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PubMed1976

Thermodynamics of the isothermal denaturation of lysozyme by guanidinium chloride.

A thermodynamic analysis of the isothermal denaturation of lysozyme by guanidinium chloride has been performed. The analysis is based on the equation which relates the equilibrium constant for denaturation to the preferential binding of denaturant. The equation has been derived previously by thermodynamic methods, whereas in this article a derivation based on statistical mechanics is given. By application of the equation the free energy of denaturation is first calculated and from it, by subtracting the calorimetrically-determined enthalpy of denaturation, the entropy of denaturation is determined.

Binding Sites↗
PubMed1978

Thermodynamics of the isothermal interaction of human immunoglobulin G with guanidinium chloride.

A thermodynamic study of the isothermal interaction of human immunoglobulin G with guanidinium chloride, a strong denaturant, has been performed. Free energies of interaction were calculated using preferential binding data obtained by measuring densities at constant chemical potential and constant composition, respectively. Enthalpies of interaction were determined calorimetrically. The values of both thermodynamic parameters as well as those of entropies of interaction have been found to depend crucially on the extent of denaturant binding.

Guanidines↗
PubMed1985

Thermodynamics of agonist and antagonist binding to the alpha 1-adrenoceptor studied using [125I]BE 2254.

The thermodynamics of binding of [125I]BE 2254 to the alpha 1-adrenoceptor in guinea pig brain membranes have been investigated at four different temperatures between 0 and 37 degrees C. The affinity and binding capacity of the radioligand did not vary with temperature. Thus, the change in enthalpy upon binding was close to zero whereas the change in entropy was large and positive (delta S degrees approximately 45 cal/mol-deg). In addition, [125I]BE 2254 has been used as a reporter ligand to probe the thermodynamics of the interaction of a variety of alpha-adrenoceptor agonists and antagonists with the alpha 1-adrenoceptor. Binding of all ligands was associated with large positive changes in entropy (delta S degrees between 18 and 48 cal/mol-deg) and little, or no, change in enthalpy, a finding that provides no convincing evidence for conformational rearrangement of alpha 1-adrenoceptors upon ligand binding.

Animals↗
PubMed1987

An ATP/2e-stoichiometry of 1 1/2 is thermodynamically possible for site 3 of oxidative phosphorylation.

Free energy changes for ATP synthesis (delta GP) and 2e(-)-transfer across Site 3 (delta GR) were determined during oxidative phosphorylation by rat liver mitochondria. At static head, -delta GR/delta GP ranged narrowly between 1.55 and 1.59 with five different respiratory substrates. Thus, an ATP/2e- of 1 1/2 at Site 3 is thermodynamically possible with regards to overall reactants and products. Using nonequilibrium thermodynamics, phenomenological stoichiometries were close to 1 1/2 for all substrates suggesting that ATP/2e- at Site 3 is, in fact, 1 1/2. An ATP/2e- of 1 1/2 can only be possible if H+/O is 4 for cytochrome oxidase.

Adenosine Triphosphate↗
PubMed1989

Regulation of adenylate cyclase by cannabinoid drugs. Insights based on thermodynamic studies.

