Thermodynamic analysis of cavity creating mutations in an engineered leucine zipper and energetics of glycerol-induced coiled coil stabilization

Protein stability in vitro can be influenced either by introduction of mutations or by changes in the chemical composition of the solvent. Recently, we have characterized the thermodynamic stability and the rate of folding of the engineered dimeric leucine zipper A(2), which has a strengthened hydrophobic core [Dürr, E., Jelesarov, I., and Bosshard, H. R. (1999) Biochemistry 38, 870-880]. Here we report on the energetic consequences of a cavity introduced by Leu/Ala substitution at the tightly packed dimeric interface and how addition of 30% glycerol affects the folding thermodynamics of A(2) and the cavity mutants. Folding could be described by a two-state transition from two unfolded monomers to a coiled coil dimer. Removal of six methylene groups by Leu/Ala substitutions destabilized the dimeric coiled coil by 25 kJ mol(-1) at pH 3.5 and 25 degrees C in aqueous buffer. Destabilization was purely entropic at around room temperature and became increasingly enthalpic at elevated temperatures. Mutations were accompanied by a decrease of the unfolding heat capacity by 0.5 kJ K(-1) mol(-1). Addition of 30% glycerol increased the free energy of folding of A(2) and the cavity mutants by 5-10 kJ mol(-1) and lowered the unfolding heat capacity by 25% for A(2) and by 50% for the Leu/Ala mutants. The origin of the stabilizing effect of glycerol varied with temperature. Stabilization of the parent leucine zipper A(2) was enthalpic with an unfavorable entropic component between 0 and 100 degrees C. In the case of cavity mutants, glycerol induced enthalpic stabilization below 50 degrees C and entropic stabilization above 50 degrees C. The effect of glycerol could not be accounted for solely by the enthalpy and entropy of transfer or protein surface from water to glycerol/water mixture. We propose that in the presence of glycerol the folded coiled coil dimer is better packed and displays less intramolecular fluctuations, leading to enhanced enthalpic interactions and to an increase of the entropy of folding. This work demonstrates that mutational and solvent effects on protein stability can be thermodynamically complex and that it may not be sufficient to only analyze changes of enthalpy and entropy at the unfolding temperature (T(m)) to understand the mechanisms of protein stabilization.     

Thermodynamic investigations of proteins. I. Standard functions for proteins with lysozyme as an example.

A direct method is proposed for obtaining thermodynamic standard functions for native and denatured proteins using experimental data from scanning calorimetry, isothermal calorimetry and potentiometric titrations. The possibility of this approach is demonstrated on the example of lysozyme in the range of pH 1.5-7.0 and temperature 0-100 degrees C. Tests for the validity of the obtained functions of enthalpy and entropy are presented in the form of cyclic processes using experimental data obtained from thermodynamically different pathways. The Gibbs function is checked by comparison with results of an independent method. The methodic problems in determining and checking standard functions for proteins are discussed in detail.     

Thermodynamic investigations of proteins. III. Thermodynamic description of lysozyme.

Standard functions of enthalpy, entropy and the Gibbs energy of native and denatured lysozyme in the range of 0-100 degrees C and pH 1.5-7.0 are represented in three-dimensional projections. The denaturational Gibbs energy change reaches 16 kcal mol-1 at conditions of maximal protein stability (0 degrees C, pH 4.5-7.0) and equals 14.5 kcal mol-1 at 25 degrees C and neutral pH. This result was found to be in agreement with the data reported from guanidine hydrochloride denaturation studies. Partial thermodynamic functions of the conformational and ionizational changes of the protein are obtained from entropy and Gibbs-energy changes in denaturation. The conformational partial entropy and Gibbs-energy change are found to be independent of pH. The pH-dependent partial ionizational entropy and Gibbs-energy changes are induced by normalization of the ionization behaviour of buried groups and cause a decrease of protein stability.     

Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds

Ribonuclease T1 has two disulfide bonds linking cysteine residues 2-10 and 6-103. We have prepared a derivative of ribonuclease T1 in which one disulfide bond is broken and the cysteine residues carboxymethylated, (2-10)-RCM-T1, and three derivatives in which both disulfides are broken and the cysteine residues reduced, R-T1, carboxamidomethylated, RCAM-T1, or carboxymethylated, RCM-T1. The RNA hydrolyzing activity of these proteins has been measured, and urea and thermal denaturation studies have been used to determine conformational stability. The activity, melting temperature, and conformational stability of the proteins are: ribonuclease T1 (100%, 59.3 degrees C, 10.2 kcal/mol), (2-10)-RCM-T1 (86%, 53.3 degrees C, 6.8 kcal/mol), R-T1 (53%, 27.2 degrees C, 3.0 kcal/mol), RCAM-T1 (43%, 21.2 degrees C, 1.5 kcal/mol), and RCM-T1 (35%, 16.6 degrees C, 0.9 kcal/mol). Thus, the conformational stability is decreased by 3.4 kcal/mol when one disulfide bond is broken and by 7.2-9.3 kcal/mol when both disulfide bonds are broken. It is quite remarkable that RNase T1 can fold and function with both disulfide bonds broken and the cysteine residues carboxymethylated. The large decrease in the stability is due mainly to an increase in the conformational entropy of the unfolded protein which results when the constraints of the disulfide bonds on the flexibility are removed. We propose a new equation for predicting the effect of a cross-link on the conformational entropy of a protein: delta Sconf = -2.1 - (3/2)R 1n n, where n is the number of residues between the side chains which are cross-linked. This equation gives much better agreement with experimental results than other forms of this equation which have been used previously.     

Basic characteristics of the process of Candida adhesion to human epitheliocytes

The adhesion of fungi belonging to the genus Candida to the epithelial cells of the mouth cavity reached its maximum at pH 6.2-7.0. The process of adhesion had similar dynamics at temperatures of 37 degrees, 28 degrees and 25 degrees C, but the adhesive activity decreased 2 times when temperature dropped from 37 degrees to 25 degrees and 4 times when temperature dropped to 4 degrees C. The introduction of the ions Ca2+ (1 and 10 mM) and Mg2+ (10 mM) led to the increase of adhesion by 80, 100 and 24% respectively. The heating of the fungal cells at 100 degrees C (for 1 hour) and at 63 degrees C (for 2 hours) decreased adhesion to 8 and 24% respectively, and treatment with formaldehyde (for 24 hours) decreased adhesion to 70% of that observed in experiments with live Candida cells.     

Characterization of the sources of protein-ligand affinity: 1-sulfonato-8-(1'')anilinonaphthalene binding to intestinal fatty acid binding protein.

1-Sulfonato-8-(1')anilinonaphthalene (1,8-ANS) was employed as a fluorescent probe of the fatty acid binding site of recombinant rat intestinal fatty acid binding protein (1-FABP). The enhancement of fluorescence upon binding allowed direct determination of binding affinity by fluorescence titration experiments, and measurement of the effects on that affinity of temperature, pH, and ionic strength. Solvent isotope effects were also determined. These data were compared to results from isothermal titration calorimetry. We obtained values for the enthalpy and entropy of this interaction at a variety of temperatures, and hence determined the change in heat capacity of the system consequent upon binding. The ANS-1-FABP is enthalpically driven; above approximately 14 degrees C it is entropically opposed, but below this temperature the entropy makes a positive contribution to the binding. The changes we observe in both enthalpy and entropy of binding with temperature can be derived from the change in heat capacity upon binding by integration, which demonstrates the internal consistency of our results. Bound ANS is displaced by fatty acids and can itself displace fatty acids bound to I-FABP. The binding site for ANS appears to be inside the solvent-containing cavity observed in the x-ray crystal structure, the same cavity occupied by fatty acid. From the fluorescence spectrum and from an inversion of the Debye-Hueckel formula for the activity coefficients as a function of added salt, we inferred that this cavity is fairly polar in character, which is in keeping with inferences drawn from the x-ray structure. The binding affinity of ANS is considered to be a consequence of both electrostatic and conditional hydrophobic effects. We speculate that the observed change in heat capacity is produced mainly by the displacement of strongly hydrogen-bonded waters from the protein cavity.     

