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At least 19 recordsLinked to original sources
PubMed1982

Thermodynamics of growth. Non-equilibrium thermodynamics of bacterial growth. The phenomenological and the mosaic approach.

Microbial growth is analyzed in terms of mosaic and phenomenological non-equilibrium thermodynamics. It turns out that already existing parameters devised to measure bacterial growth, such as YATP, mu, and Q substrate, have as thermodynamic equivalents flow ratio, output flow and input flow. With this characterisation it becomes possible to apply much of the already existing knowledge of phenomenological non-equilibrium thermodynamics to bacterial growth. One of the conclusions is that the frequent observation that YATP is only 50% of its theoretical maximum does not mean that the microbe corresponds to a thermodynamic system that has been optimized for maximal output power, as has been suggested. Rather, at least in some cases, it corresponds to a system that has been optimized towards maximum growth rate. When the degree of reduction of the (single) carbon source is significantly smaller than that of the biomass produced, the efficiency of biomass synthesis has been kept as high (i.e., about 24%) as is consistent with maximization of the growth rate at optimal efficiency. Mosaic thermodynamics allows an analysis of processes which in microbial metabolism may be responsible for any particular growth behaviour. Equations are derived that predict the effect of uncoupling through leaks, futile cycling, or 'slip' on microbial growth. It turns out that uncoupling is expected to affect both the growth rate-independent and the growth rate-dependent 'maintenance coefficient'. The effect on the latter is different when catabolic substrate limits growth than when anabolic substrate limits growth. In the latter case, the growth rate-dependent maintenance coefficient is negative. It is concluded that mosaic non-equilibrium thermodynamics will be a powerful theoretical tool especially in future experimental analyses of the metabolic basis for microbial growth characteristics and growth regulation.

Adenosine Triphosphate↗
PubMed2004

Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization.

Classification of the amounts and types of lower order structural elements in proteins is a prerequisite to effective comparisons between protein folds. In an effort to provide an additional vehicle for fold comparison, we present an alternative classification scheme whereby protein folds are represented in statistical thermodynamic terms in such a way as to illuminate the energetic building blocks within protein structures. The thermodynamic relationship is examined between amino acid sequences and the conformational ensembles for a database of 159 Homo sapiens protein structures ranging from 50 to 250 amino acids. Using hierarchical clustering, it is shown through fold-recognition experiments that (1) eight thermodynamic environmental descriptors sufficiently accounts for the energetic variation within the native state ensembles of the H. sapiens structural database, (2) an amino acid library of only six residue types is sufficient to encode >90% of the thermodynamic information required for fold specificity in the entire database, and (3) structural resolution of the statistically derived environments reveals sequential cooperative segments throughout the protein, which are independent of secondary structure. As the first level of thermodynamic organization in proteins, these segments represent the thermodynamic counterpart to secondary structure.

Computer Simulation↗
PubMed2002

Thermodynamics of biological evolution and aging. Supramolecular thermodynamics is a key to understanding phenomena of life. What is life from a physical chemist's viewpoint.

The law of temporal hierarchies of the biological world allows us to pick out of the biomass quasi-closed thermodynamic systems with a given hierarchy. It has been established, that the use of this law of Nature as applied to supramolecular structures of organisms allows us the opportunity of using the methods of equilibrium supramolecular thermodynamics in the examination of open living systems. It has been shown that supramolecular thermodynamics is one of the "keys", which allows us to explain the origin of life and evolution of living beings. The second law of thermodynamics in its classic formulation (R. Clausius, J.W. Gibbs) is easy to apply in order to make calculations, carried out through methods of chemical, supramolecular and overall hierarchical thermodynamics.

Aging↗
PubMed1984

[Thermodynamics of life from the point of view of technical thermodynamics and exergy].

All living beings are, from the thermodynamic point of view, open, well regulated, and optimized systems with considerable internal irreversibilities. However scientific research is mainly based on closed systems. The theory of open systems is very well developed in engineering thermodynamics. Here the concept of "exergy"--the thermodynamic potential related to given surroundings--clearly distinguishes between the two concepts of the word "energy".

Animals↗
PubMed1979

Thermodynamic compensation process in interacting protein systems: definition of thermodynamic compensatory temperature, (Tc).

In our thermodynamic analysis of the non-linear Van't Hoff expression as applied to several self-associating systems -- specifically in the cases of bovine liver L-glutamate dehydrogenase (GDH), glucagon and S-carboxymethylated apo A-II protein from human high density lipoprotein -- we have examined the interrelationships of a number of thermodynamic temperatures as they affect the association process. We found the principal determinants of the linear thermodynamic compensation process to be delta S0(T)/delta C0p(T) = (delta T'C)/(Texp), where (delta T'C) = Texp). We have defined the unique compensatory temperature, (TC), for any interacting system, at which the contributions of enthalpy and entropy to the association process are balanced.