The abilities of lipophilic cannabinoid drugs to regulate adenylate cyclase activity in neuroblastoma cell membranes were analyzed by thermodynamic studies. Arrhenius plots of hormone-stimulated adenylate cyclase activity exhibited a break point at 20 degrees. The break point was reduced to 14 degrees by benzyl alcohol, consistent with results from other laboratories that have correlated this response with the increase in membrane fluidity induced by benzyl alcohol. Because cannabinoid drugs partition into membrane lipids and alter membrane fluidity parameters in a number of model systems, it was of interest to examine the influence of delta 9-tetrahydrocannabinol and cannabidiol on enzyme activity analyzed by the Arrhenius plot. delta 9-Tetrahydrocannabinol, known to inhibit adenylate cyclase, failed to decrease the transition temperature either at 1 microM or at concentrations exceeding its aqueous solubility (30 microM), suggesting that delta 9-tetrahydrocannabinol could not mimic the effects observed with benzyl alcohol. In contrast, 30 microM cannabidiol, which stimulated enzyme activity slightly, decreased the Arrhenius plot break point to 17.5 degrees. The decrease in the transition temperature in response to benzyl alcohol or cannabidiol was not accompanied by a change in activation energies above or below the transition temperature. delta 9-Tetrahydrocannabinol inhibits adenylate cyclase activity via Gi as does the muscarinic agonist carbachol (Howlett et al., Mol Pharmacol 29: 307-313, 1986). Both carbachol and delta 9-tetrahydrocannabinol decreased the enthalpy and entropy of activation. The net free energy of activation at 37 degrees was increased in the presence of both of these inhibitory agonists. These data suggest that, for the entropy-driven hormone-stimulated adenylate cyclase enzyme, less disorder of the system occurs in the presence of regulators that inhibit the enzyme via Gi. In summary, thermodynamic data suggest that cannabidiol can influence adenylate cyclase by increasing membrane fluidity, but that the inhibition of adenylate cyclase by delta 9-tetrahydrocannabinol is not related to membrane fluidization.

Adenylyl Cyclase Inhibitors↗
PubMed1995

A thermodynamic analysis of estrogen regulation of alpha 2-adrenoceptor binding.

We previously demonstrated that in vivo estradiol treatment markedly attenuates alpha 2-adrenoceptor function and coupling to G-proteins in the hypothalamus of female rats. Ligand binding studies indicated that 48 h exposure to estradiol decreases the number of alpha 2-adrenergic receptors in the agonist high affinity state. In the present studies, when [3H]RX821002 was used to label brain alpha 2-adrenoceptors, the density of binding sites significantly increased in the hypothalamus and preoptic area 48 h after estrogen treatment. Moreover, the thermodynamics of ligand binding to alpha 2-adrenergic receptors in membranes of female rat hypothalamus were modified by the same estradiol treatments that reduce alpha 2-adrenoceptor function. In hypothalamic membranes from ovariectomized control rats, antagonist (RX821002)-receptor binding was primarily entropy-driven while agonist (oxymetazoline) binding had a higher enthalpy component. In membranes from estradiol-exposed animals, the entropic contribution to both agonist and antagonist bindings was markedly increased, and the enthalpy component was reduced. Since the thermodynamic characteristics of ligand-receptor binding are strongly correlated with efficacy in activating signal transduction [36], these data raise the intriguing possibility that steroids regulate transmembrane signaling by stabilization of a receptor conformation with reduced intrinsic efficacy.

Adrenergic alpha-Antagonists↗
PubMed1977

Amphipathic helixes and plasma lipoproteins: thermodynamic and geometric considerations.

In this paper analyses are made of the thermodynamic and geometric properties of the predicted association between amphipathic helixes and phospholipid vesicles. From thermodynamic considerations it is proposed that a major driving force for such an association is the negative free energy gained by the transfer of a number of hydrophobic residues (contained within the non-polar faces of amphipathic helixes), from water to the interior of a phospholipid bilayer. The mechanism proposed is that in the aqueous state a potentially amphipathic sequence forms a non-helical hydrophobic patch on the surface of the apolipoprotein. Formation of an amphipathic helix and simultaneous burial of the hydrophobic residues in the surface of a phospholipid bilayer provides the driving force for lipid association. From this model an estimate of the upperlimit for the hydrophobically driven free energy of lipid association (-40-65 kcal/mol) is calculated for the 4 apolipoproteins with known sequences. On the basis of geometrical considerations a model for an intermediate state of high density lipoprotein (HDL) synthesis is proposed. This model consists of a cholesterol-containing phospholipid bilayer disc whose 'naked" hydrophobic edges are shielded from the aqueous phase by amphipathic helixes of the apolipoproteins. Exposure of these 'bicycle tire" miscelles to the enzyme lecithin : cholesterol acyl transferase (LCAT) is postulated to result in the formation of mature spherical HDL particles with cholesteryl ester forming a neutral lipid core.

