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PubMed1990

Thermodynamic nonideality in macromolecular solutions. Evaluation of parameters for the prediction of covolume effects.

Second virial coefficients and hence covolumes for self-interaction of five proteins, viz. ribonuclease, ovalbumin, bovine serum albumin, catalase and alpha-crystallin, have been determined by analyzing the concentration dependence of the partition coefficient obtained from frontal chromatographic studies on either Fractogel TSK HW55 or porous glass beads. The resulting estimates of the effective radii essentially duplicate their Stokes counterparts and thereby provide further justification for assuming the approximate identity of the thermodynamic and hydrodynamic radii of hydrated globular proteins. Gel chromatographic evaluation of second virial coefficients for protein/dextran systems has led to elimination of the sphere/sphere model as a valid thermodynamic description of the space-filling effects in protein/polymer mixtures, since it does not predict the observed independence of covolume, expressed per unit mass of polymer, upon size of the polymer. This requirement is met by the sphere/rod model [Edmond, E. & Ogston, A. G. (1968) Biochem. J. 109, 569-576] and also by the sphere/flexible-segment model [Hermans, J. (1982) J. Chem. Phys. 77, 2193-2203]. Furthermore, similar studies of the effect of solute radius on covolume for interaction with dextran T70 attest to the adequacy of either model for predicting the thermodynamic nonideality arising from the inclusion of dextrans in protein solutions, and also provide the relevant calibration of the model.

Catalase↗
PubMed1993

On the activation mechanism of the H(+)-ATP synthase and unusual thermodynamic properties in the alkalophilic cyanobacterium Spirulina platensis.

The activation requirements and thermodynamic characteristics of ATP synthase from the alkalophilic cyanobacterium Spirulina platensis were studied in coupled membrane vesicles. Activation by methanol increased the Vmax, while the Km for MgATP was unaffected (0.7 mM). We propose that in Sp. platensis, as in chloroplasts, the activating effect of methanol is based on perturbation of the gamma-epsilon subunit interaction. Light-driven ATP synthesis by membrane vesicles of Sp. platensis was stimulated by dithiothreitol. The characteristics of the activation of the ATP synthase by the proton electrochemical potential difference (delta mu H+) were analyzed on the basis of the uncoupled rates of ATP hydrolysis as a function of a previously applied proton gradient. Two values of delta mu H+, at which 50% of the enzyme is active, were found; 13-14 kJ.mol-1 for untreated membrane vesicles, and 4-8 kJ.mol-1 for light-treated and dithiothreitol-treated membrane vesicles. These values are lower than the corresponding values for the oxidized and reduced forms, respectively, of the chloroplast enzyme. Although no bulk proton gradient could be observed, membrane vesicles of Sp. platensis were able to maintain an equilibrium phosphate potential (delta Gp) of 40-43.5 kJ.mol-1, comparable to values found for Synechococcus 6716 and Anabaena 7120 membrane vesicles. Acid/base-transition experiments showed that the thermodynamic threshold, delta mu H+, for ATP synthesis, catalyzed by light-treated and dithiothreitol-treated Spirulina membrane vesicles, was less than 5 kJ.mol-1. The activation characteristics and the low thermodynamic threshold allow ATP synthesis to occur at low delta mu H+ values. The findings are discussed, both with respect to differences and similarities with the enzymes from chloroplasts and other cyanobacteria, and with respect to the alkalophilic properties of Sp. platensis.

Adenosine Triphosphate↗
PubMed1996

A thermodynamic analysis of conformational change due to the alpha 2 beta 2 complex formation of tryptophan synthase.

A characteristic property of the tryptophan synthase alpha 2 beta 2 complex is the mutual activation of the alpha and beta subunit upon complex formation. It has been speculated that this mutual activation results from the conformational change due to the alpha/beta subunit interaction. To elucidate this mechanism, we investigated the thermodynamic parameters of association for the various combinations of the alpha and beta subunits from Escherichia coli and Salmonella typhimurium using isothermal titration calorimetry. The negative association enthalpy of the S. typhimurium alpha subunit with the beta subunit from E. coli (or S. typhimurium) was about 20 kJ mol-1 larger than that of the E. coli alpha subunit at 40 degrees C. However, the favorable enthalpy of the S. typhimurium alpha subunit was perfectly compensated by the unfavorable association entropy, therefore, the Gibbs energy of association was similar to that of the E. coli alpha subunit. Furthermore, the site-directed mutagenesis study revealed that a single mutation (K109N; [Asn109] alpha subunit) of the E coli alpha subunit at the subunit interface from E. coli to the S. typhimurium type could change the characteristics of the thermodynamic parameters of association to the S. typhimurium alpha subunit type. The heat-capacity changes of the association of the alpha subunit with the beta subunit were quite great, 6.37-8.21 kJ mol-1 K-1, compared with that due to a decrease in accessible surface area in the subunit interface. The analysis of the thermodynamic parameters of association suggested that the complex formation couples with the folding (rearrangements) of the alpha subunit monomer or/and beta subunit dimer.

