Effects of five-tryptophan mutations on structure, stability and function of Escherichia coli dihydrofolate reductase

To elucidate the roles of tryptophan residues in the structure, stability, and function of Escherichia coli dihydrofolate reductase (DHFR), its five tryptophan residues were replaced by site-directed mutagenesis with leucine, phenylalanine or valine (W22F, W22L, W30L, W47L, W74F, W74L, W133F, and W133V). Far-ultraviolet circular dichroism (CD) spectra of these mutants reveal that exciton coupling between Trp47 and Trp74 strongly affects the peptide CD of wild-type DHFR, and that Trp133 also contributes appreciably. No additivity was observed in the contributions of individual tryptophan residues to the fluorescence spectrum of wild-type DHFR, Trp74 having a dominant effect. These single-tryptophan mutations induce large changes in the free energy of urea unfolding, which showed values of 1.79-7.14 kcal/mol, compared with the value for wild-type DHFR of 6.08 kcal/mol. Analysis of CD and fluorescence spectra suggests that thermal unfolding involves an intermediate with the native-like secondary structure, the disrupted Trp47-Trp74 exciton coupling, and the solvent-exposed Trp30 and Trp47 side chains. All the mutants except W22L (13%) retain more than 50% of the enzyme activity of wild-type DHFR. These results demonstrate that the five tryptophan residues of DHFR play important roles in its structure and stability but do not crucially affect its enzymatic function.

High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase

A high-pressure (15)N/(1)H two-dimensional NMR study has been carried out on folate-bound dihydrofolate reductase (DHFR) from Escherichia coli in the pressure range between 30 and 2000 bar. Several cross-peaks in the (15)N/(1)H HSQC spectrum are split into two with increasing pressure, showing the presence of a second conformer in equilibrium with the first. Thermodynamic analysis of the pressure and temperature dependencies indicates that the second conformer is characterized by a smaller partial molar volume (DeltaV = -25 mL/mol at 15 degrees C) and smaller enthalpy and entropy values, suggesting that the second conformer is more open and hydrated than the first. The splittings of the cross-peaks (by approximately 1 ppm on (15)N axis at 2000 bar) arise from the hinges of the M20 loop, the C-helix, and the F-helix, all of which constitute the major binding site for the cofactor NADPH, suggesting that major differences in conformation occur in the orientations of the NADPH binding units. The Gibbs free energy of the second, open conformer is 5.2 kJ/mol above that of the first at 1 bar, giving an equilibrium population of about 10%. The second, open conformer is considered to be crucial for NADPH binding, and the NMR line width indicates that the upper limit for the rate of opening is 20 s(-)(1) at 2000 bar. These experiments show that high pressure NMR is a generally useful tool for detecting and analyzing "open" structures of a protein that may be directly involved in function.

Single amino acid substitutions in flexible loops can induce large compressibility changes in dihydrofolate reductase

To address the effects of single amino acid substitutions on the flexibility of Escherichia coli dihydrofolate reductase (DHFR), the partial specific volume (v(o)) and adiabatic compressibility (beta(s)(o)) were determined for a series of mutants with amino acid replacements at Gly67 (7 mutants), Gly121 (6 mutants), and Ala145 (5 mutants) located in three flexible loops, by means of precise sound velocity and density measurements at 15 degrees C. These mutations induced large changes in v(o) (0.710-0.733 cm(3). g(-1)) and beta(s)(o) (-1.8 x 10(-6)-5.5 x 10(-6) bar(-1)) from the corresponding values for the wild-type enzyme (v(o)=0.723 cm(3). g(-1), beta(s)(o) = 1.7 x 10(-6) bar(-1)), probably due to modifications of internal cavities. The beta(s)(o) value increased with increasing v(o), but showed a decreasing tendency with the volume of the amino acid introduced. There was no significant correlation between beta(s)(o) and the overall stability of the mutants determined from urea denaturation experiments. However, a mutant with a large beta(s)(o) value showed high enzyme activity mainly due to an enhanced catalytic reaction rate (k(cat)) and in part due to increased affinity for the substrate (K(m)), despite the fact that the mutation sites are far from the catalytic site. These results demonstrate that the flexibility of the DHFR molecule is dramatically influenced by a single amino acid substitution in one of these loops and that the flexible loops of this protein play important roles in determining the enzyme function.

Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility

The partial specific volume, v, and adiabatic compressibility, beta(s), of Escherichia coli dihydrofolate reductase were measured at 30 degrees C in the presence of various ligands (folate, dihydrofolate, tetrahydrofolate, NADPH, NADP, methotrexate, and KCl). Binding of these ligands (binary and ternary complexes) brought about large changes of v (0.734-0.754 cm(3) g(-1)) and beta(s) (6. 6x10(-6)-9.8x10(-6) bar(-1)), keeping a linear relationship between the two parameters. The values of v and beta(s) increased with an increase in internal cavity, V(cav), and a decrease in accessible surface area, ASA, which were calculated from the X-ray crystal structures of the complexes. A large variation of V(cav) relative to ASA by ligand binding suggested that the cavity is a dominant factor and the effect of hydration might be small for the ligand-induced changes of v and beta(s). The beta(s) values of the binary and ternary complexes suggested a characteristic conformational flexibility of the kinetic intermediates in the enzyme reaction coordinate. Comparison of beta(s) with the cavity distribution in the crystal structures revealed that the flexibility of the intermediates was mainly determined by the total cavity volume with minor contributions of the number, position, and size of cavities. These results demonstrate that the compressibility is a useful measure of the conformational flexibility of the intermediates in the enzyme reaction and that the combined study of compressibility and X-ray crystallography gives new insight into the protein dynamics through the behavior of the cavities.

Nitrilase of Rhodococcus rhodochrous J1. Conversion into the active form by subunit association

Nitrilase-containing resting cells of Rhodococcus rhodochrous J1 converted acrylonitrile and benzonitrile to the corresponding acids, but the purified nitrilase hydrolyzed only benzonitrile, and not acrylonitrile. The activity of the purified enzyme towards acrylonitrile was recovered by preincubation with 10 mM benzonitrile, but not by preincubation with aliphatic nitriles such as acrylonitrile. It was shown by light-scattering experiments, that preincubation with benzonitrile led to the assembly of the inactive, purified and homodimeric 80-kDa enzyme to its active 410-kDa aggregate, which was proposed to be a decamer. Furthermore, the association concomitant with the activation was reached after dialysis of the enzyme against various salts and organic solvents, with the highest recovery reached at 10% saturated ammonium sulfate and 50% (v/v) glycerol, and by preincubation at increased temperatures or enzyme concentrations.

Polyol-induced molten globule of cytochrome c: an evidence for stabilization by hydrophobic interaction

To address the contribution of hydrophobic interaction to the stability of molten globule (MG) of proteins, the effects of various polyols (ethylene glycol, glycerol, erythritol, xylitol, sorbitol, and inositol) on the structure of acid-unfolded horse cytochrome c were examined at pH 2, by means of circular dichroism (CD), partial specific volume, adiabatic compressibility, and differential scanning calorimetry (DSC). Addition of polyols induced the characteristic CD spectra of MG, the effect being enhanced with an increase in their concentration and chain length (the number of OH groups) of polyols except for ethylene glycol. The free energy change of MG formation by sorbitol was comparable with those for the salt-induced MG formation but the heat capacity change was negligibly small. The partial specific volume did not change within the experimental error but the adiabatic compressibility largely increased by MG formation. The sorbitol-induced MG showed a highly cooperative DSC thermogram with a large heat capacity change in comparison with the salt-induced one. These results demonstrate that polyols can stabilize the MG state of this protein through the enhanced hydrophobic interaction overcoming the electrostatic repulsion between charged residues. The stabilizing mechanism and structure of MG state induced by polyols were discussed in terms of the preferential solvent interactions and osmotic pressure of the medium, in comparison with the salt-induced one.

Protective roles of bacterioruberin and intracellular KCl in the resistance of Halobacterium salinarium against DNA-damaging agents

Halobacterium salinarium, a member of the extremely halophilic archaebacteria, contains a C50-carotenoid namely bacterioruberin. We have previously reported the high resistance of this organism against the lethal actions of DNA-damaging agents including ionizing radiation and ultraviolet light (UV). In this study, we have examined whether bacterioruberin and the highly concentrated salts in this bacterium play protective roles against the lethal actions of ionizing radiation, UV, hydrogen peroxide, and mitomycin-C (MMC). The colourless mutant of H. salinarium deficient in bacterioruberin was more sensitive than the red-pigmented wild-type to all tested DNA-damaging agents except MMC. Circular dichroism (CD) spectra of H. salinarium chromosomal DNA at various concentrations of KCl (0-3.5 M) were similar to that of B-DNA, indicating that no conformational changes occurred as a result of high salt concentrations. However, DNA strand-breaks induced by ionizing radiation were significantly reduced by the presence of either bacterioruberin or concentrated KCl, presumably due to scavenging of free radicals. These results suggest that bacterioruberin and intracellular KCl of H. salinarium protect this organism against the lethal effects of oxidative DNA-damaging agents.