Apolipoproteins↗
PubMed1988

Cryomicroscope investigation and thermodynamic modeling of the freezing of unfertilized hamster ova.

Thermodynamic computer modeling was used to predict the freezing response of single-celled unfertilized hamster ova. The cell membrane transport characteristics were investigated, using a microscope diffusion chamber system. The mean osmotically inactive cell volume was determined to be 21.6% of the initial cell volume. An overall mean value of 0.8 +/- 0.1 micron3/micron2.min.atm (= 18 +/- 2.5 micron/sec) was determined for the membrane hydraulic coefficient, Lp. The effect of the extracellular solute concentration on Lp was determined at room temperature (approximately 23 degrees C). A thermodynamic computer model was used to predict the cell response to freezing. The predicted response was compared to the actual volumetric response observed during freezing on a temperature-controlled cryomicroscope conduction stage. The effect of the cooling rate on the nucleation temperature of unprotected ova and protected ova suspended in a 1.5 M DMSO solution was investigated. Overall mean nucleation temperatures of -13 and -57.1 degrees C were observed for unprotected and protected ova, respectively, where the mean nucleation temperature for protected ova was strongly cooling rate dependent.

Animals↗
PubMed1996

Binding thermodynamics of 5-HT1A receptor ligands.

The thermodynamic parameters delta G degree, delta H degree and delta S degree of the binding equilibrium of 15 ligands (eight agonists and seven antagonists) to the 5-HT1A receptor subtype have been determined by affinity measurements carried out on rat cortex membranes (minus striatum) at six different temperatures (0, 10, 20, 25, 30, 35 degrees C), and by van't Hoff plots. Most of the compounds studied are tryptamine, phenylpiperazine and tetralin derivatives. Affinity constants were measured by saturation experiments for the selective 5-HT1A receptor agonist [3H]8-hydroxy-N,N-dipropyl-2-aminotetralin ([3H]8-OH-DPAT) and by inhibition assays of [3H]8-OH-DPAT binding for the other compounds. Scatchard plots were monophasic in the full range of temperatures, indicating a single class of high affinity binding sites. Van't Hoff plots of all ligands were linear in the temperature range investigated (0-30 degrees C or 0-35 degrees C). 5-Hydroxytryptamine (serotonin) and 5-methoxy-tryptamine (mexamine) displayed a positive slope. Experimental data indicate that for 5-HT1A receptor subtype agonists and antagonists are not thermodynamically discriminated. The results are discussed from a quantitative point of view with the aim of obtaining new details on the nature of the forces driving the 5-HT1A binding at a molecular level.

8-Hydroxy-2-(di-n-propylamino)tetralin↗
PubMed1994

The molten globule is a third thermodynamical state of protein molecules.

Analysis of published data on conformational transitions in relatively small proteins shows that the slopes of these transitions are proportional to the protein molecular weight. It is true both for transitions from the native (N) to the unfolded (U) states (when protein denaturation is coupled to its unfolding) and for transitions from the native to the molten globule (MG) states and from the molten globule to the unfolded state (when protein denaturation is decoupled from protein unfolding). This is precisely the behaviour predicted by thermodynamics for first order phase transitions ('all-or-none' transitions) in small systems. It follows that N-->U, N-->MG and MG-->U transitions in proteins are all of the 'all-or-none' type. Thus the molten globule state of protein molecules is separated by an 'all-or-none' transition both from the native and the unfolded state, i.e. the molten globule state is a third thermodynamic state of protein molecules in addition to the two previously established states--the native and the unfolded.

Mathematics↗
PubMed1995

Comparative thermodynamic analyses of the Fv, Fab* and Fab fragments of anti-dansyl mouse monoclonal antibody.

In order to investigate the role of the constant domains on the antigen-binding property of the variable domains, we have carried out a comparative thermodynamic study of the anti-dansyl Fv, Fab* and Fab fragments that possess the identical amino acid sequence of the variable domains. The thermodynamic analyses have shown that binding constants, enthalpy changes and entropy changes are similar for the three antigen-binding fragments, whereas the thermal stability of Fab is much higher than that of Fv and Fab*. We have concluded that (i) the variable domains of the three antigen-binding fragments possess identical intrinsic capability for antigen binding and (ii) the two constant domains serve to improve the stability of the variable domains.

