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At least 973 records · Page 54Linked to original sources
PubMed1983

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp.

The thermodynamics of double-helix formation in 1 M NaCl have been measured spectrophotometrically for CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. The results indicate additional double-helical stability is conferred by the terminal unpaired bases. The 3' A stabilizes the double helix more than the 5' A or the 3' U. The increased stability is due to a more favorable enthalpy change for double-helix formation. Comparison of the thermodynamics for CCGG, ACCGGp, CCGGUp, and ACCGGUp indicates stacking interactions are somewhat more important than pairing interactions in determining the stability of the terminal AU base pairs in ACCGGUp.

Base Composition↗
PubMed1983

Thermodynamic binding constants for gallium transferrin.

Gallium-67 is widely used as an imaging agent for tumors and inflammatory abscesses. It is well established that Ga3+ travels through the circulatory system bound to the serum iron transport protein transferrin and that this protein binding is an essential step in tumor localization. However, there have been conflicting reports on the magnitude of the gallium-transferrin binding constants. Therefore, thermodynamic binding constants for gallium complexation at the two specific metal binding sites of human serum transferrin at pH 7.4 and 5 mM NaHCO3 have been determined by UV difference spectroscopy. The conditional constants calculated for 27 mM NaHCO3 are log K1 = 20.3 and log K2 = 19.3. These results are discussed in relation to the thermodynamics of transferrin binding of Fe3+ and to previous reports on gallium binding. The strength of transferrin complexation is also compared to that of a series of low molecular weight ligands by using calculated pM values (pM = -log [Ga-(H2O)6]) to express the effective binding strength at pH 7.4.

Edetic Acid↗
PubMed1983

Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A.

General thermodynamic models are presented that can account for the existence of heat capacity changes and compensation between the enthalpy and entropy changes in protein-ligand interactions. The models involve the coupling between some type of transition in the state of the protein (or ligand) and the binding process. The coupled transition may be a proton dissociation, the binding of a second ligand, a change in the degree of aggregation, or a conformational change in either the protein or ligand. Both mandatory coupling and nonmandatory coupling between the binding process and the transition are considered. The model is also extended to include a multistate transition of the protein. Computer simulations show that apparently linear compensation plots (plots of delta H degrees vs. delta S degrees) with a slope approximately equal to the experimental temperature are to be expected for the binding of a ligand to a protein when such coupled reactions exist. Also heat capacity changes, which may be either positive or negative, are to be expected to accompany the reaction. Experimental thermodynamic data for the binding of cytidine 3'-phosphate to ribonuclease A are presented. These data demonstrate apparent enthalpy-entropy compensation when pH and ionic strength are varied. A negative heat capacity change, ranging from -145 (at mu = 1.0 M) to -225 cal/(mol X deg) (at mu = 0.05 M), is also observed for this protein-ligand interaction. The apparent compensation and heat capacity change data are interpreted according to the models presented.

Computers↗
PubMed1984

Thermodynamic equation of state for cholesteryl esters in surface phases.

Phase behavior at the air-water interface for binary mixtures of cholesteryl esters with several phospholipids was determined and combined with a large body of data from other similar studies. Analysis of areas along the phase boundary between the monolayer phase and either a double layer or a bulk phase revealed a simple, additive relationship between lipid components. This indicates that at its limits the monolayer phase behaves as an ideal mixture of components with fixed partial molecular areas. This concept is supported by the independence of the values of the partial molecular areas from the nature of the other lipid component. General agreement with the model was also found for data from the double-layer-bulk phase boundary. However, in contrast to the monolayer phase boundary, the double-layer phase behaves as if comprised of components with not only fixed but also identical partial molecular areas. The lack of a surface pressure dependency for partial molar areas apparently contradicts earlier thermodynamic descriptions of surfaces. However, satisfactory resolution with theory can be obtained if along the phase boundary each lipid species has a stoichiometric number of water molecules associated with it. This concept is supported by the consistency and values of the parameters calculated from the data by using this model. In both phases, the activity coefficient of interfacial water was constant, and the cholesteryl esters were relatively more hydrated than the other lipids. Overall, this thermodynamic equation of state for phase boundaries provides the basis for modeling the surfaces of natural, cholesteryl ester rich lipid inclusions like lipoproteins and arterial lipid deposits.

