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PubMed2002

Thermodynamics of systems of biochemical reactions.

When a reaction system described in terms of species is in a certain state, the Gibbs energy G provides the means for determining whether each reaction will go to the right or the left, and the equilibrium composition of the whole system can be calculated using G. When the pH is specified, a system of biochemical reactions is described in terms of reactants, like ATP (a sum of species), and the transformed Gibbs energy G' provides the means for determining whether each reaction will go to the right or the left. The equilibrium composition of the whole system can be calculated using G'. Since metabolism is complicated, the thermodynamics of systems of reactions like glycolysis and the citric acid cycle can also be considered at specified concentrations of coenzymes like ATP, ADP, NAD(ox), and NAD(red). This is of interest because coenzymes tend to be in steady states because they are involved in many reactions. When the concentrations of coenzymes are constant, the further transformed Gibbs energy G" provides the means for calculating whether each reaction will go to the right or the left, and the equilibrium composition of the whole system can be calculated using G". Under these conditions, a metabolic reaction system can be reconceptualized in terms of sums of reactants; for example, glycolysis can be represented by C(6)=2C(3), where C(6) is the sum of the reactants with six carbon atoms and C(3) is the sum of the reactants with three carbon atoms. These calculations can also be described by use of semigrand partition functions. Semigrand partition functions have the advantage of containing all the thermodynamic information on a series of reactions at specified pH or at specified pH and specified concentrations of coenzymes.

Animals↗

PubMed1989

Kinetics and thermodynamic transitions of N-acetyl-beta-D-glucosaminidase A and B in free and bound forms: role of cellulose ion-exchangers.

The kinetic and thermodynamic properties of N-acetyl-beta-D-glucosaminidase A (Hex A) and N-acetyl-beta-D-glucosaminidase beta (Hex B) from goat testes were investigated in free and bound (after binding them on ion-exchangers such as DEAE- or CM-cellulose respectively) forms. The optimum pH of free Hex A and Hex B was at 4.2 and 5.4, whereas the bound forms showed the optimum pH at 4.0 and 5.2 respectively. While apparent Km of free and bound Hex A (0.8 and 1.0 mM respectively) did not differ, the Km of Hex B increased when bound on CM-cellulose (Km of free Hex B = 0.96 mM versus bound Hex B = 1.6 mM). Though the free Hex A was more thermo-labile than the free Hex B, both isozymes, on insoluble matrices decayed at faster rates on heating. Activation analysis revealed that the energy of activation (Eoa) for transition state of free Hex B (81 Kcal deg-1 mole-1) did not differ from Eoa of bound Hex B. On the other hand, Eoa of free Hex A declined from 77.2 to 71.1 Kcal deg-1 mole-1 when heat transitions were carried out in free and bound state respectively. Thermodynamic analysis suggested a change in entropy of activation (delta S) of free Hex A and Hex B as 200 and 211 eu respectively. While delta S of Hex B did not change after heat transitions, delta S of Hex A was 182.5 eu.

Animals↗

PubMed1987

Thermodynamics of the two step formation of horseradish peroxidase compound I.

The effects of temperature (20 to -38 degrees C), pressure (normal pressures to 1.2 kbar) and solvent (water, 60% DMSO and 50% methanol) on the reaction of hydrogen peroxide or ethyl peroxide with horseradish peroxidase were studied. The formation of compound I was followed at 403 nm in a stopped flow apparatus adapted for high pressure and low temperature work. As with the alkaline form (Job and Dunford 1978), the neutral form of the peroxidase binds peroxide substrates in two steps. It was the combined use of organic solvents and low temperatures which revealed saturation kinetics: (Formula: see text) compound I, where E = horseradish peroxidase and S peroxide substrate. In water and organic solvents at temperatures above -10 degrees C, K1 was too small and k2 too large to be measured, here K1 X k2 was obtained. k-2 was too small for measurement under all conditions. Whereas K1 was insensitive to the peroxide substrate and solvent composition, k2 was very sensitive. The thermodynamic parameters delta H, delta S and delta V for K1 and k2 were obtained under different experimental conditions and the data are interpreted within the available thermodynamic theories.

Cold Temperature↗

PubMed1984

The thermodynamic efficiency of the Ca2+-Mg2+-ATPase is one hundred percent.