Animals↗
PubMed1979

Computation as a thermodynamic process applied to biological systems.

A physical quantity, 'information,' can be defined and must be included in the second law of thermodynamics. This quantity is different from entropy, though closely related to it. Acquisition and use of information is characteristic of most systems, especially those of biological orgin. Treatment of information as a physical quantity permits many types of machines (in the most general sense) to be understood in respect of a thermodynamic function, and as well an investigation of the extent to which the laws governing information are or may limit their behavior. This limitation is most important at the molecular level, such as in the process of DNA and RNA synthesis. However, it may ultimately have a significant impact on all areas of biology including the theory of evolution, which in light of the concept of information can now be addressed in an important new way.

Computers↗
PubMed1989

Equivalent multi-tissue and thermodynamic decompression algorithms.

Multi-tissue and thermodynamic decompression algorithms are described and a computational equivalence is established between the two approaches. Eigenvalues and weighted eigenfunctions of the Fick-Fourier equation effectively define response functions from which Haldane half-lives can be extracted from arbitrary exposures, operationally bridging the two approaches. Decompression criteria for the algorithms are also described and coupled. Comparisons of similarities and differences of approaches are given from both theoretical and applied viewpoints. A seven-parameter set, spanning both models, forms the basis of analysis. We find that representative thermodynamic parameters in a perfusion-diffusion model effectively recover Haldane half-lives in a bootstrap and that critical parameters overlap, though ranges differ in the two cases.

Algorithms↗
PubMed1986

Thermodynamic restrictions on the elastic constants of bone.

The thermodynamic restrictions on the elastic coefficients of linear orthotropic elasticity and linear transversely isotropy elasticity are recorded and it is shown that previously reported data for the elastic orthotropic constants of bone satisfy these thermodynamic restrictions.

Bone and Bones↗
PubMed1975

Thermodynamic study of a liquid crystal as a liquid phase in gas-liquid chromatography. II. A cholesteric liquid crystal.

Gas-liquid chromatography is utilized for the determination of thermodynamic solution parameters for various organic solutes at infinite dilution in the meso- and isotropic phases of cholesteryl palmitate. The thermodynamic data and trends in values of the activity coefficients for the solutes are discussed in relation to their structure and to the orientations of the liquid crystal.

Cholesterol↗
PubMed1991

Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme.

Packing interactions in bacteriophage T4 lysozyme were explored by determining the structural and thermodynamic effects of substitutions for Ala98 and neighboring residues. Ala98 is buried in the core of T4 lysozyme in the interface between two alpha-helices. The Ala98 to Val (A98V) replacement is a temperature-sensitive lesion that lowers the denaturation temperature of the protein by 15 degrees C (pH 3.0, delta delta G = -4.9 kcal/mol) and causes atoms within the two helices to move apart by up to 0.7 A. Additional structural shifts also occur throughout the C-terminal domain. In an attempt to compensate for the A98V replacement, substitutions were made for Val149 and Thr152, which make contact with residue 98. Site-directed mutagenesis was used to construct the multiple mutants A98V/T152S, A98V/V149C/T152S and the control mutants T152S, V149C and A98V/V149I/T152S. These proteins were crystallized, and their high-resolution X-ray crystal structures were determined. None of the second-site substitutions completely alleviates the destabilization or the structural changes caused by A98V. The changes in stability caused by the different mutations are not additive, reflecting both direct interactions between the sites and structural differences among the mutants. As an example, when Thr152 in wild-type lysozyme is replaced with serine, the protein is destabilized by 2.6 kcal/mol. Except for a small movement of Val94 toward the cavity created by removal of the methyl group, the structure of the T152S mutant is very similar to wild-type T4 lysozyme. In contrast, the same Thr152 to Ser replacement in the A98V background causes almost no change in stability. Although the structure of A98V/T152S remains similar to A98V, the combination of T152S with A98V allows relaxation of some of the strain introduced by the Ala98 to Val replacement. These studies show that removal of methyl groups by mutation can be stabilizing (Val98----Ala), neutral (Thr152----Ser in A98V) or destabilizing (Val149----Cys, Thr152----Ser). Such diverse thermodynamic effects are not accounted for by changes in buried surface area or free energies of transfer of wild-type and mutant side-chains. In general, the changes in protein stability caused by a mutation depend not only on changes in the free energy of transfer associated with the substitution, but also on the structural context within which the mutation occurs and on the ability of the surrounding structure to relax in response to the substitution.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acids↗
PubMed1992