Animals↗
PubMed1995

Analyses of thermodynamic data for concentrated hemoglobin solutions using scaled particle theory: implications for a simple two-state model of water in thermodynamic analyses of crowding in vitro and in vivo.

Quantitative description of the thermodynamic consequences of macromolecular crowding (excluded volume nonideality) is an important component of analyses of the thermodynamics and kinetics of noncovalent interactions of biopolymers in vivo and in concentrated polymer solutions in vitro. By analyzing previously published thermodynamic data, we have investigated extensively the comparative applicability of two forms of scaled particle theory (SPT). In both forms, macromolecules are treated as hard spheres, but MSPT, introduced by Ross and Minton, treats the solvent as a structureless continuum, whereas bulk water molecules are included explicitly as hard spheres in BSPT, an approach developed by Berg. Here we use both MSPT and BSPT to calculate the excluded volume component of the macromolecular activity coefficient of hemoglobin (Hb) at concentrations up to 509 mg/ml by fitting osmotic pressure data for Hb and sedimentation equilibrium data for Hb and sickle-cell Hb (HbS). Both forms of SPT also are used here to analyze the effects of other globular proteins (BSA and Hb) on the solubility of HbS. In applying MSPT and BSPT to analyze macromolecular crowding, the extent of hydration delta Hb (in gH2O/gprotein) is introduced as an adjustable parameter to specify the effective (hard sphere) radius of hydrated Hb. In our nonlinear least-squares fittings based on BSPT, the hard sphere radius of bulk water molecules is either fixed at 1.375 A or floated. Although both forms of SPT yield good fittings (with different values of delta Hb) at Hb concentrations up to 350 mg/ml, only BSPT gives good fittings of all available Hb osmotic pressure data as well as of the sedimentation equilibrium and solubility data. Only BSPT predicts values for delta Hb (approximately 0.5-0.6 g/g) in the range obtained for Hb from hydrodynamic measurements (approximately 0.36-0.78 g/g). These findings indicate the applicability, at least in the context of BSPT, of a simple two-state classification of water (bulk water and water of macromolecular hydration) as a basis for interpreting excluded volume nonideality in concentrated solutions of globular proteins.

Biophysical Phenomena↗
PubMed1990

Thermodynamics of information transfer between subunits in oligomeric enzymes and kinetic cooperativity. 2. Thermodynamics of kinetic cooperativity.

The principles of structural kinetics allow one to define the thermodynamic conditions that are sufficient to generate a certain type of kinetic behavior. If subunits are loosely coupled, that is if no quaternary constraint exists between them, the kinetic behavior of the polymeric enzyme is qualitatively defined by the behavior of an ideal dimer. The nature and the extent of the kinetic cooperativity are defined by the energy of interaction, delta G rho, between two subunits. This energy of interaction is that of an ideal dimer relative to that of the A2 and B2 states. This thermodynamic formulation of a given type of cooperativity holds whatever the degree of polymerization of the enzyme. Under these conditions of loose coupling between subunits, positive kinetic cooperativity cannot be associated with any sigmoidicity of the rate curve. The range of energy coupling where positive kinetic cooperativity must, of necessity, be observed becomes more and more narrow as the number of subunit interactions is increased. This range, however, is independent of the number of subunits. The same situation is not observed for negative cooperativity which appears to be independent of both the number of subunits and the number of subunit interactions. If the subunits are tightly coupled, that is if quaternary constraints exist between them, three thermodynamic parameters, delta G' rho, delta G lambda, delta G mu, are required to define the nature of kinetic cooperativity. delta G' rho is the free energy of an ideal strained dimer relative to that of strained A2 and B2 states. delta G lambda and delta G mu represent the difference of strain energies between conformations A and B and B and B relative to that existing between conformations A and A. One may determine in the parametric space (delta G' rho, delta G lambda, delta G mu) the boundaries between the sufficient conditions that generate a certain type of cooperativity and the lack of these conditions. The kinetic parameters of the rate equation are not all independent. A number of constraint conditions exist between them which depend upon the subunit design of the polymeric enzyme. The existence of these constraint conditions may be diagnostic of a certain type of subunit interactions.

Enzymes↗
PubMedDate not supplied

[Disorders of information exchange as a basis for disease formation and the second law of thermodynamics for living thermodynamic systems].

The second law of thermodynamics and the adaptation law have been utilized for analysis of thermodynamic systems functioning in humans. Disturbances in the information exchange are thought to play a pathogenetic role in the disease onset. A new informational-thermodynamic approach to assessment of the system condition (steady, unsteady) is proposed which may help to develop methods of the disease course prognosis.

Adaptation, Physiological↗
PubMed2004

Thermodynamic length in a two-dimensional thermodynamic state space.

The main goal of this paper is to reach an explicit formulation and possible interpretation of thermodynamic length in a thermodynamic state space with two degrees of freedom. Using the energy and entropy metric in a general form, we get explicit results about thermodynamic length along isotherms, its relation with work and with speed of sound. We also look at the relation between the determinants of the energy and entropy metrics and find that they differ by a factor of T4.