Acetonitrile-protein interactions: amino acid solubility and preferential solvation

The solubility of amino acids and the preferential solvent interaction of hen-egg lysozyme in acetonitrile (AN)-water mixtures (<60 w/v% AN) were investigated by means of densimetric and refractometric methods at 25 degreesC. The free energy of transfer from water to aqueous AN was negative for most nonpolar side-chains of amino acids and positive for the peptide group, the extent being comparable to those for methanol and ethanol systems. Addition of AN to an aqueous solvent was thus suggested to weaken the hydrophobic interaction and to enhance the peptide-peptide hydrogen bond therein leading to the denaturation of proteins. A parallel examination by circular dichroism confirmed that the conformation of lysozyme (pH 3) remains native in aqueous AN up to 40% but changes to the helix-rich form at higher AN concentrations. At all solvent compositions up to 50% AN (pH 3), however, lysozyme was preferentially hydrated probably due to a local salting-out of the AN molecules from the charges on the protein surface, indicating the increase of the chemical potential of the protein. These results are discussed in relation to the role of AN as an eluting organic solvent in reverse-phase chromatography.

Effects of point mutations at the flexible loop alanine-145 of Escherichia coli dihydrofolate reductase on its stability and function

To elucidate the role of a flexible loop (residues 142-149) in the stability and function of Escherichia coli dihydrofolate reductase, alanine-145 in this loop was substituted by site-directed mutagenesis with ten amino acids (Glu, Phe, Gly, His, Ile, Leu, Arg, Ser, Thr, and Val). The amount of three mutant proteins (A145E, A145I, and A145L) in cells was too small to allow the measurement of circular dichroism (CD) spectra and urea unfolding. The CD spectra of other seven mutants were identical with those of the wild-type DHFR, indicating that the native conformation of DHFR was not affected by the mutations. The free energy change of unfolding by urea decreased with an increase in the hydrophobicity of amino acid residues introduced, A145T>A145R>A145G>=A145S>=A145H>A145V++ +>wild-type>=A145F. The steady-state kinetic parameters for the enzyme reaction, Km and ksub, were only slightly influenced by the mutations. These results suggest that site 145 in the flexible loop plays an important role in the stability but has little or no effect on the native structure and function of this enzyme. The characteristics of the mutations are discussed in comparison with those of mutations at site 67 [Ohmae et al. (1996) J. Biochem. 119, 703-710] and at site 121 [Gekko et al. (1994) J. Biochem. 116, 34-41] in two other flexible loops.

Nonadditive effects of double mutations at the flexible loops, glycine-67 and glycine-121, of Escherichia coli dihydrofolate reductase on its stability and function

The structure, stability, and enzymatic function of dihydrofolate reductase (DHFR) from Escherichia coli are influenced by point mutations at sites 67 and 121 in two flexible loops [Gekko et al. (1994) J. Biochem. 116, 34-41; Ohmae et al. (1996) J. Biochem. 119, 703-710]. In the present study, eight double mutants at sites 67 and 121 (G67V/G121S, G67V/G121A, G67V/G121C, G67V/G121D, G67V/G121V, G67V/G121H, G67V/G121L, and G67V/G121Y) were constructed in order to identify interactions between the two sites of DHFR. The far-ultraviolet circular dichroism spectra of double mutants were clearly different from those of the respective single mutants, with significant changes being observed for three mutants, G67V/G121A, G67V/G121L, and G67V/G121S. The Gibbs free energy change of urea unfolding of double mutants could not be expressed by the sum of those of the respective single mutants except for G67V/G121H. The steady-state kinetic experiments showed that the effect of double mutations manifests itself not in Km but in k(cat), and the transition-state stabilization energy for G67V/G121A, G67V/G121C, and G67V/G121L is not equal to the sum of those for the single mutants. These results indicate that the additivity rule essentially does not hold for these double mutants, and that long-range interactions occur between sites 67 and 121, even though they are separated by 27.7 A. This is evidence that the flexible loops play important roles in the stability and function of this enzyme through structural perturbations, in which a small alteration in local atomic packing due to amino acid substitution is cooperatively magnified over almost the whole molecule.