Conformational and thermodynamic properties of supercoiled DNA.

We used Monte Carlo simulations to investigate the conformational and thermodynamic properties of DNA molecules with physiological levels of supercoiling. Three parameters determine the properties of DNA in this model: Kuhn statistical length, torsional rigidity and effective double-helix diameter. The chains in the simulation resemble strongly those observed by electron microscopy and have the conformation of an interwound superhelix whose axis is often branched. We compared the geometry of simulated chains with that determined experimentally by electron microscopy and by topological methods. We found a very close agreement between the Monte Carlo and experimental values for writhe, superhelix axis length and the number of superhelical turns. The computed number of superhelix branches was found to be dependent on superhelix density, DNA chain length and double-helix diameter. We investigated the thermodynamics of supercoiling and found that at low superhelix density the entropic contribution to superhelix free energy is negligible, whereas at high superhelix density, the entropic and enthalpic contributions are nearly equal. We calculated the effect of supercoiling on the spatial distribution of DNA segments. The probability that a pair of DNA sites separated along the chain contour by at least 50 nm are juxtaposed is about two orders of magnitude greater in supercoiled DNA than in relaxed DNA. This increase in the effective local concentration of DNA is not strongly dependent on the contour separation between the sites. We discuss the implications of this enhancement of site juxtaposition by supercoiling in the context of protein-DNA interactions involving multiple DNA-binding sites.

Computer Simulation↗
PubMed1992

Thermodynamics of DNA branching.

Branched DNA molecules arise transiently as intermediates in genetic recombination or on extrusion of cruciforms from covalent circular DNA duplexes that contain palindromic sequences. The free energy of these structures relative to normal DNA duplexes is of interest both physically and biologically. Oligonucleotide complexes that can form stable branched structures, DNA junctions, have made it possible to model normally unstable branched states of DNA such as Holliday recombinational intermediates. We present here an evaluation of the free energy of creating four-arm branch points in duplex DNA, using a system of two complementary junctions and four DNA duplexes formed from different combinations of the same set of eight 16-mer strands. The thermodynamics of formation of each branched structure from the matching pair of intact duplexes have been estimated in two experiments. In the first, labeled strands are allowed to partition between duplexes and junctions in a competition assay on polyacrylamide gels. In the second, the heats of forming branched or linear molecules from the component strands have been determined by titration microcalorimetry at several temperatures. Taken together these measurements allow us to determine the standard thermodynamic parameters for the process of creating a branch in an otherwise normal DNA duplex. The free energy for reacting two 16-mer duplexes to yield a four-arm junction in which the branch site is incapable of migrating is + 1.1 (+/- 0.4) kcal mol-1 (at 18 degrees C, 10 mM-Mg2+). Analysis of the distribution of duplex and tetramer products by electrophoresis confirms that the free energy difference between the four duplexes and two junctions is small at this temperature. The associated enthalpy change at 18 degrees C is +27.1 (+/- 1.3) kcal mol-1, while the entropy is +89 (+/- 30) cal K-1 mol-1. The free energy for branching is temperature dependent, with a large unfavorable enthalpy change compensated by a favorable entropy term. Since forming one four-stranded complex from two duplexes should be an entropically unfavorable process, branch formation is likely to be accompanied by significant changes in hydration and ion binding. A significant apparent delta Cp is also observed for the formation of one mole of junction, +0.97 (+/-0.05) kcal deg-1 mol-1.

Base Composition↗