Differential scanning calorimetric studies of a Bacillus halodurans alpha-amylase

The thermal unfolding of Amy 34, a recombinant alpha-amylase from Bacillus halodurans, has been investigated using differential scanning calorimetry (DSC). The denaturation of Amy 34 involves irreversible processes with an apparent denaturation temperature (T(m)) of 70.8 degrees C at pH 9.0, with four transitions, as determined using multiple Gaussian curves. The T(m) increased by 5 degrees C in the presence of 100-fold molar excess of CaCl2 while the aggregation of Amy 34 was observed in the presence of 1000-fold molar excess of CaCl2. Increase in the calcium ion concentration from 1- to 5-fold molar excess resulted in an increase in calorimetric enthalpy (DeltaH(cal)), however, at higher concentrations of CaCl2 (up to 100-fold), DeltaH(cal) was found to decrease, accompanied by a decrease in entropy change (DeltaS), while the T(m) steadily increased. The presence of 100-fold excess of metal chelator, EDTA, resulted in a decrease in T(m) by 10.4 degrees C. T(m) was also decreased to 61.1 degrees C and 65.9 degrees C at pH 6.0 and pH 11.0, respectively.     

Entropy principle for human development, growth and aging

Entropy productions within nude subjects in respiration calorimeters are calculated from the corresponding energetic data obtained by Du Bois et al. (1952, J. Nutr. 48, 257-293.). The entropy production for men is constant at environmental temperatures from 24-34 degrees C. The metabolic entropy production comprises 98.6% of the total entropy production. The entropy production for women shows a minimum at 30 degrees C (the middle of the neutral zone), a small rise in the cold zone and a trend toward a rise in the warm zone; the average entropy production for women is 8.7% smaller than that for men. The entropy production rises from 0-2 years of age, and decreases rapidly from 2-25 years of age and then gradually to 85 years of age. The entropy production does not seem to achieve a minimum or a level in the lives of men and women. Based on these results, a three-stage hypothesis of entropy production in human life is proposed.     

Statistical aspects of van't Hoff analysis: a simulation study

The thermodynamics of biological interactions is frequently studied by the van't Hoff analysis whereby data on variation of the binding constant K(D) with temperature are used to obtain estimates of standard enthalpy (Delta H degrees ), entropy (Delta S degrees ), and heat capacity (Delta C degrees P) of complex formation. A Monte Carlo simulation demonstrates that the absolute error of the above parameters is proportional to the relative error of KD and independent of the actual values of KD and of the way they vary with temperature. The error of Delta H degrees is approximately the same as that of T Delta S degrees (within 14% in the temperature range 5-45 degrees C). The error depends both on the number of temperature points within the experimental temperature range and on the size of the range, but it is more sensitive to the latter. Using the linear form of the van't Hoff equation to fit data with non-zero Delta C degrees P gives erroneous Delta H degrees and DeltaS degrees estimates at standard temperature except for the case when the T points are placed symmetrically with respect to the standard temperature. With the range of Delta C degrees P values usual for protein-protein interactions, the KD error must be very low to confidently infer that Delta C degrees P is non-zero or to claim that two interactions have different Delta C degrees P.     

Mixed monolayers of straight-chain/branched-chain phospholipids. I. Mixed monolayers of distearoyl phosphatidylcholine and diisoeicosanoyl phosphatidylcholine