Adiabatic compressibility of flagellin and flagellar filament of Salmonella typhimurium

The partial specific volume and adiabatic compressibility of flagellin, its F40 fragment deprived of the disordered terminal regions, from Ala-1 to Arg-65 and from Ser-451 to Arg-494, and the flagellar filament of Salmonella typhimurium were determined from the density and the sound velocity measurements at 15 degrees C. The partial specific volumes were 0.728 cm3/g, 0.745 cm3/g, and 0.734 cm3/g, and the partial specific adiabatic compressibilities were 4.0 x 10(-12) cm2/dyn, 6.7 x 10(-12) cm2/dyn, and 4.7 x 10(-12) cm2/dyn, for flagellin, F40, and the filament, respectively. The smaller values of flagellin than those of F40 are reasonably explained by the presence of disordered terminal regions, which are supposed to be highly hydrated by water molecules. The volume increase upon polymerization of flagellin into the filament is also confirmed by depolymerization under a high pressure. The smaller volume and compressibility of the filament compared with those of F40 suggest an extensive hydration of the filament on its complex surface structure, which surpasses the effect on the volume and compressibility by a possible increase in the cavity volume at intersubunit interfaces upon polymerization.

High-salt effects on the structure and damage of chromosomal DNA in Halobacterium salinarium, an extremely halophilic bacterium

High concentration salt effects on the structure and radiation-induced damages of DNA were studied to elucidate the biochemical mechanism of the resistance of halophilic H. salinarium against DNA damaging agents. High concentration of KCl did not induce significant conformational changes in H. salinarium chromosomal DNA, but exhibited an extensive protective effect on the radiation-induced single-strand breaks of plasmid DNA.

Acid and thermal unfolding of Escherichia coli dihydrofolate reductase

The acid and thermal unfolding of Escherichia coli dihydrofolate reductase (DHFR) were studied by means of circular dichroism (CD) and fluorescence spectroscopy. There existed at least one intermediate around pH 4 in the acid unfolding process at 15 degrees C, in which the tertiary structure was disrupted before unfolding of the secondary structure. The fluorescence energy transfer from intrinsic tryptophan residues to 1-anilinonaphthalene-8-sulfonate suggested the disruption of the tertiary structure around some tryptophan residues of the intermediate. The thermal unfolding process at pH 7.0 also involved at least one intermediate having a disrupted tertiary structure and a folded secondary structure. The three-state thermodynamic analysis showed that the intermediate in thermal unfolding was less stable by 1.8 kcal/mol than the native state. The similarity of the far-ultraviolet CD spectra of acid and thermally unfolded forms suggests that both types of unfolding produce the same structure, which may be a molten globule intermediate such as that in the folding kinetics of DHFR. The acid and thermal unfolding were depressed in the presence of KCl due to stabilization of the native form.

Effects of point mutations at the flexible loop glycine-67 of Escherichia coli dihydrofolate reductase on its stability and function

To elucidate the role of a flexible loop (residues 64-72) in the stability and function of Escherichia coli dihydrofolate reductase, glycine-67 in this loop was substituted by site-directed mutagenesis with seven amino acids (Ala, Cys, Asp, Leu, Ser, Thr, and Val). The circular dichroism spectra suggested that the confirmation of the native structure was affected by the mutations in both the presence and absence of NADPH. The free energy change of unfolding by urea decreased in the order of G67A > G67S > or = wild-type > or = G67D > G67T > G67C > or = G67L > G67V. The steady-state kinetic parameters for the enzyme reaction, Km and kcat, were only slightly influenced, but the rate of the hydride transfer reaction was significantly changed by the mutations, as revealed by the deuterium isotope effect on the enzyme activity. These results suggest that site 67 in the flexible loop, being very far from the active site, plays an important role in the stability and function of this enzyme. The characteristics of the mutations were discussed in terms of the modified flexibility of the native structure, compared with the results of mutations at site 121 in another flexible loop.

A large compressibility change of protein induced by a single amino acid substitution

The adiabatic compressibility (beta s) was determined, by means of the precise sound velocity and density measurements, for a series of single amino acid substituted mutant enzymes of Escherichia coli dihydrofolate reductase (DHFR) and aspartate aminotransferase (AspAT). Interestingly, the beta s values of both DHFR and AspAT were influenced markedly by the mutations at glycine-121 and valine-39, respectively, in which the magnitude of the change was proportional to the enzyme activity. This result demonstrates that the local change of the primary structure plays an important role in atomic packing and protein dynamics, which leads to the modified stability and enzymatic function. This is the first report on the compressibility of mutant proteins.