Cholesterol Esters↗
PubMed1985

Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp.

The thermodynamics of ACCGGCp, ACCGGAp, and ACCGGGp helix formation have been measured in 1 M NaCl. The terminal mispairs stabilize the CCGG core duplex at 10(-4) M in the order AC approximately equal to AA less than AG approximately equal to AU. The data reported provide thermodynamic parameters for RNA structure prediction and suggest useful approximations for including other mismatches in current algorithms.

Base Sequence↗
PubMed1986

Thermodynamics of dimer and tetramer formations in rabbit muscle phosphofructokinase.

The self-association of rabbit muscle phosphofructokinase (PFK) was monitored as a function of temperature, pH, and ionic strength in order to understand the thermodynamics of this aggregation process. Thermodynamic parameters obtained from the temperature study show that the dimerization of PFK is characterized by negative entropy and enthalpy changes of -270 +/- 5 eu and -87 +/- 1 kcal/mol, respectively, with no observable change in heat capacity. This is in contrast to the formation of the tetramer, which is governed by positive entropy and enthalpy changes and a positive heat capacity change of 5000 +/- 2000 cal/mol. Low ionic strength also favors the formation of the dimer without a significant influence on the tetramerization, which is enhanced by increasing the pH from 6.00 to 8.55. Furthermore, Wyman linkage analysis [Wyman, J. (1964) Adv. Protein Chem. 19, 224-285] reveals that the formation of the tetramer from the monomer between pH 6.00 and pH 8.55 involves the loss of 3.3 protons. Further analysis shows that ionization of residues with an apparent pKa of 6.9 is linked to the formation of PFK tetramers. The conclusion of this study indicates that the major noncovalent forces governing the formation of the dimer are different from those for the association of the tetramer.

Animals↗
PubMed1987

Alamethicin incorporation in lipid bilayers: a thermodynamic study.

Interaction of the peptide antibiotic alamethicin with phospholipid vesicles has been monitored by changes in its circular dichroic and fluorescent properties. The data are consistent with an incorporation of the peptide in the lipid bilayer. Aggregation of alamethicin in the membrane phase is evident from a characteristic concentration dependence of the incorporation, reflecting the existence of a critical concentration. The data can be fully understood in terms of a theoretical approach that includes aggregation and thermodynamic nonideality. Thermodynamic parameters of the peptide-lipid interaction have been evaluated under a variety of conditions of temperature, ionic strength, and lipid type (saturated and unsaturated fatty acid chains). From the results obtained in this study, one can extrapolate to the incorporation behavior of alamethicin at low concentrations, as they are typical for measurements of conductance across planar lipid films. This leads to a simple explanation of the voltage-gating mechanism of alamethicin in a straightforward way.

Alamethicin↗
PubMed1988

Sigmoidal relation between mitochondrial respiration and log ([ATP]/[ADP])out under conditions of extramitochondrial ATP utilization. Implications for the control and thermodynamics of oxidative phosphorylation.

Except for close to state 3, mitochondrial respiration has been observed to vary almost linearly with the extramitochondrial phosphorylation potential. For the understanding of the control, thermodynamics, and stoichiometries of oxidative phosphorylation, it is important if this linearity corresponds to an extension of a near-equilibrium flow-force relationship. Using three methods to determine the extramitochondrial ATP/ADP ratio, we observed that at high ATP/ADP ratios the relationship between respiratory rate and log (ATP/ADP) deviated in a sigmoidal fashion from linearity, if the amount of hexokinase present was modulated. In a titration with uncoupler, the sigmoidicity at high ATP/ADP ratios was absent. This difference between the flow-force relationships of these two experiments suggests that the sigmoidicity in the former case reflects a nonproportional flow-force relationship of the adenine nucleotide translocator. In the latter case, one measures the flow-force relationship of the redox-driven proton pumps alone, which turns out to be virtually linear. We determined the flow-force relation of the adenine nucleotide translocator for two ways of varying the force and confirmed the sigmoidicity in both cases. The implication is that the near-linearity of the flow-force relationships at intermediary respiratory rates does not correspond to an Onsager-type (near equilibrium) linearity. We discuss that this phenomenon requires the application of nonclassical forms of nonequilibrium thermodynamics and may be responsible for some of the control over oxidative phosphorylation that is exerted by the cytosolic ATP consuming processes.