The temperature dependence of the force/area isotherms of monolayer of distearoyl phosphatidylcholine (DSPC), diisoeicosanoyl phosphatidylcholine (DIEPC) and a complete mixed compositional range of these two lecithins are reported. The isotherms for DSPC closely resemble those previously reported for dipalmitoyl phosphatidylcholine but are shifted to higher temperatures by 16 degrees C. The isotherms of DIEPC, an iso-branched lecithin, show differences from these obtained for similar straight-chain lecithins in that the full condensed isotherms are more expanded, the fully expanded isotherms are more condensed and therefore the liquid expanded (LE)/liquid condensed (LC) intermediate region is significantly reduced. This means that the condensed state is more disordered and the expanded state is less disordered than the corresponding states in straight-chain lecithins. Data for the mixed films are interpreted in terms of surface pressure/mole fraction phase diagrams and both energies and entropies of compression associated with the LE/LC transition. The phase diagrams at 34.1 degrees C, 35.8 degrees C and 38.5 degrees C are all of the negative azeotropic type with the surface pressure minimum point shifting with temperature. The thermodynamic analysis indicates that from 34.1 degrees C to 38.5 degrees C the driving force for mixing changes from the entropy to the energy of the transition. It would seem that at the lower temperature the packing of the distearoyl lecithin is perturbed by the diisoeicosanoyl lecithin, while at higher temperatures the very high entropy of pure or nearly pure diisoeicosanoyl lecithin results in other mixtures having less entropy than would be expected on an ideal mixing basis.     

In vitro, rapid assembly of gap junctions is induced by cytoskeleton disruptors

We report here rapid assembly of gap junctions in prostate epithelial cells in vitro. Assembly of gap junctions can be induced by incubation at 0 degrees C followed by incubation at 37 degrees C. Colchicine (10(- 5) M, 10(-3) M) and cytochalasin B (25 micrograms/ml), 100 micrograms/ml) at room temperature or at 37 degrees C also induce assembly of gap junctions. Assembly of the junctions proceeds even in the presence of a metabolic inhibitor (dinitrophenol) or of an inhibitor of protein synthesis (cycloheximide). We conclude that assembly of gap junctions can proceed from a pool of pre-existing precursors. The experimental conditions that result in gap-junction assembly involve perturbation of the cytoskeleton. Therefore, we propose that the assembly of gap junctions requires convergent migration of precursor molecules whose positional control in the membrane is released by perturbation of the cytoskeleton. Aggregates of particles and rugosities, whose distribution size and shape is similar to that of gap junctions, may represent intermediate assembly stages. This would indicate that the final stages in the assembly take place only after convergence of the precursor molecules to the junctional site and involve profound conformational changes required for establishment of fully assembled connexons.     

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.     

Kinetic modelling of the degradation of the alpha-tocopherol in biodiesel-rape methyl ester

The aim of this work was to study the influence of three major factors (light, atmospheric oxygen, temperature) responsible for the degradation of tocopherols. The evolution of alpha-tocopherol contents was analysed by high-performance liquid chromatography. Taguchi's experimental design was applied to establish a mathematical model of alpha-tocopherols degradation in function of the studied parameters especially in a domain of temperature between 50 degrees C and 150 degrees C. The results show that the major factor is the temperature, especially above 100 degrees C. Light is a negligible factor, meaning that degradation is mainly due to an autoxidation phenomenon. Moreover, only interactions between temperature and atmospheric oxygen have been observed especially above 100 degrees C. The mathematical model was validated for a temperature of 75 degrees C and permits to calculate a predictive speed of degradation in this domain.     

Interaction of local and reflex thermal effects in control of forearm blood flow

We measured forearm blood flow (ABF) bilaterally on six subjects during 15-min periods of leg exercise and the first 10 min of recovery. One forearm (control) was kept at about 33 degrees C skin temperature in all experiments. In experiments at ambient temperature (Ta) of 15 degrees C, the other arm (experimental) was kept at about 26, 33, and 40 degrees C, respectively, during three successive cycles of exercise and recovery. ABF in the 26 degrees C forearm was linearly related to and averaged 42% of control. The relation of ABF in the 40 degrees C forearm to control ABF showed a bend at control ABF of 4-5 ml X 100 ml-1 X min-1. Below the bend, experimental ABF average 213% of control. Above the bend, experimental ABF averaged 5.09 ml X 100 ml-1 X min-1 above control. In four subjects, after heating the experimental forearm to 40 degrees C, we measured ABF for 25-30 min at rest in Ta of both 15 and 25 degrees C. At 25 degrees C Ta, ABF in the heated forearms rose gradually, but control ABF showed little change. At 15 degrees C Ta, the effect on ABF of local heating to 40 degrees C was much reduced, apparently due to reflex vasoconstrictor signals.     