The thermodynamic efficiency of the Ca2+ -Mg2+ -ATPase of skeletal sarcoplasmic reticulum has been evaluated by comparing the Ca2+ gradient established with the ATP/(ADP*Pi) ratio. The evaluation was made at an external Ca2+ level (4.7 X 10(-8) M) which is below the Km value of 7 X 10(-8) M. The Mg-ATP and phosphate concentrations were held constant (0.1 mM) and the ADP concentration was varied. Maximal uptake to an internal free Ca2+ concentration of 17 mM was observed at infinite ATP/(ADP*Pi) ratio (absence of ADP). This corresponds to a [Ca2+] i/[Ca2+] 0 gradient of 3.6 X 10(5). A Ca2+ gradient one-half as large was observed at an ATP/(ADP*Pi) ratio of 3.5 X 10(3) M-1. The square of the Ca2+ gradient is shown to be proportional to the ATP/(ADP*Pi) ratio, for finite values of the latter. The proportionality constant is identical to the equilibrium constant for hydrolysis of ATP (9.02 X 10(6) M) under these conditions (0.1 mM Mg2+, 30 degrees C). The intrinsic thermodynamic efficiency of the pump is shown to be 100%, with a maximal uncertainty of 3%. The efficiency is lower under less optimal conditions, when the pump is inhibited and passive leak processes compete.

Adenosine Diphosphate↗

PubMed1995

Thermodynamics of Strecker synthesis in hydrothermal systems.

Submarine hydrothermal systems on the early Earth may have been the sites from which life emerged. The potential for Strecker synthesis to produce biomolecules (amino and hydroxy acids) from starting compounds (ketones, aldehydes, HCN and ammonia) in such environments is evaluated quantitatively using thermodynamic data and parameters for the revised Helgeson-Kirkham-Flowers (HKF) equation of state. Although there is an overwhelming thermodynamic drive to form biomolecules by the Strecker synthesis at hydrothermal conditions, the availability and concentration of starting compounds limit the efficiency and productivity of Strecker reactions. Mechanisms for concentrating reactant compounds could help overcome this problem, but other mechanisms for production of biomolecules may have been required to produce the required compounds on the early Earth. Geochemical constraints imposed by hydrothermal systems provide important clues for determining the potential of these and other systems as sites for the emergence of life.

Aldehydes↗

PubMed1987

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.

A new and promising development in the field of computer simulation of molecular systems is the so-called thermodynamic cycle integration technique, which combines well-known results from statistical thermodynamics with powerful computer simulation methods. The basic formulas, the development and the applications in the areas of drug design, protein engineering and conformational analysis of this elegant technique are discussed.

Computer Simulation↗

PubMed1978

Thermodynamics of peptide bond formation at clay mineral surfaces.

The possibility of surface catalysed condensation of unsubstituted amino acids on kaolinite in aqueous systems at elevated temperatures was investigated; no evidence of clay catalysed polycondensation has been found. The thermodynamic feasibility of the hypothetical lysine/dilysine condensation reaction in the temperature-range up to 90 degrees C was evaluated for a range of experimental conditions by the combination of measured free energies of lysine/dilysine cation exchange on kaolinite and on montmorillonite, and free energies for the analogous condensation reaction in homogeneous solution. The results indicate that, in spite of the high selectivity of the clays for the adsorption of cation dimers from dilute solutions, the thermodynamic barrier to the surface condensation of unsubstituted amino acids on clay minerals in aqueous systems up to 90 degrees C is not lower than it is in homogeneous solution.

Amino Acids↗

PubMed1978

A thermodynamic analysis of the correlation between active Na+ transport and the rate of oxygen consumption in epithelia.

Active transport in epithelia is discussed in terms of the relationships between oxygen consumption and sodium flux as affected by each of the two corresponding thermodynamic forces. Analysis is presented of the use of nonequilibrium thermodynamics as a total in elucidating coupling and stoichiometry, and in evaluating drug action in the system. The analysis leads to the quantitative characterization of active transport in "two-flow" systems in terms of two plots: oxygen consumption nad sodium flow, each as a function of electrical potential difference, at constant affinity and constant concentrations. The relevant characteristic parameters are then shown to be represented by the slopes and intercepts of the two plots, the ratios of the slopes and of the intercepts, and by the difference--as well as the ratio--of the ratios. Distinction is made between experimental conditions in which the phenomenological coefficients remain constant and those in which these coefficients undergo appreciable changes. In terms of the above analysis, and examination is made of the effect of commonly used drugs. It is shown that while drugs may effect both the affinity and the phenomenological coefficients, they invariably affect the latter--at least in the cases hitherto reported.

Animals↗

PubMed1978

A thermodynamic analysis of the amorphous to crystalline calcium phosphate transformation.

A thermodynamic analysis of the precipitation of amorphous calcium phosphate (ACP) and its transformation to crystalline apatite had been made. A nearly constant ion product, over a wide variety of conditions, was obtained for a tricalcium phosphate (TCP)-like phase suggesting that the molecular unit which governs the solubility of ACP may be similar in composition to TCP. The introduction of 10% acid phosphate into the formula for the TCP ion product improves the fit of experimental data and results in an invariant ion product. The stability of ACP in solution was found to be dependent upon its thermodynamic instability with respect to an octacalcium phosphate (OCP)-like phase. The dependence of the induction period for the amorphous to crystalline transformation upon the pH and the Ca/P ratio of the solution is best explained by the assumption that an OCP-like phase is initially nucleated on the surfaces of the ACP particles. The events that occur in the immediate post-transition period suggest the hydrolysis of this OCP-like material to an apatitic phase.