Adenosine Diphosphate↗
PubMed1990

Kinetics and thermodynamics of oxygen and carbon monoxide binding to the T-state hemoglobin of Urechis caupo.

The tetrameric hemoglobin from Urechis caupo is nearly ideal for studying ligation to the T-state. Our previous EXAFS study had shown that the Fe is displaced 0.35 A from the mean plane of the porphyrin in the HbCO derivative. We have carried out detailed kinetic studies of oxygen and CO ligation as a function of temperature in order to characterize both the kinetics and thermodynamics of ligation in this hemoglobin. The entropy change associated with ligation essentially corresponds to simple immobilization of the ligand and is virtually the same as that we have determined for leghemoglobin, an extreme R-state-type hemoglobin. The low ligand affinities thus derive from small enthalpies of ligation, which can be correlated with the large out of plane displacement of the Fe. Only oxygen pulse measurements revealed kinetic evidence for cooperative oxygen binding, but a direct measurement of oxygen binding gave a Hill number of 1.3. An allosteric analysis gave L = 2.6 and c = 0.048 (oxygen) and c = 0.77 (CO). The higher affinity state in this weakly cooperative hemoglobin is denoted T*, and it is for this state that thermodynamic quantities have been determined. The small differences between T and T* in CO binding were nevertheless sufficient to allow us to measure by flash photolysis the rate of the T*----T conformational change in terms of an allosteric model. The half-time for this transition was calculated to be 8-14 ms at 20 degrees C.

Allosteric Regulation↗
PubMed1990

Thermodynamic data from drug-DNA footprinting experiments.

Sequence-dependent thermodynamic quantities for the antiviral agent netropsin and a related bis(N-methylimidazole) dipeptide, lexitropsin, have been determined by DNase I footprinting techniques. The primary data are autoradiographic spot intensities derived from 10 footprinting experiments carried out in the temperature range 0-45 degrees C. After exclusion effects due to overlapped drug sites on DNA and redistribution phenomena associated with the enzyme were accounted for, sequence-dependent binding constants for the two ligands were calculated. Our approach does not require an independent determination of the free drug concentration, which is calculated, with individual site binding constants, by using only footprinting data. The temperature dependence of the binding constants for netropsin implied that the binding enthalpies for all the sites but one on a 139 base pair restriction fragment of pBR 322 DNA are exothermic. Their values roughly correlate with the free energies of binding, which are smaller for sites including a 5'-TA-3' sequence. The binding enthalpies for the lexitropsin to all its sites were exothermic and more negative than those of netropsin. This may be due to the greater ability of the lexitropsin, when compared to netropsin, to form hydrogen bonds with sites on DNA. The binding constants of the lexitropsin toward its GC interaction sequences were much lower than those of netropsin, as can be explained by the reduced charge of the former ligand. Although it is difficult to determine the specific origin of the thermodynamic effects measured, comparison between netropsin and the lexitropsin suggests that the degree of solvation in the minor groove of DNA may be a factor influencing the entropy of the binding process.

Base Sequence↗
PubMed1990

Size and structure of antigen-antibody complexes: thermodynamic parameters.