Asparagine↗
PubMed2005

Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein.

NMR and visible spectroscopy coupled to redox measurements were used to determine the equilibrium thermodynamic properties of the four haems in cytochrome c3 under conditions in which the protein was bound to ligands, the small anion phosphate and the protein rubredoxin with the iron in the active site replaced by zinc. Comparison of these results with data for the isolated cytochrome shows that binding of ligands causes only small changes in the reduction potentials of the haems and their pairwise interactions, and also that the redox-sensitive acid-base centre responsible for the redox-Bohr effect is essentially unaffected. Although neither of the ligands tested is a physiological partner of cytochrome c3, the small changes observed for the thermodynamic properties of cytochrome c3 bound to these ligands vs. the unbound state, indicate that the thermodynamic properties measured for the isolated protein are relevant for a physiological interpretation of the role of this cytochrome in the bioenergetic metabolism of Desulfovibrio.

Bacterial Proteins↗
PubMed1985

Correlation of thermodynamic activity and vapour diffusion through human skin for the model compound, benzyl alcohol.

This work tested the potential for predicting percutaneous absorption rates of a volatile penetrant from any vehicle by using thermodynamic activity measurements. Benzyl alcohol was chosen as a non-ideal, hydrogen bonding, volatile model penetrant. A manual headspace gas chromatography method measured benzyl alcohol vapour concentrations and thermodynamic activities above binary mixtures with vehicles: butanol, butyl acetate, isopropyl myristate, isophorone, toluene and propylene carbonate. Benzyl alcohol vapour diffusion through human, abdominal skin was also measured in-vitro for these mixtures. The benzyl alcohol vapour flux was linearly related to the activity, suggesting that percutaneous absorption is controlled by thermodynamic activity when the vehicle has no effect on the stratum corneum barrier.

Benzyl Alcohol↗
PubMed1985

Vapour and liquid diffusion of model penetrants through human skin; correlation with thermodynamic activity.

This work investigates vapour and liquid permeation through human skin of model penetrants benzyl alcohol, benzaldehyde, aniline, anisole and 2-phenylethanol applied in model vehicles butanol, butyl acetate, isophorone, isopropyl myristate, propylene carbonate, toluene, n-heptane and water. Vapour permeation was a linear function of thermodynamic activity as measured by headspace gas chromatography, except when the vehicle was n-heptane. Liquid permeation did not always follow simple thermodynamic predictions, e.g. for the penetrant, benzyl alcohol, when the vehicle damaged the skin (toluene, n-heptane) or when propylene carbonate produced low fluxes and isopropyl myristate, high values. At comparable thermodynamic activities, liquid fluxes were often ten-fold higher than vapour fluxes, and these differences were reflected by the partition coefficients and the amount of penetrant entering the stratum corneum membrane. The conclusion was that liquid fluxes were membrane controlled, whereas an interfacial effect probably contributed to low vapour permeation.

Benzyl Alcohol↗
PubMedDate not supplied

Thermodynamic considerations of acrylic cement implant at the site of giant cell tumors of the bone.

A discussion of the thermodynamic aspects of a relatively new treatment method for giant cell tumors of the bone is presented in this paper. The advantages of implanting methylmethacrylate acrylic bone cement into a curetted tumor site are briefly discussed and placed in perspective relative to more prevalent surgical treatments. As the bone cement self-heats while curing, the possibility of heat necrosis in the bone exists. However, the damage due to heat may be beneficial in reducing the rate of tumor recurrence. A thermodynamic consideration of the treatment situation appears to be warranted. After a general introduction and a brief literature review, the theoretical thermodynamic equations are developed. Once the basic equations for the heat transfer from the cement or the bone are derived, there is then a discussion of the various characteristics of bone and methylmethacrylate crucial to the analysis, such as, thermal conductivity, specific heat, density, and heat generation parameters. Finally, in order to reduce the theory to a form which may be used practically, the equations derived are written in terms of finite-difference equations, which approximate them numerically. Different equations are written for each type of heat transfer condition encountered in the cement-bone system as spacial variances in material and geometry occur. The equations derived may be used to model the system allowing one to predict the time-dependent temperature distribution in bone during the curing of acrylic cement. Using computer techniques to reduce the equations obtained from this analysis, and knowing the temperature at which adjacent cells die, a zone of necrosis may be mapped surrounding the acrylic impact.