Thermodynamic analysis of binding between mouse major urinary protein-I and the pheromone 2-sec-butyl-4,5-dihydrothiazole

The mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT) binds to an occluded, nonpolar cavity in the mouse major urinary protein-I (MUP-I). The thermodynamics of this interaction have been characterized using isothermal titration calorimetry (ITC). MUP-I-SBT binding is accompanied by a large favorable enthalpy change (DeltaH = -11.2 kcal/mol at 25 degrees C), an unfavorable entropy change (-TDeltaS = 2.8 kcal/mol at 25 degrees C), and a negative heat capacity change [DeltaC(p)() = -165 cal/(mol K)]. Thermodynamic analysis of binding between MUP-I and several 2-alkyl-4,5-dihydrothiazole ligands indicated that the alkyl chain contributes more favorably to the enthalpy and less favorably to the entropy of binding than would be expected on the basis of the hydrophobic desolvation of short-chain alcohols. However, solvent transfer experiments indicated that desolvation of SBT is accompanied by a net unfavorable change in enthalpy (DeltaH = +1.0 kcal/mol) and favorable change in entropy (-TDeltaS = -1.8 kcal/mol). These results are discussed in terms of the possible physical origins of the binding thermodynamics, including (1) hydrophobic desolvation of both the protein and the ligand, (2) formation of a buried water-mediated hydrogen bond network between the protein and ligand, (3) formation of strong van der Waals interactions, and (4) changes in the structure, dynamics, and/or hydration of the protein upon binding.     

Thermodynamics of the temperature-induced unfolding of globular proteins.

The heat capacity, enthalpy, entropy, and Gibbs energy changes for the temperature-induced unfolding of 11 globular proteins of known three-dimensional structure have been obtained by microcalorimetric measurements. Their experimental values are compared to those we calculate from the change in solvent-accessible surface area between the native proteins and the extended polypeptide chain. We use proportionality coefficients for the transfer (hydration) of aliphatic, aromatic, and polar groups from gas phase to aqueous solution, we estimate vibrational effects, and we discuss the temperature dependence of each constituent of the thermodynamic functions. At 25 degrees C, stabilization of the native state of a globular protein is largely due to two favorable terms: the entropy of non-polar group hydration and the enthalpy of interactions within the protein. They compensate the unfavorable entropy change associated with these interactions (conformational entropy) and with vibrational effects. Due to the large heat capacity of nonpolar group hydration, its stabilizing contribution decreases quickly at higher temperatures, and the two unfavorable entropy terms take over, leading to temperature-induced unfolding.     

Temperature dependence of the energy-linked monosaccharide transport across the cell membrane of Rhodotorula gracilis.

The temperature dependence of the active monosaccharide transport across the cell membrane of the yeast Rhodotorula gracilis has been studied between 0 and 55 degrees C with D-xylose as the transported substrate: (i) Between 0 and 10 degrees C there is virtually no transport. (ii) The initial velocity of transport increases exponentially from 15 to 30 degrees C (deltaE equal to 32 plus or minus 2 kcal/mol). (iii) At 30 degrees C a sharp "break" occurs in the Arrhenius plot and with increasing temperature the transport becomes inactivated, with a positive slope of the corresponding straight line ("deltaE equal to minus 15 kcal/mol"). (iv) In the temperature range of 50-55 degrees C, both the transport and the metabolic activity cease. In order to account for the abrupt changes of the membrane permeability, we attempted to ascribe them to phase transitions in the membrane structure: the first one, between 10 and 15 degrees C, to the crystalline: liquid-crystalline phase change; the second one, around 30 degrees C, to a change from highly ordered (low entropy) to less ordered (high entropy) membrane structure. Whereas the former phase transition is reversible, the latter appears to be irreversible. Arrhenius plots of the cell respiration exhibit a "break" at 30 degrees C, as well. However, at higher temperatures there is no thermal inactivation of the respiratory activity. The importance of a proper organization of the cell membrane constituents for the efficient transport function is discussed.     