The role of antigen-antibody (Ag-Ab) complexes in the immune response depends, in part, on the size of the complexes. Previously, we combined electron microscopy with classical and quasi-elastic light scattering to characterize the molecular weight distribution and the conformation of Ag-Ab complexes made from bovine serum albumin (BSA) and pairs of anti-BSA monoclonal antibodies at a single concentration and Ag:Ab molar ratio. In this report, the molecular weight distribution of Ag-Ab complexes was determined by classical light scattering at a single Ag:Ab ratio and over a range of concentrations, and binding of BSA to pairs of MAb was determined by radioimmunoassay at several Ag:Ab molar ratios. A thermodynamic model was developed for the equilibrium size distribution of Ag-Ab complexes formed between a pair of MAb, each with unique affinity and specificity, and an Ag containing a single epitope for each of the pair of MAb. The combined experimental data were used in conjunction with the model to determine the values of cyclization and polymerization constants. Successful determination of the parameters required data from both classical light scattering and electron microscopy. Cyclization constants were lower than those reported in other studies of Ag-Ab complexes; this may be attributable to our use of a protein Ag, as compared to a divalent hapten. In two out of three cases, cyclization constants increased with increasing number of Ab in the complex, in contrast to previous assumptions. The validity of the thermodynamic model was further shown by its ability, in combination with conformational and hydrodynamic model, to predict the hydrodynamic radius of the complexes over a wide range of experimental conditions.

Animals↗
PubMed1981

Thermodynamics of concanavalin A dimer-tetramer self-association: sedimentation equilibrium studies.

The effects of temperature and pH on the reversible dimer-tetramer association of concanavalin A were studied by the high-speed sedimentation equilibrium technique. Both commercial and highly purified preparations of concanavalin A were used. Equilibrium constants were analyzed as a Wyman linked function by using truncated van't Hoff temperature dependence. In the concentration range 0.1-3.0 mg/mL, from 5 to 35 degrees C and between pH 5.5 and pH 7.5 at 0.5 M ionic strength, only dimer and tetramer species were present in both preparations. For purified concanavalin A, association constants ranged from 1.5 X 10(3) to 8.0 X 10(7) M-1. Constants for our commercial preparation were approximately 10-fold lower due to the decrease competency of some subunits to self-associate. From the fit of the Wyman model to the experimental data, delta G degree, delta H degree, delta S degree, and delta Cp degree were calculated for the association and association-linked ionization reactions. From the values of the ionization thermodynamic parameters, the association is governed by the ionization of a histidine side chain on each subunit, either histidine-51 or histidine-121. The association is characterized by large entropy (66.3 cal.mol-1.deg-1 at 25 degrees C) and heat capacity (-821 cal.mol-1.deg-1) changes in accordance with the large hydrophobic association surface observed in crystallographic studies [Reeke, G. N., Jr., Becker, J. W., & Edelman, G. M. (1975) J. Biol. Chem. 250, 1525-1547]. In addition, there is a large enthalpy change (10.4 kcal.mol-1 at 25 degrees C). We propose a model for the interaction based on a more detailed thermodynamic description than was obtained in an earlier, incomplete study [Huet, M., & Clavarie, J. M. (1978) Biochemistry 17, 236-241].

Concanavalin A↗
PubMed1980

Reversible dissociation of wheat germ ribosomal subunits: cation-dependent equilibria and thermodynamic parameters.

The influence of magnesium ion concentration upon the equilibrium between the wheat germ ribosome and its subunits has been studied by light scattering. The curves obtained for ribosome dissociation and subunit reassociation were identical and were independent of the origin and direction of the magnesium ion titration, suggesting that the wheat germ ribosomes are behaving as a homogeneous population equivalent to Escherichia coli type A ribosomes. Increasing K+ concentrations in the presence of Mg2+ favored ribosome dissociation. Polyamines favored subunit reassociation, with 0.1 mM spermine acting as effectively as 1 mM spermidine. Thermodynamic parameters have been determined from the temperature-dependent equilibria and have been compared to those of E. coli type A ribosomes. The association of the 40S and 60S subunits is exothermic. At 1.5 mM Mg2+ and 100 mM K+, the entropy term is negative, favoring ribosome dissociation, and contributes less to the free energy than the enthalpy term. The determination of these thermodynamic parameters was based on molecular weights of 1.2 x 10(6) and 2.3 x 10(6) for the 40S and 60S subunits, respectively, calculated from laser light scattering data.