Compactness of thermally and chemically denatured ribonuclease A as revealed by volume and compressibility

The conformational changes of ribonuclease A due to thermal and guanidine hydrochloride denaturation were monitored by means of precise density and sound velocity measurements. It was found that the apparent molar volume decreased but the adiabatic compressibility increased on thermal denaturation under acidic conditions (pHs 1.60, 1.90, and 2.08). On the other hand, guanidine hydrochloride denaturation (pH 2.00) brought about large decreases in the compressibility and apparent molar volume. These results indicate that the conformation of the denatured protein is greatly different between the two types of denaturation: the thermally denatured state corresponds to the structure with enhanced thermal fluctuation having a residual secondary structure and a high local concentration of nonpolar groups exposed, but the guanidine hydrochloride denaturation leads to exposure of a large amount of amino acid residues, resulting in an increase in hydration and a decrease in the internal cavity. The compressibility changes due to both types of denaturation were not correlated to a loss of the secondary structure, as judged by means of circular dichroism. These findings suggest that the compactness and thermal fluctuation of the protein cannot be described by a two-state denaturation model and that there are some molten-globule-like intermediates in the denaturation processes.

Point mutations at glycine-121 of Escherichia coli dihydrofolate reductase: important roles of a flexible loop in the stability and function

To elucidate the role of a flexible loop in the stability and function of Escherichia coli dihydrofolate reductase, glycine-121 in a flexible loop (residues 117-131), separated by 19 A from active site Asp27, was substituted by site-directed mutagenesis with eight amino acids (Ala, Val, Leu, Asp, Ser, Cys, Tyr, and His). The free energy change of unfolding decreased in the order of G121A > G121D > G121C > G121S, wild-type > G121H > G121Y > G121L > G121V. The thermal denaturation temperature decreased with all mutations, accompanied by a decrease in the calorimetric enthalpy of denaturation. The steady-state kinetic parameter for the enzyme reaction, Km, was only slightly influenced, but kcat was significantly decreased by the mutations, there being 3- (G121C) to 42-fold (G121L) decreases in kcat/Km compared to that of the wild-type enzyme. The effects of mutations on the stability and enzyme activity were statistically examined as a function of the hydrophobicity and volume of amino acids introduced. The diminished stability and activity with increases in the hydrophobicity and volume of amino acids suggest that the main effect of the mutations would be modification of the flexibility of the loop due to overcrowding of the bulky side chains, overcoming the enhancement of the hydrophobic interaction.

Effects of point mutation in a flexible loop on the stability and enzymatic function of Escherichia coli dihydrofolate reductase

To elucidate the role of a flexible loop in the stability and function of Escherichia coli dihydrofolate reductase, glycine-121 in the flexible loop (117-131) was substituted to valine and leucine by site-directed mutagenesis. Despite the increased hydrophobicity of the side chains, the free energy changes of unfolding of the two mutants (G121V and G121L) determined by urea denaturation at 15 degrees C were decreased by 1.22 and 0.38 kcal/mol, respectively, compared with that of the wild-type. Thermal denaturation temperature, as monitored by differential scanning calorimetry, was decreased by 2.4 and 5.2 degrees C for G121V and G121L, respectively, accompanying the decrease in enthalpy change of denaturation. These findings indicate that the structure of DHFR is destabilized by the mutations, predominantly due to the large decrease in enthalpy change of denaturation relative to entropy change of denaturation. The steady-state kinetic parameter in the enzyme reaction, Km, was not influenced but kcat was greatly decreased by these mutations, resulting in 240- and 52-fold decreases in kcat/Km for G121V and G121L, respectively. The main effect of the mutations appeared to be modification of the flexibility of the loop due to overcrowding of the bulky side chains, overcoming the enhancement of hydrophobic interaction.

Effect of pressure on the sol-gel transition of gelatin

The effects of hydrostatic pressure on the sol-gel transition of gelatins were studied in the concentration range 1.5-12.5% under high pressures up to 300 MPa. The gelatin gels were stabilized by pressure: the pressure-induced elevation of melting temperature, (dT/dP)m, was 3.89 x 10(-2), 3.17 x 10(-2) and 2.92 x 10(-2) K/MPa for gelatins of Bloom No. 60, 225 and 304, respectively. The enthalpy, entropy and volume changes accompanying the gel formation were calculated from the Eldridge-Ferry plots and the Clausius-Clapeyron equation. The volume changes of gelation were estimated to be -25.7, -20.8 and -18.3 ml/mol of cross-links for gelatins of Bloom No. 60, 225 and 304, respectively, which were almost independent of pressure. The kinetic process of gelation was suppressed under high pressure, indicating the positive activation volume of gelation. These volume changes were discussed in terms of the characteristic hydration modes of cross-linking junctions of gelatin gels, comparing them with those of native collagen.