A calorimetric study of the folding-unfolding of an alpha-helix with covalently closed N and C-terminal loops.

The thermal melting of a dicyclic 29-residue peptide, having helix-stabilizing side-chain to side-chain covalent links at each terminal, has been studied by circular dichroism spectropolarimetry (CD) and differential scanning calorimetry (DSC). The CD spectra for this dicyclic peptide indicate that it is monomeric, almost fully alpha-helical at -10 degrees C, and undergoes a reversible transition from the folded to the disordered state with increasing temperature. The temperature dependencies of the ellipticity at 222 nm and the excess heat capacity measured calorimetrically are well fit by a two-state model, which indicates a cooperative melting transition that is complete within the temperature ranges of these experiments (from -10 degrees C to 100 degrees C). This allows a complete analysis of the thermodynamics of helix formation. The helix unfolding is found to proceed with a small positive heat-capacity increment, consistent with the solvation of some non-polar groups upon helix unfolding. It follows that the hydrogen bonds are not the only factors responsible for the formation of the alpha-helix, and that hydrophobic interactions are also playing a role in its stabilization. At 30 degrees C, the calorimetric enthalpy and entropy values are estimated to be 650(+/-50) cal mol(-1)and 2.0(+/-0.2) cal K(-1)mole(-1), respectively, per residue of this peptide. Comparison with the thermodynamic characteristics obtained for the unfolding of double-stranded alpha-helical coiled-coils shows that at that temperature the enthalpic contribution of non-polar groups to the stabilization of the alpha-helix is insignificant and the estimated transition enthalpy can be assigned to the hydrogen bonds. With increasing temperature, the increasing magnitude of the negative enthalpy of hydration of the exposed polar groups should decrease the helix-stabilizing enthalpy of the backbone hydrogen bonds. However, the helix-stabilizing negative entropy of hydration of these groups should also increase in magnitude with increasing temperature, offsetting this effect.     

A comparison of solution conformation and hydrodynamic properties of equine, porcine and rabbit serum albumin using viscometric measurements

This paper presents the results of viscosity determinations on aqueous solutions of equine, porcine and rabbit serum albumin over a wide range of concentrations and at temperatures ranging from 5 degrees C to (42-45) degrees C. The results are compared with human and bovine serum albumin previously studied. Viscosity-temperature dependence is discussed on the basis of the modified Arrhenius formula. The effective specific volume, the activation energy and entropy of viscous flow for all investigated albumins are compared. Viscosity-concentration dependence, in turn, is discussed on the basis of Mooney equation. Based on the assumption that theoretical and experimental values of Simha factor--at high temperature limit--are equal to each other, the hydrodynamic volume of the studied albumins has been calculated. The numerical values of a self-crowding factor were also obtained. At low concentration limit, the numerical values of the intrinsic viscosity and of Huggins coefficient were compared.     

Heat denaturation of immunoglobin G in monomolecular layers

Studies were carried out of viscous-elastic properties of monomolecular layers of human immunoglobulin IgG formed at the interface water solutions of NaCl--air within 20 degrees C to 50 degrees C at NaCl concentration in sublayer from 0.3 to 1.0 M. It has been shown that at concentrations from 0.3 to 0.5 M of NaCl IgG macromolecules keep the tertiary structure, and in the region 35 +/- 5 degrees C a conformation transition is observed. The recorded conformation transition is reversible and of entropy nature. At NaCl concentration 0.75 in the sublayer and temperature close to 35 degrees C IgG macromolecules undergo irreversible structural changes due to the destruction of hydrogen and disulfide bonds in IgG molecules. Macromolecules dissociate to fragments with molecular mass 49,000 +/- 2000. At NaCl concentration 1.0 M and temperatures 30-50 degrees C IgG macromolecules of the monolayer are in a dissociated state. Changes in entropy, enthalpy and heat capacity as well as areas occupied by the macromolecules at dense packing, molecular mass and efficient electric dipole moment of the monolayer are calculated.