Kinetics↗
PubMed1979

Thermodynamics of the denaturation of lysozyme in alcohol--water mixtures.

The thermal denaturation of lysozyme was studied at pH 2 in aqueous mixtures of methanol, ethanol, and 1-propanol by high sensitivity differential scanning calorimetry (DSC). The most obvious effect of alcohols was the lowering of Td, the temperature of denaturation, increasingly with higher alcohol concentration and longer alkyl chain. Both the calorimetric and van't Hoff enthalpies of denaturation initially increased and then decreased with increasing alcohol concentration, the ratio of the two enthalpies being nearly unity, 1.007 +/- 0.011, indicating the validity of the two-state approximation for the unfolding of lysozyme in these solvent systems. The reversibility of the denaturation was demonstrated by the reversibility of the DSC curves and the complete recovery of enzymic activity on cooling. The changes in heat capacity on unfolding decreased with increasing alcohol concentration for each alcohol. Experimentally determined values of denaturation temperature and of entropy and heat capacity changes were used to derive the additional thermodynamic parameters delta G degrees and delta S degrees for denaturation as a function of temperature for each alcohol--water mixture. Comparison of the thermodynamic parameters with those reported [Pfeil, W., & Privalov, P.L. (1976) Biophys. Chem. 4, 23--50] in aqueous solution at various values of pH and guanidine hydrochloride concentration showed that these latter changes have no effect on the heat capacity changes, whereas the addition of alcohols causes a sharp decrease.

Alcohols↗
PubMed1979

Effects of anions on the activation thermodynamics and fluorescence emission spectrum of alkaline phosphatase: evidence for enzyme hydration changes during catalysis.

The effect of anions on the thermodynamic activation functions for a model enzyme, calf intestinal alkaline phosphatase (EC 3.1.3.1), have been studied in order to examine the role of protein hydration changes in establishing the energetics of enzyme catalysis. The influences of these anions on the activation volume (delta V) and activation free energy (delta G) reflected clear Hofmeister (lyotropic) series effects, in the order F- greater than Cl- greater than Br- greater than I- (order of increasing salting-out potential). A pronounced covariation was observed between the influences of these anions on Vmax, which is proportional to delta G, and on the negative activation volume of the reaction. Fluoride was able to counteract the influences of Br- and I- on both Vmax and delta V when combinations of these anions were employed. The effects of Br- and I- on Vmax and delta V were more pronounced at lower temperatures. The control delta V was increasingly negative at reduced temperatures. The effects of the neutral salts and propanol on delta V and delta G, as well as the effects of salting-in anions on the activation enthalpy and the negative activation entropy of the reaction, are consistent with a model which proposes that peptide groups or polar side chains on the native enzyme exergonically increase their exposure to solvent during the catalytic activation event. These conclusions are in accord with the known free energy, enthalpy, entropy, and volume changes which occur when model peptide groups are transferred between water and concentrated salt solutions. Consistent with the kinetic results, the fluorescence emission wavelength maximum of alkaline phosphatase increased in the presence of anions in the order F- greater than Cl- greater than Br- greater than I-. The salting-out ion (F-) and the salting-in ions (Br- and I-) shifted lambda max in different directions, and these lambda max shifts could be counterbalanced by using equimolar combinations of salting-in and salting-out anions. Control experiments with a model compound, N-acetyltryptophanamide, showed that the spectra shifts caused by the salts did not result solely from differential quenching by the anions of the solvent-exposed tryptophan(s) on the enzyme. Hofmeister additivity phenomena indicated that the solvent is at the basis of these salt-induced enzyme structural changes. It is concluded that changes in protein solvation during enzymic reactions contribute significantly to the thermodynamic activation parameters in both the native and the salt-perturbed enzyme.

Alkaline Phosphatase↗
PubMed1977

Thermodynamic limits on the size and size distribution of nucleic acids synthesized in vitro: the role of pyrophosphate hydrolysis.