Apatites↗

PubMed1978

A thermodynamic analysis of the secondary transition in the spontaneous precipitation of calcium phosphate.

A thermodynamic analysis has been made of the secondary transition stage in the spontaneous precipitation of calcium phosphate following the amorphous-crystalline transformation. The first formed crystalline material has a solubility similar to that of octacalcium phosphate (OCP) and the computed thermodynamic solubility product remains invariant in the pH range 7.00--8.60. The duration of the secondary stage is sensitive to pH and the transition appears to occur by hydrolysis of the first formed OCP-like phase to a more basic apatitic phase with a tricalcium phosphate (TCP) stoichiometry. The crystalline material at the end of this transition has an invariant solubility product, in the pH range 7.00 to 8.60, when the TCP-like molecular formula is assumed. Changes in the solution chemistry which accompany the solid-to-solid transitions are consistent with the above conclusions. The results of this study are also consistent with those of a previous study which suggest that the stability of the amorphous calcium phosphate phase is dependent upon the instability of the solution phase with respect to OCP formation.

Calcium↗

PubMed1979

Preparation of cupric palmitate membrane, its characterization and evaluation of thermodynamically effective fixed charge density.

Membrane potentials have been measured across parchment-supported cupric palmitate membrane separating various 1:1 electrolytes at concentrations C1 and C2 such that C2 = 10 C1. Membrane potential data have been used to calculate transference number of ions, permselectivity and also to derive the thermodynamically effective fixed charge density which is an important characteristic governing the membrane phenomena by utilizing the generally accepted and most widely used theory of Teorell-Meyer and Sievers as well as the recent theories for membrane potential of Kobatake et al. and Nagasawa et al. based on the principles of nonequilibrium thermodynamics. The values of charge densities derived from different theories were almost the same, confirming thereby the validity of the recently developed theories of membrane potential.

Electrochemistry↗

PubMed1980

Surface thermodynamics of normal and pathological human granulocytes.

Surface tensions of normal and pathological granulocytes were determined by (1) adhesion to solid substrates of different surface tensions while suspended in liquid media of different surface tensions, and by (2) measurement of cell-liquid-vapor contact angles obtained with sessile drops of saline water on cell monolayers. The results obtained by the two different methods were in close conformation with one another. With the cell adhesion method some residual leukocyte adhesion still persists even under conditions where there no longer is a van der Waals attraction between cells and solid substrate. At low ionic strength and by the abolishment of all multivalent cations through the admixture of EDTA, that residual cell adhesion virtually disappears (with normal as well as with pathological granulocytes), indicating that the earlier residual cell adhesion did indeed arise from electrostatic interactions mediated by multivalent cations (probably Ca2+). Comparison of the capacities for engulfment and the surface thermodynamics data of normal and pathological granulocytes obtained in this study leads to the novel observation that the phagocytic episode from half to complete engulfment of bacterial particles by granulocytes appears to be the crucial step from the thermodynamic point of view.

Cell Adhesion↗

PubMed1990

Thermodynamics of industrially-important, enzyme-catalyzed reactions.

The thermodynamics of 10 industrially-important, enzyme-catalyzed reactions are examined. The reactions discussed are: the conversions of penicillin G to 6-amino-penicillinic acid using the enzyme penicillin acylase; starch to glucose using amylases; glucose to fructose using glucose (xylose) isomerase; cellulose to glucose using cellulase; fumaric acid and ammonia to L-aspartic acid using L-aspartase; transcinnamic acid and ammonia to L-phenylalanine using L-phenylalanine ammonia lyase; L-histidine to urocanic acid and ammonia using L-histidine ammonia lyase; lactose to glucose and galactose using lactase; and the reactions catalyzed by amino acylases and proteases. The selection of these processes was based on the economic value of the products and their intrinsic industrial importance. The available thermodynamic properties, such as equilibrium constants, Gibbs energies (delta G degrees), enthalphies (delta H degrees), and heat capacity changes (delta Cp degrees) of these enzyme-catalyzed reactions, are reviewed and summarized. Recommendations are made for future research in this area.

Aldose-Ketose Isomerases↗

PubMedDate not supplied

Modulation of membrane potential in algal cells by temperature gradients. A thermodynamic approach.