Bone Neoplasms↗
PubMed1983

Surface thermodynamics of bacterial adhesion.

The adhesion of five strains of bacteria, i.e., Staphylococcus aureus (strain 049), Staphylococcus epidermidis (strain 047), Escherichia coli (strains 055 and 2627), and Listeria monocytogenes, to various polymeric surfaces was studied. The design of the experimental protocol was dictated by thermodynamic considerations. From the thermodynamic model for the adhesion of small particles from a suspension onto a solid substratum, it follows that the extent of adhesion is determined by the surface properties of all three phases involved, i.e., the surface tensions of the adhering particles, of the substrate, and of the suspending liquid medium. In essence, adhesion is more extensive to hydrophilic substrata (i.e., substrata of relatively high surface tension) than to hydrophobic substrata, when the surface tension of the bacteria is larger than that of the suspending medium. When the surface tension of the suspending liquid is larger than that of the bacteria, the opposite pattern of behavior prevails. Suspensions of bacteria at a concentration of 10(8) microorganisms per ml were brought into contact with several polymeric surfaces (Teflon, polyethylene, polystyrene, and acetal and sulfonated polystyrene) for 30 min at 20 degrees C. After rinsing, the number of bacteria adhering per unit surface area was determined by image analysis. The surface tension of the suspending medium. Hanks balanced salt solution, was modified through the addition of various amounts of dimethyl sulfoxide. It was found that the number of bacteria adhering per unit surface area correlates well with the thermodynamic predictions and that these data may be used to determine the surface tension of the different bacterial species. The surface tensions of the bacteria obtained in this fashion are in excellent agreement with those obtained by other methods.

Acetals↗
PubMed1998

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Computer Simulation↗
PubMed1989

Water movement: does thermodynamic interpretation distort reality?

In a recent theoretical analysis of water flow, Finkelstein (Water Movement Through Lipid Bilayers, Pores, and Plasma Membranes: Theory and Reality, 1987) has attacked the contributions of irreversible thermodynamics, stating that "the thermodynamic treatment of uphill water flow completely distorts reality." Instead he presents a mechanistic formulation. For a porous membrane, water flow is attributed to convection generated by a favorable hydrostatic pressure gradient within pores, even when in the presence of permeant solutes water moves against its chemical potential gradient; water flow may "drag", solute, to an extent determined by the solute partition coefficient, but the possibility that solute flow may drag water is excluded. We argue that this formulation violates the second law of thermodynamics. Water cannot move against its chemical potential gradient because of the influence of only part of the chemical potential gradient. Furthermore, the proposed mechanism requires that at one of the membrane-solution interfaces water must move against both its concentration gradient and the hydrostatic pressure gradient. Also considered by Finkelstein is the nature of the reflection coefficient sigma, a kinetic variable, which he concludes can be evaluated (in a porous membrane) by measurement of the (equilibrium) solute partition coefficient. We claim that in general it is not possible to evaluate a kinetic variable from measurements of equilibrium parameters alone. A valid kinetic analysis must incorporate the contribution of all coupled flows.

Body Water↗
PubMed1992

Cascade of cell swelling: thermodynamic potential discharge of brain cells after membrane injury.

This paper illustrates the principles of volume regulation in brain cells. Animal experiments were first performed ex vivo. Brains of gerbils were removed and incubated in 3 ml of physiological saline for 1 h. Control (0.86 g, n = 8) and swollen hemispheres (1.11 g, n = 8) were analyzed for tissue hydration, electrolytes and osmolality. The incubation media were also analyzed for gains or losses of electrolytes and water. Na+ and Cl- moved into and K+ moved out of the tissue. The ratio of Na+ influx to K+ efflux was calculated to be approximately 2:1. Water shifted into the tissue accompanying the net movements of small ions. In a simulated "cell" model constructed on the basis of the above observations with an outside saline and an inside colloid solution separated by a dialysis membrane, fluid shifts were demonstrated in the absence of (or even against) an osmotic gradient across the membrane under isobaric and isothermal conditions. Such paradoxical fluid shifts, presumably occurring in a similar manner to those in living cells, were shown to be due to the discharge of a huge thermodynamic potential accumulated by the cell as a condensation of ions outside and of proteins inside the cell membrane. We conclude that a loss in barrier function of the cell membrane ignites such a thermodynamic potential discharge causing an environmental fluid shift into the cells even under conditions of no (or even a contrary) osmotic gradient. Under such circumstances, countercotransporters and ion exchangers such as Na(+)-K(+)-2Cl- may work as modulators of the fluid shift, limiting its rate. The thermodynamic potential can explain the cascade of cell swelling (cytotoxic edema) as well as the spontaneous increase in osmolality in the ischemic cell when the cell volume increase is somehow restricted.