The free-energy change of phosphodiester bond formation from nucleoside triphosphates is more favorable than with nucleoside diphosphates as substrates. Base-stacking interactions can make significant contributions to both delta G degrees ' values. Pyrophosphate hydrolysis when it accompanies the former reaction dominates all thermodynamic considerations. Three experimental situations are discussed in which high-molecular-weight polynucleotides are synthesized without a strong driving force for covalent bond formation. For one of these, a kinetic scheme is presented which encompasses an early narrow Poisson distribution of chain lengths with ultimate passage to a disperse equilibrium population of chain sizes. Hydrolytic removal of pyrophosphate expands the time scale for this undesirable process by a factor of 10(9), while it enormously elevates the thermodynamic ceiling for the average degrees of polymerization in the other two examples. The electron micrographically revealed broad size population from an early study of partial replication of a T7 DNA template is found to adhere (fortuitously) to a disperse most probable representation. Some possible origins are examined for the branched structures in this product, as well as in a later investigation of replication of this nucleic acid. The achievement of both very high molecular weights and sharply peaked size distributions in polynucleotides synthesized in vitro will require coupling to inorganic pyrophosphatase action as in vivo.

Calorimetry↗
PubMed1977

Thermodynamic studies of the reversible association of Escherichia coli ribosomal subunits.

The kinetics of association of Escherichia coli 30S and 50S ribosomal subunits have been carried out as a function of temperature after a magnesium jump from 1.5 to 3 mM. Turbidimetric recordings combined with a stopped-flow apparatus were used to follow the kinetics. The data show that the rates of formation and dissociation of the 70S particles at 3 mM Mg2+ and +25 degrees C were, respectively: k2 = 10(5) M-1 s-1, k1 = 4,5 X 10(-3) s-1; lowering the temperature decreases the rate constants with activation energies equal to E2 = 7.5 kcal/mol, E1 = 26.5 kcal/mol and enhances the association equilibrium towards the 70S species with an enthalpy change (delta H degrees assoc = -19.9 kcal/mol) dominant over the entropy change (delta S degrees assoc = -33 cal/(deg mol)). These thermodynamic parameters were compared to those obtained from studies on the interactions of codon-anticodon in yeast phenylalanine transfer RNA as well as of ribooligonucleotides. The kinetic and thermodynamic data are shown to be consistent with 16S-23S RNA interaction.

Binding Sites↗
PubMed1976

Thermodynamic studies of binary and ternary complexes of pig heart lactate dehydrogenase.

The thermodynamics of the reaction catalyzed by pig heart muscle lactate dehydrogenase (LDH; EC1.1.1,27) have been studied in 0,2 M potassium phosphate buffer, pH 7, over the temperature range of 10 to 35 degrees C by using oxamate and oxalate to simulate the corresponding reactions of the substrates pyruvate and lactate, respectively. The various complexes formed are characterized by Gibbs free energies, enthalpies, and entropies. The Gibbs free energies were determined by equilibrium dialysis investigations, fluorescence titrations, and ultraviolet difference spectroscopy, while the reaction enthalpies stem from direct calorimetric measurements, Formulas are given for both the temperature dependence of the equilibrium constants and the variation with temperature of the enthalpies involved in the four reactions between LDH and NADH or NAD, LDH-NADH and oxamate, and LDH-NAD and oxalate. All reactions show a marked negative temperature coefficient, deltacp, of the binding enthalpies indicating partial refolding to be associated with binary and ternary complex formation. This interpretation appears very probable in view of recent x-ray crystallographic studies on lactate dehydrogenase from dogfish, which demonstrate a volume decrease to occur on binding of oxamate to the LDH-NADH complex. The validity of the thermodynamic parameters, as derived with substrate analogues, for the actual catalytic reaction, gains strong support from the agreement between the sum of the heats involved in the four intermediary reactions reported in this study and direct determinations of the overall enthalpy associated with the catalytic process published in the literature.

Animals↗