The aim of the present study is to ascertain whether transmembrane temperature gradients couple with transport of electric charge in living cells of Valonia utricularis and eventually measure the thermodynamic coupling coefficient (s). Simple experimental procedures are described that allow generation of temperature gradients of predetermined sense and intensity across the cell membrane. Simultaneous measurement of the potential difference is ensured by standard electrophysiological methods. The mathematical expressions that allow quantitative treatment of experimental results are indicated in the article and are based on standard nonequilibrium thermodynamic and electrophysiological formalism. The value of the coupling coefficient between temperature gradient and flow of electric charge is indicated and concisely discussed in terms of possible mechanisms of ionic membrane transport.

Biological Transport↗

PubMed2005

Thermodynamics of an ideal generalized gas: II. Means of order alpha.

The property that power means are monotonically increasing functions of their order is shown to be the basis of the second laws not only for processes involving heat conduction, but also for processes involving deformations. This generalizes earlier work involving only pure heat conduction and underlines the incomparability of the internal energy and adiabatic potentials when expressed as powers of the adiabatic variable. In an L-potential equilibration, the final state will be one of maximum entropy, whereas in an entropy equilibration, the final state will be one of minimum L. Unlike classical equilibrium thermodynamic phase space, which lacks an intrinsic metric structure insofar as distances and other geometrical concepts do not have an intrinsic thermodynamic significance in such spaces, a metric space can be constructed for the power means: the distance between means of different order is related to the Carnot efficiency. In the ideal classical gas limit, the average change in the entropy is shown to be proportional to the difference between the Shannon and Rényi entropies for nonextensive systems that are multifractal in nature. The L potential, like the internal energy, is a Schur convex function of the empirical temperature, which satisfies Jensen's inequality, and serves as a measure of the tendency to uniformity in processes involving pure thermal conduction.

Entropy↗

PubMed2002

Ion passage pathways and thermodynamics of the amphotericin B membrane channel.

Amphotericin B is a polyene macrolide antibiotic used to treat systemic fungal infections. Amphotericin B's chemotherapeutic action requires the formation of transmembrane channels, which are known to transmit monovalent ions. We have investigated the ion passage pathways through the pore of a realistic model structure of the channel and computed the associated thermodynamic properties. Our calculations combined the free energy computations using the Poisson equation with a continuum solvent model and the molecular simulations in which solvent molecules were present explicitly. It was found that there are no substantial structural barriers to a single sodium or chloride ion passage. Thermodynamic free energy calculations showed that the path along which the ions prefer to move is off center from the channel's central axis. In accordance with experiments, Monte Carlo molecular simulations established that sodium ions can pass through the pore. When it encounters a chloride anion in the channel, the sodium cation prefers to form a solvent-bridged pair configuration with the anion.

Amphotericin B↗

PubMed2004

An equilibrium thermodynamic model of the sequestration of calcium phosphate by casein micelles and its application to the calculation of the partition of salts in milk.

An equilibrium thermodynamic model of the interaction of calcium, phosphate and casein in milk is described in which the micellar calcium phosphate is assumed to be in the form of calcium phosphate nanoclusters. A generalized empirical formula for the nanocluster is used to define the molar ratios of small ions (Ca, Mg, P(i) and citrate) to a casein phosphorylated sequence (phosphate centre, PC). From this model, a method of calculating the partition of milk salts into diffusible and non-diffusible fractions is obtained. No arbitrary assumptions are made, no fitting of adjustable parameters is done and the PCs in the caseins are defined by inspection of their primary structures. In addition to the salt partition, the mole fractions of the individual caseins not complexed to the calcium phosphate through one or more of their PCs are computed and a generic stability rule for milks is derived. The use of the model is illustrated by calculations of the partition of salts in a standard milk and by comparison with experimental data on the partition of salts in the milk of individual cows. The generic stability rule is applied to the individual milks to determine whether the micellar calcium phosphate is thermodynamically stable. According to the calculations, compositions that might lead to pathological calcification in the lumen of the mammary gland were seldom found in primiparous healthy cows in early or mid lactation but occurred more often in multiparous animals, in late lactation and during mastitic infection.

Animals↗

PubMed2003

A thermodynamic interpretation of cell hydrophobicity in aerobic granulation.

Aerobic granulation can be regarded as a microorganism-to-microorganism self-immobilization process, in which cell hydrophobicity could be a decisive parameter in determining the microorganism-to-microorganism interaction and structural compactness of aerobic granules. This study looked into the thermodynamic interpretation of cell hydrophobicity in aerobic granulation; and a model that correlates microbial interaction and relative cell hydrophobicity defined as the ratio of cell hydrophobicity over cell hydrophilicity was derived. This model describes how cell hydrophobic and hydrophilic interactions affect aerobic granulation and offers deep insights into the thermodynamic mechanisms of microbial aggregation. The model prediction was in good agreement with experimental data. Results showed that aerobic granulation was a function of cell hydrophobicity over cell hydrophilicity, i.e. a high cell hydrophobicity strongly favors microbial aggregation and results in a more compact structure.

Aerobiosis↗