjunction with hydrophobic patches and directly related to 'hydrophobic bonding' changes. Water amounts greater than 1.4 g H2O per g lysozyme are sufficiently distant from the macromolecule for motion to revert to that typical of water in bulk. The typical correlation times for water motion in the four fraction are: over 10(-6) s (superbound); 10(-9) s (polar bound); 10(-11) s (structured) and 10(-12) s (bulk). These results correlate well with results from other measurement techniques found in the literature.

A pH titration study on the ionic bridging within lipopolysaccharide aggregates

The packing of lipopolysaccharide aggregates from rough strains of Escherichia coli was examined at different pH values. Lipopolysaccharide head-group motion, measured with an electron spin resonance probe, was found to be dependent on pH, and indicated the existence of multiple ionizable groups. Lipopolysaccharide from a rough (Ra) and a heptose-less (Re) mutant were more rigid at pH 5 than at pH 10.5. In addition, head-group mobility of the magnesium salt of Ra lipopolysaccharide was substantially less than that of the sodium salt at pH 7.0, whereas at high pH (pH 12) the two salts were equally fluid. Changes in head-group packing were also reflected in pH-dependent changes in the phase transition measured with differential scanning calorimetry. The enthalpy of the transition, delta Ht, for the sodium salt of Re lipopolysaccharide was greatest at pH 7.5 and approached zero in both the acidic and the basic pH ranges. We propose that fixed charges in the core and lipid A regions significantly influence lipopolysaccharide head-group motion and the lipopolysaccharide aggregation state. Furthermore, ionic bridging among phosphate groups dramatically rigidifies head group interactions in the neutral to acidic pH ranges.

Effect of ethanol on prostacyclin and thromboxane A2 synthesis in rat aortic rings in vitro

Spontaneous 6-keto-PGF1 alpha and TXB2 levels in isolated rat aortic rings increased in a concentration dependent manner after a 0.5 hour incubation with moderate or high ethanol concentrations (11 mM to 218 mM). After a 1 hour incubation with moderate concentrations of ethanol less than or equal to 22 mM) spontaneous prostaglandin (PG) production did not increase although high concentrations (87 mM and 218 mM) increased both 6-keto-PGF1 alpha and TXB2 levels. Similarly, in the presence of 40 microM Na-arachidonate, high ethanol concentrations increased PG production after 0.5 and 1 hour incubation. In addition, either a 4 or an 8 hour exposure to high ethanol concentrations increased spontaneous PG production. A moderate concentration of ethanol (22 mM) increased the 6-keto-PGF1 alpha/TXB2 ratio whereas high levels (greater than or equal to 87 mM) depressed the ratio after 0.5 and 1 hour exposure. This effect was short-lived since after 4 or 8 hours incubation with high ethanol concentrations the 6-keto-PGF1 alpha/TXB2 ratio was markedly increased. The alcohol-induced changes in both spontaneous and arachidonate-stimulated PG levels were concentration dependent and related to the incubation time. Furthermore, these data suggest that there may be unbalanced production of PGI2 and thromboxane A2 in vascular tissue exposed to alcohol.