Electroviscosity of polyelectrolyte solutions

A theoretical expression for the electroviscous effect in polyelectrolyte solutions, caused by the distortion of counterion-distribution and counterion flow around a polyion under a velocity gradient of solvent flow, was obtained to elucidate the characteristic behaviour of the viscosity of highly charged polyelectrolyte solutions observed at low salt concentration. The derivation of the theory was performed on the basis of the Navier-Stokes-Onsager equation, Poisson equation, and diffusion equations for low molecular ions by the use of a cell model (free-volume model) for a polyion. Energy dissipation was obtained without directly solving these equations. It was found that the derived expression of viscosity explained the experimental results satisfactorily, and that the streaming potential effect caused by the counterion flow played an essential role in the increase in viscosity of polyelectrolyte solutions at finite polymer concentration and low salt concentration ranges.

Flexibility of globular proteins in water as revealed by compressibility

In order to elucidate the flexibility-structure-function relationships of proteins, the adiabatic compressibility of about 30 globular proteins, including food proteins, was determined by means of sound velocity and density measurements in aqueous solutions. Most proteins studied showed positive compressibility, indicating the large internal flexibility of the molecules. The volume fluctuation was in the range of 30-200 ml/mol, which corresponded to about 0.3% of the total protein volume. From the statistical analyses of the compressibility data, it was found that the flexibility of proteins is closely related to structural factors such as hydrophobicity, helix element, and amino acid composition, and to functional properties such as digestibility and foaming capacity. These results indicate that the dynamics of protein structure should be taken into account in predicting precisely the functions and properties of a protein from its primary or tertiary structure.

Competing solvent effects of polyols and guanidine hydrochloride on protein stability

The denaturation of lysozyme and ribonuclease A by guanidine hydrochloride was followed in the presence and absence of glycerol and sorbitol by means of circular dichroism measurements at 25 degrees C. The protein-solvent interactions in the presence of these polyols were also studied by means of density measurements, for discussion of the mechanism of protein stabilization by polyols in terms of the multicomponent thermodynamic theory. The free energy of denaturation depends linearly on the molarity of guanidine hydrochloride at a given polyol concentration, without modification of the cooperativity of the transition. The free energy of denaturation at an infinite dilution of guanidine hydrochloride increases in proportion to the polyol concentration. These results indicate the competing solvent effects of polyols and guanidine hydrochloride on the structures of proteins. In water-protein-polyol systems, protein is preferentially hydrated to elevate its chemical potential, predominantly due to the unfavorable interaction of polyols with the exposed nonpolar amino acid residues. By linkage with the free energy of denaturation, it was quantitatively determined that the chemical potential of denatured protein is more extensively elevated by addition of polyols than that of native protein. These results demonstrate that polyols stabilize the protein structure through strengthening of the hydrophobic interaction, competing with the effect of guanidine hydrochloride.

Changes in physicochemical properties of mitochondrial membranes during the formation process of megamitochondria induced by hydrazine

Changes in some biochemical and physico-chemical properties of rat liver mitochondrial membranes during the formation process of megamitochondria induced by hydrazine were analyzed. Hepatic mitochondria obtained from rats placed on a 1% hydrazine diet for 3 days became slightly enlarged and sometimes elongated, while they became gigantic after 7 days of hydrazine intoxication. Changes were observed in mitochondria from rats treated with hydrazine for 3 days. Total amounts of phospholipids extracted from mitochondria and submitochondrial fractions were increased. Among phospholipid species, relative amounts of acidic phospholipids were increased. Contents of Ca2+ in mitochondria were increased. Differential scanning calorimetric analysis of mitochondria, especially that of the outer membrane fraction, showed that the thermotropic lipid phase transition temperatures were elevated accompanying the broadening of thermograms and the increase in transition enthalpy. Contents of water in mitochondria were increased significantly with the ratio of freezable water to unfreezable water unchanged. Among the changes observed was that the total amount of phospholipids (except for that of the outer membrane fraction) and the contents of water and Ca2+ nearly returned to normal in megamitochondria after 7 days of hydrazine intoxication. Relative amounts of phospholipids and thermotropic lipid phase transition temperatures of megamitochondria did not return to normal levels and yet changes were smaller than those obtained from 3 days of hydrazine intoxication. The fluidity of mitochondrial membranes was not affected by hydrazine treatment. These data would suggest that hydrazine-induced megamitochondrial formation is not due simply to the swelling of mitochondria, but might be due to the fusion of adjacent mitochondria by Ca2+-acidic phospholipid interactions, and once megamitochondria are formed the mitochondrial membranes are stabilized.