Animals↗
PubMed1996

Relationship between PVA and myocardial oxygen consumption can be derived from thermodynamics.

The pressure-volume area (PVA) has been shown to be an excellent, linear index of myocardial oxygen consumption. The thermodynamic basis for this result, however, has not been elucidated. The present study was undertaken to determine what information could be gained from analyzing the cardiac pressure-volume (P-V) cycle as an approximation to some "ideal" thermodynamic cycle operating under the constraints imposed by cardiovascular anatomy and physiology. The myocardium was approximated as a linear, chemically driven elastance in accordance with the time-varying elastance model. Analysis provided descriptions of a Carnot cycle for myocardium and a suboptimal ideal cycle, including isovolumic phases. Further analysis of the ideal cycle indicated that the end-systolic P-V relationship (ESPVR) is an approximation to the adiabatic P-V trajectory that primarily determines total energy consumption. Analysis also indicated possible explanations of current results that seem to be at odds with the time-varying elastance model. These results suggest that thermodynamic cycle analysis may provide a useful analytic tool for investigation of the cardiac cycle.

Animals↗
PubMed1983

Thermodynamics of living matter: physical foundations of biology.

All major functions of life are exerted by reversible conformational changes of living matter, the genetically coded, giant molecules of proteins, polynucleotides, and biological membranes. Only thermodynamics can answer the questions why these reversible actions occur, why they are inevitable, and what the physical foundations may be on which biology rests. Classical Gibbs-Helmholtz thermodynamics was found to be inapplicable to the interpretation of reactions in living matter, because copious flows of heat without exchange of work obscure the subtle bond-forming or bond-breaking energy transformations that are driving the actions of living matter. An alternative thermodynamic formulation that is universally applicable was developed and applied to numerical examples: formation of a diatomic molecule from the elements, and two conformational changes, a protein folding and the winding of a polynucleotide helix. The subtle energy transformations, bond-forming or bond-breaking, that were causing the two reactions of living matter to proceed in vitro forward or in reverse have been identified as the thermal work function delta Wto(T) and the chemical bond energy delta Ho0. Since the chemical bond energies and the heat capacities delta CoP(T) between reaction temperature and the absolute zero, unchangeable attributes of matter, were the only ingredients used for the treatment, the complexity of the reactions has been reduced--as far as effects and ultimate causes are concerned--to the simplicity of low temperature physics, a solid physical foundation for all biological and medical sciences.

Animals↗
PubMed1998

Mitochondrial oxidative phosphorylation thermodynamic efficiencies reflect physiological organ roles.

Mitochondria cannot maximize energy production, efficiency, and the cellular ATP phosphorylation potential all at the same time. The theoretical and observed determinations of coupling of oxidative phosphorylation in mitochondria from rat liver, heart, and brain were compared using classical and nonequilibrium thermodynamic measures. Additionally, the optimal thermodynamic efficiency and flow ratios were determined for control of the two energy-converting complexes of the respiratory chain: complex I (NADH), which reflects the integrated cellular pathway, and complex II (FADH2), the predominantly tricarboxylic acid (TCA) cycle pathway. For all three organs, the cellular respiratory pathway was more tightly coupled than the TCA pathway and resulted in a greater optimal efficiency. Liver mitochondria are the most thermodynamically efficient at ATP production using oxidative phosphorylation. Heart and brain mitochondrial systems utilize more oxygen, but can produce ATP at a faster rate than liver systems. Per the theory of economic degrees of coupling, isolated rat liver mitochondrial systems are designed for the economic production of ATP for use in cellular processes. In the brain, the mitochondrial TCA cycle pathway promotes the maximal maintenance of the cellular energy state for cellular viability, whereas in the heart the TCA cycle pathway maximizes the production of ATP. The coupling of oxidative phosphorylation not only can be expected to change with substrate availability but may also reflect an ontogenetic response of mitochondria to fit specific organ roles in the rat.