The Hofmeister effect and the behaviour of water at interfaces

Starting from known properties of non-specific salt effects on the surface tension at an air-water interface, we propose the first general, detailed qualitative molecular mechanism for the origins of ion-specific (Hofmeister) effects on the surface potential difference at an air-water interface; this mechanism suggests a simple model for the behaviour of water at all interfaces (including water-solute interfaces), regardless of whether the non-aqueous component is neutral or charged, polar or non-polar. Specifically, water near an isolated interface is conceptually divided into three layers, each layer being I water-molecule thick. We propose that the solute determines the behaviour of the adjacent first interfacial water layer (I1); that the bulk solution determines the behaviour of the third interfacial water layer (I3), and that both I1 and I3 compete for hydrogen-bonding interactions with the intervening water layer (I2), which can be thought of as a transition layer. The model requires that a polar kosmotrope (polar water-structure maker) interact with I1 more strongly than would bulk water in its place; that a chaotrope (water-structure breaker) interact with I1 somewhat less strongly than would bulk water in its place; and that a non-polar kosmotrope (non-polar water-structure maker) interact with I1 much less strongly than would bulk water in its place. We introduce two simple new postulates to describe the behaviour of I1 water molecules in aqueous solution. The first, the 'relative competition' postulate, states that an I1 water molecule, in maximizing its free energy (--delta G), will favour those of its highly directional polar (hydrogen-bonding) interactions with its immediate neighbours for which the maximum pairwise enthalpy of interaction (--delta H) is greatest; that is, it will favour the strongest interactions. We describe such behaviour as 'compliant', since an I1 water molecule will continually adjust its position to maximize these strong interactions. Its behaviour towards its remaining immediate neighbours, with whom it interacts relatively weakly (but still favourably), we describe as 'recalcitrant', since it will be unable to adjust its position to maximize simultaneously these interactions.(ABSTRACT TRUNCATED AT 400 WORDS)

Circular dichroism study of the unfolding-refolding of a cardiotoxin from Taiwan cobra (Naja naja atra) venom

Circular dichroism spectroscopy has been used to study the unfolding-refolding process of a cardiotoxin from Taiwan cobra (Naja naja atra) venom upon addition of fluoroalcohols or sodium dodecyl sulfate (SDS) to its aqueous solution. In these experiments, the disulfide bridges remained intact. The unfolding process has been found to be reversible both for fluoroalcohols and for SDS unfolding. The reversibility of the unfolding-refolding process of cardiotoxin in aqueous mixtures of fluoroalcohols was dependent on the volume per volume ratio of alcohol to water. SDS did not unfold the secondary structures of cardiotoxin whereas its tertiary structure was affected. If the SDS concentration in aqueous solution exceeded the critical micelle concentration value of SDS, a quasi-refolded state of cardiotoxin was observed. The mechanism of unfolding-refolding is discussed in terms of molecular interactions which might govern the protein conformation in solution.

Solubilization of the alternative oxidase of cuckoo-pint (Arum maculatum) mitochondria. Stimulation by high concentrations of ions and effects of specific inhibitors

Selective solubilization of cyanide- and antimycin-insensitive duroquinol oxidase activity from cuckoo-pint (Arum maculatum) mitochondria was achieved using taurocholate. Inhibitor-sensitivities and water-forming DQH2 (tetramethyl-p-hydroquinone, reduced form): O2 stoichiometry were the same for the alternative oxidase of intact Arum mitochondria. Cyanide-insensitive oxidation of DQH2 by intact and solubilized mitochondria was stimulated by up to four-fold by high concentrations of anions high in the Hofmeister series, such as phosphate, sulphate or citrate. Optimal (0.7 M) sodium citrate increased Vmax. for DQH2 oxidation by the solubilized preparation from 450 to 2400 nmol of O2 X min-1 X mg of protein-1 and decreased the apparent Km for DQH2 from 0.53 to 0.38 mM. Inhibition of solubilized DQH2 oxidase activity by CLAM (m-chlorobenzhydroxamic acid) and SHAM (salicylhydroxamic acid) was mixed competitive/non-competitive, with apparent inhibition constants for CLAM of 25 microM (Ki) and 81 microM (KI) and for SHAM of 53 microM (Ki) and 490 microM (KI). Propyl gallate and UHDBT were non-competitive inhibitors with respect to DQH2 (apparent Ki = 0.3 microM and 12 nM respectively). Low concentrations of C18 fatty acids selectively inhibited cyanide-insensitive oxidation by intact and solubilized mitochondria, and inhibition was reversed by 1% (w/v) bovine serum albumin. Inhibition was competitive with DQH2, suggesting that fatty acids interfere reversably with the binding of DQH2 to the oxidase. These results tend to support the view that quinol oxidation by the alternative pathway of Arum maculatum mitochondria is catalysed by a quinol oxidase protein, rather than by a non-enzymic mechanism involving fatty acid peroxidative reaction. [Rustin, Dupont & Lance (1983) Trends Biochem. Sci. 8, 155-157; (1983) Arch. Biochem. Biophys. 225, 630-639].