Compressibility-structure relationship of globular proteins

The adiabatic compressibility, -beta s, of 11 globular proteins in water was determined by means of sound velocity measurements at 25 degrees C. All the proteins studied except for subtilisin showed positive -beta s values, indicating the large internal compressibility of the protein molecules. The intrinsic compressibility of proteins free from the hydration effect appeared to be comparable to that of normal ice. The compressibility data for 25 proteins, including 14 reported previously [Gekko, K., & Noguchi, H. (1979) J. Phys. Chem. 83, 2706-2714], were statistically analyzed to examine the correlation of the compressibility with some structural parameters and the amino acid compositions of proteins. It was found that -beta s increases with increasing partial specific volume and hydrophobicity of proteins. The helix element also seemed to be a dynamic domain to increase -beta s. Four amino acid residues (Leu, Glu, Phe, and His) greatly increased -beta s, and another four (Asn, Gly, Ser, and Thr) decreased it. Some empirical equations were derived for the estimation of the -beta s values of unknown proteins on the basis of their amino acid compositions. The volume fluctuations of proteins revealed by the compressibility data were in the range of 30-200 mL/mol, which corresponded to about 0.3% of the total protein volume. The conformational fluctuation seemed to enhance the thermal stability of proteins.

Increased thermal stability of collagen in the presence of sugars and polyols

The effects of sugars and polyols on the thermal denaturation temperature, Tm, of acid-soluble collagen from calf skin were studied at pH 4.0 under atmospheric pressure as well as high pressures up to 4,000 atm. Addition of these compounds invariably raised Tm with increases in their concentration over the whole range of pressure. The extent of stabilization by different sugars and polyols is discussed in terms of their different influences on the structure of water. The hydroxymethyl chain length of polyols and equatorial OH groups of the sugars were found to be decisive factors for their stabilizing effect on collagen structure. The similarity in their stabilizing effects on collagen and globular proteins suggests that our stabilization mechanism proposed for globular proteins can be essentially extended to fibrous proteins: such protein stabilization would be dominantly mediated through a preferential hydration of protein, originating in the water-structure-making character of sugars and polyols.

Calorimetric study on thermal denaturation of lysozyme in polyol-water mixtures

In order to clarify the mechanism of polyol-induced stabilization of protein, the thermal denaturation of lysozyme was studied at pH 4 in aqueous mixtures of some polyols (ethylene glycol, glycerol, erythritol, xylitol, and sorbitol) by a differential scanning calorimetry (DSC). The denaturation temperature, Td, increased with increasing the polyol concentration and the number of hydroxymethyl groups per polyol molecule. The calorimetric enthalpy or denaturation, delta H cal, increased with the increase in polyol concentration, but it was not significantly affected by the chain length of the polyol: delta H cal was about 30 kcal/mol larger in 30% (w/w) aqueous polyols than in water. The standard thermodynamic parameters for denaturation, delta G degrees, delta S degrees, and delta H degrees, which were calculated for glycerol and sorbitol systems using Td and delta H cal and assuming a constant heat capacity change, were an increasing function of polyol concentration. According to the thermodynamics of three component systems, it appeared that one or two polyol molecules are preferentially excluded from the domain of this protein on thermal denaturation. These thermodynamic data support the hypothesis that the thermal stabilization of lysozyme by polyols is due to a preferential solvent interaction effect which strengthens the hydrophobic interaction of the protein.

Mechanism of polyol-induced protein stabilization: solubility of amino acids and diglycine in aqueous polyol solutions

The solubilities of several amino acids and diglycine have been measured in water and at several concentrations of methanol and various polyols (glycerol, erythritol, xylitol, sorbitol, and inositol). The solubility data were used to calculate the free energy of transfer of amino acid side chains and peptide group from water to the aqueous alcohol solutions. The results for methanol systems were similar to those reported for ethanol and dioxane systems. The free energy of transfer to aqueous solutions of linear polyols was positive for most nonpolar side chains and peptide group, but high concentrations of the polyols may disrupt the hydrophobic interactions of large nonpolar side chains. Moreover, the linear polyols appeared to stabilize the hydrophobic interaction more effectively and the peptide-peptide hydrogen bond less effectively with increasing hydroxymethyl chain length of polyols. A cyclic polyol, inositol, had a very strong stabilizing ability on hydrophobic interactions of nonpolar side chains, but it may act as a destabilizing reagent for peptide-peptide hydrogen bonds. From these results, it was concluded that the protein stabilization by polyols is a manifestation of polyol-induced strengthening of the hydrophobic interaction of protein molecules.