Animals↗
PubMed2006

Contraction-relaxation coupling mechanism characterization in the thermodynamic phase plane: normal vs. impaired left ventricular ejection fraction.

Using simultaneous pressure-volume measurements obtained during cardiac catheterization, we employ the thermodynamic phase-plane (TPP) method to characterize global contraction-relaxation coupling (CRC) between normal and impaired left ventricular (LV) ejection fraction (LVEF) groups. The cardiac cycle inscribes a closed loop in the TPP defined by the coordinates "potential" power [V(dP/dt), ergs/s] and "kinetic" power [P(dV/dt), ergs/s]. The TPP-derived indexes kappa and rho define the chamber's contractile and CRC attributes, respectively. Data from 33 subjects dichotomized as normal control (n = 22, >50% LVEF) and impaired LVEF (n = 11, <50% LVEF) were analyzed. The results were as follows: kappa = 3.0 +/- 1.1 and rho = -0.38 +/- 0.21 for controls and kappa = 5.4 +/- 1.6 and rho = -1.14 +/- 0.47 for the impaired LVEF group; kappa and rho are significantly higher for impaired LVEF than for control (P < 0.001 for both). As kappa increased, rho decreased (r = -0.69) for all subjects. Hence, ventricles with impaired LVEF are thermodynamically less efficient because they require more potential power per unit of delivered kinetic power than controls. We conclude that TPP-derived indexes of CRC facilitate assessment of chamber efficiency in thermodynamic terms and elucidate the dominant differentiating features in terms of CRC indexes.

Animals↗
PubMed1990

Electrode radius predicts lesion radius during radiofrequency energy heating. Validation of a proposed thermodynamic model.

Myocardial heating by transcatheter delivery of radiofrequency (RF) energy has been proposed as an effective means of arrhythmia ablation. A thermodynamic model describing the radial temperature gradient at steady state during RF-induced heating is proposed. If one assumes that RF power output is adjusted to maintain a constant electrode-tissue interface temperature at all times, then this thermodynamic model predicts that the radius of the RF-induced lesion will be directly proportional to the electrode radius. A total of 76 RF-induced lesions were created in a model of isolated canine right ventricular free wall perfused and superfused with oxygenated Krebs-Henseleit buffer. Electrode radius was varied between 0.75 and 2.25 mm. RF energy (500 kHz) was delivered for 90 seconds, and the power output was adjusted to maintain a constant electrode-tissue interface temperature of 60 degrees C. A strong linear correlation was observed between electrode radius and lesion radius in two dimensions: transverse (p = 0.0001, r = 0.85) and transmural (p = 0.0001, r = 0.89). With these data, the temperature correlation with irreversible myocardial injury in this model was calculated at 46.6-48.8 degrees C. Therefore, the proposed thermodynamic model closely predicts the observed relation between electrode radius and lesion size during RF myocardial heating.

Animals↗
PubMedDate not supplied

Quantum-chemical model evaluations of thermodynamics and kinetics of oxygen atom additions to narrow nanotubes.

This paper reports a computational study of oxygen additions to narrow nanotubes, a problem frequently studied with fullerenes. In fact, fullerene oxides were the first observed fullerene derivatives, and they have naturally attracted the attention of both experiment and theory. C60O had represented a long-standing case of experiment-theory disagreement, and there has been a similar problem with C60O2. The disagreement has been explained by kinetic rather than thermodynamic control. In this paper a similar computational approach is applied to narrow nanotubes. Recently, very narrow nanotubes have been observed with a diameter of 5 A and even with a diameter of 4 A. It has been supposed that the narrow nanotubes are closed by fragments of small fullerenes like C36 or C20. In this report we perform calculations for oxygen additions to such model nanotubes capped by fragments of D2d C36, D4d C32, and Ih C20 fullerenic cages (though the computational models have to be rather short). The three models have the following carbon contents: C84, C80, and C80. Both thermodynamic enthalpy changes and kinetic activation barriers for oxygen addition to six selected bonds are computed and analyzed. The lowest isomer (thermodynamically the most stable) is never of the 6/6 type, that is, the enthalpically favored structures are produced by oxygen additions to the nanotube tips. Interestingly enough, the lowest energy isomer has, for the D2d C36 and D4d C32 cases, the lowest kinetic activation barrier as well.

Computer Simulation↗
PubMed2006

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.

BACKGROUND: Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. RESULTS: We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. CONCLUSION: Convenience kinetics can be used to translate a biochemical network--manually or automatically--into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases.

Energy Metabolism↗