Early stages in the trifluoroethanol-induced unfolding of hen egg-white lysozyme and its complex with (GlcNAc)3

The trifluoroethanol-induced unfolding of hen egg-white lysozyme was studied by circular dichroism. It was shown that if the H2O/trifluoroethanol ratio is above 10:1 (v/v), the unique three-dimensional structure of the protein is not affected, whereas within the ration 10:1-2.8:1 (v/v), this structure is partially unfolded. At the ratio 2.4:1 (v/v), the native conformation of lysozyme is completely disrupted and the conformational transition fits a two-state model. A similar effect was observed for the trifluoroethanol-induced unfolding of the lysozyme-(GlcNAc)3 complex. Within the H2O2 trifluoroethanol ratio 15:1-5.5:1 (v/v), the characteristic intensities of the Cotton effects which arise from the association of (GlcNAc)3 with the active site of lysozyme, diminished and approached those exhibited by lysozyme itself at the same H2O trifluoroethanol ratios. This shows that (GlcNAc)3 is released from the protein surface in early stages of the unfolding process. At the ratio 2.4:1 (v/v), the lysozyme-(GlcNAc)3 complex was completely disrupted and the protein unfolded. It is suggested that a considerable alteration in hydration of the lysozyme molecule caused by trifluoroethanol increases protein surface fluctuations, causing the release of (GlcNAc)3 from the active site of lysozyme.

Protein conformation and reversed-phase high-performance liquid chromatography

The structure of a series of proteins has been investigated by circular dichroism, fluorescence and visible spectroscopy as well as by differential scanning calorimetry under reversed-phase high-performance liquid chromatography elution conditions. These studies show that 1-propanol, a typical eluent, induces a reversible conformational change in proteins to an apparently ordered, helical form. This structural transition occurs in the range of propanol concentrations that produces elution of a particular protein. The possible relationship between this conformational change and protein elution is considered.

Effects of hydration on the surface morphology of urediospores

Changes in the surface morphology of mature urediospores of Uromyces viciae-fabae have been studied with respect to different preparative procedures for the scanning electron microscope. Specimens were examined in the critical point-dried, freeze-dried and frozen-hydrated states. Dried urediospores were significantly different in appearance from those which were hydrated. Shrinkage probably accounted for some of the surface features of dried spores, particularly amongst those which had been critical point-dried. No significant effects on spore surface texture resulted from chemical immersion fixation, chemical vapour fixation, dehydration or the mode of sputter-coating. It is suggested that the presence or absence of unfreezable water, involved in maintaining the structural stability of polymers which provide the specimen surface with its characteristic morphology, may have an important influence on the gross texture of cell surfaces as viewed with the scanning electron microscope.

The influence of experimental conditions on the association constant for binding of vitamin B12 by human intrinsic factor coupled to Sepharose 4B

The association constant for binding of vitamin B12 (cyanocobalamin) by human intrinsic factor coupled to Sepharose 4B and the concentration of binding sites of the coupled intrinsic factor have been measured as a function of pH, temperature, ionic strength and the presence of various (ionic and non-ionic) components in the solution.

Unfolding processes of small globular proteins: the two-state vs multi-state model

1. The alcohol-induced unfolding of two homologous proteins, neurotoxin and cardiotoxin from Taiwan cobra (Naja naja atra) venom has been analysed. 2. It is postulated that the unfolding process for both proteins is a multi-state conformational transition. 3. It has been hypothesized that between the compact native state of the protein and its fully unfolded state there exists a quasi-continuous spectrum of conformational metastates of protein species. 4. The population distribution of these metastates is partially dependent on the nature of unfolding factors as well as the amino acid composition and sequence. 5. The sum of all transient conformational states and the protein species being in the folded and unfolded states respectively, can be detected by means of circular dichroism spectroscopy since the absorption of circularly polarized light is rapid relative to the rate of fluctuations of the protein structure.