Enthalpy and entropy of transfer of amino acids and diglycine from water to aqueous polyol solutions

The enthalpies of transfer of several amino acids and diglycine from water to aqueous polyols (glycerol, xylitol, sorbitol, and inositol) have been calorimetrically determined in order to clarify the mechanism of polyol-induced stabilization of proteins. The obtained enthalpy data were combined with the data on free energy of transfer previously determined to calculate the corresponding entropy of transfer. The enthalpies of transfer of nonpolar side chains of amino acids and peptide group were positive and negative, respectively, depending on the polyol concentration and hydrophobicity of the side chains. This indicates that the non-spontaneous transfer of nonpolar side chains to aqueous polyols is due to an enthalpy effect while that of peptide group is due to an entropy effect. These thermodynamic data are discussed in terms of changes in water structure or solvent ordering around the solute molecules. It was found that the polyol-induced stabilization of proteins is a result of a complicated enthalpy-entropy compensation phenomenon closely related to the solvent ordering around the solute molecules; consequently, the polyol effects on nonpolar side chains do not necessarily dominate those on peptide groups in an enthalpic sense.

Mechanism of protein stabilization by glycerol: preferential hydration in glycerol-water mixtures

A densimetric investigation of the interactions between solvent components in glycerol-water mixtures (between 10 and 40 vol % glycerol) and seven proteins have been carried out in the acid pH region. All the proteins were found to be preferentially hydrated at all conditions used, i.e., addition of the proteins to the mixed solvent results in an increase in the chemical potential of glycerol. It is considered that this thermodynamically unfavorable interaction should tend to minimize the surface of contact between proteins and glycerol and in this way stabilize the native structure of globular proteins.

Thermodynamic and kinetic examination of protein stabilization by glycerol

The effect of concentrated glycerol on the thermal transitions of chymotrypsinogen and ribonuclease has been examined by differential spectrophotometry at 293 and 287 mm, respectively. It was found that for both proteins addition of glycerol raises the transition temperature, the increase in Tm being greater for ribonuclease than for chymotrypsinogen. This increase in the free energy of denaturation appears to reflect primarily a decrease in the entropy change. Analysis in terms of the Wyman linkage equation shows that, for both proteins, the exclusion of glycerol from the protein domain increases on denaturation i.e., the chemical potential of glycerol becomes even more positive when the protein unfolds relative to the native structure. This provides the thermodynamic stabilization free energy. Results of the kinetic examination of the slow unfolding reaction are consistent with the concept that the preferential exclusion of glycerol is related, at least in part, to enhanced solvent ordering.

Preferential hydration of bovine serum albumin in polyhydric alcohol-water mixtures

The preferential solvent interaction with bovine serum albumin in aqueous solution of polyhydric alcohols (ethylene glycol, glycerol, xylitol, sorbitol, mannitol, and inositol) was investigated by a densimetric method with the application of multicomponent theory. This proteins was preferentially hydrated in all solvent systems examined: the extent depended on the number and the steric configuration of the hydroxyl groups of alcohols. The absolute interactions of these alcohols with the protein were estimated by assuming that the amount of hydration of protein at every solvent composition used is identical with that in pure water. The preferential hydration of the protein in 30% aqueous solutions of glycerol and sorbitol was found to decrease as the temperature was increased, indicating that the increase in chemical potential of protein on transferring it from water to both aqueous solvents is generated by a large positive enthalpy change, sufficient to compensate for the positive entropy change in the transfer process. On the basis of these results, and mechanism of stabilization of protein structure by these alcohols was discussed from the viewpoint of the solvation of protein.

Thermodynamics of polyol-induced thermal stabilization of chymotrypsinogen

In order to clarify the mechanism of polyol-induced stabilization of protein, the thermodynamic parameters (delta G degree, delta H degree, and delta S degree) of thermal denaturation of chymotrypsinogen have been measured in aqeous solutions of some polyols (ethylene glycol, erythritol, adonitol, sorbitol, mannitol, and inositol) by a differential spectrophotometric method. On increasing the alcohol concentration and the number of hydroxymethyl groups of the alcohols, delta G degree increased as a result of a large decrease in delta S degree compensating for a decrease in delta H degree. This result means that the stabilization of this protein by polyols is due to the entropy effect, and that the free energy change of transfer of the denatured protein from water to aqueous media containing these alcohols must be larger than that of the native protein. This strongly supports the previous proposal that the driving force of protein stabilization induced by polyols is a solvent medium effect or a solvent ordering effect. The decreases in delta H degree and delta S degree with polyols are expected to be more due to the effects of polyols on peptide-water interactions than to exposed nonpolar groups of denatured protein.