Journal Article↗
PubMed1989

Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: three-state and four-state thermodynamic models.

Chemical shifts of base and H1' protons of the single-stranded hexamers d(ATTACC) and d(GGTAAT), of the 1:1 mixtures of these complementary hexamers, and of the self-complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation. Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B-DNA duplex or a hairpin-loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin-loop formation. In the analysis of the duplex formation of the hexamers, a two-state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three-state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two-state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual delta Hd degrees and delta Sd degrees values. Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an average Tmd value of 341 K (1M DNA) and delta Hd degrees of - 121 kJ.mol-1 for the dimer/random-coil transition of the hexamer duplex d(ATTACC).d(GGTAAT). For the duplex in equilibrium random-coil transition of the 12-mer d(ATTACCGGTAAT) an average Tmd value of 336 K (1M DNA) and delta Hd degrees of -372 kJ.mol-1 are found. The hairpin/random-coil transition of d(ATTACCGGTAAT) is characterized by a rather large delta Hh degrees value, -130 kJ.mol-1, and an average Tmh value of 304 K.

Magnetic Resonance Spectroscopy↗
PubMed1990

High-performance liquid chromatography of amino acids, peptides and proteins. XCV. Thermodynamic and kinetic investigations on rigid and soft affinity gels with varying particle and pore sizes: comparison of thermodynamic parameters and the adsorption behaviour of proteins evaluated from bath and frontal analysis experiments.

The thermodynamic constants, associated with the interaction of three proteins with triazine dye affinity sorbents, have been derived from bath and frontal analysis experiments. In cases where mass-transfer restrictions are very high, calculation of the thermodynamic constants directly from frontal analysis experiments could not be achieved. In such cases, a portion of the adsorbate was always present in the effluent, a situation which has its effect as the split peak phenomenon. With Fractogel-based triazine dye affinity sorbents none of the test proteins applied in frontal analysis were adsorbed. A similar behaviour was observed for a Cellufine sorbent during the adsorption of human serum albumin and the Blue Sepharose CL6B sorbent during the adsorption of alcohol dehydrogenase, which displayed much slower apparent adsorption kinetics than observed in the bath experiments. These phenomena were shown to be associated with changes in the gel structure, caused in part by the column packing procedure. Silica-based sorbents performed better in the adsorption of lysozyme in the column mode than soft-gel affinity sorbents, as was evident in the higher capacities and steeper breakthrough curves. At high protein concentrations (feedstock concentration greater than 0.2 mg/ml) breakthrough curves obtained with small- and large-particle-size sorbents, but of constant pore size, were found to be identical. This finding demonstrates that the use of small-particle-size sorbents (e.g. particle diameter, dp less than or equal to 5 microns) for the preparative isolation of proteins may not be justified when operating in the overload mode. With other higher-molecular-weight proteins and the silica-based sorbent systems examined, the small-particle-size sorbents (dp = 5 microns) displayed less symmetrical shapes of their breakthrough curves than the larger-particle-size and soft-gel sorbents. This behaviour was further exacerbated when non-porous glass or silica-based sorbents were utilized. These non-porous affinity sorbents displayed nearly rectangular breakthrough shapes at the onset of the adsorption process, but comparatively slow adsorption kinetics became evident as saturation was approached. This phenomenon has been attributed to surface rearrangement and/or reorientation of the adsorbed proteins, particularly with sorbents of high ligand densities.

Amino Acids↗
PubMed1990

Thermodynamics of information transfer between subunits in oligomeric enzymes and kinetic cooperativity. 1. Thermodynamics of subunit interactions, partition functions and enzyme reaction rate.

The strength of quaternary constraints between two subunits of a polymeric enzyme depends upon the number of neighboring subunits and upon whether these subunits are liganded or not. These quaternary constraints between two subunits of a complex polymeric enzyme may be expressed, however, in terms of quaternary constraints that exist within ideal dimers. The influence of quaternary constraints on the reaction rate of a complex polymeric enzyme may thus be expressed in terms of the intersubunit strain that exists within dimers. This conclusion, that was far from evident, appears to be the consequence of the postulates of structural kinetics, and derive as well from usual thermodynamic principles. The structural steady-state equations may be expressed in terms of partition and sub-partition functions. As applied to structural kinetic models, a partition function expresses how, during the steady state, the energy of a population of enzyme molecules is distributed over n states. Similarly a sub-partition function describes how, during the steady state, the energy of these enzyme molecules is partitioned among only n-k of these states. Although the concept of partition function was initially formulated for equilibrium processes, it may be extended without any loss of generality to non-equilibrium processes. Moreover it is reminiscent of the concept of binding polynomial presented some years ago by Wyman for the equilibrium binding of a ligand to a protein. With this formalism derived from statistical mechanics, a structural rate equation may be derived from the ratio of a sub-partition function of degree n-1 and of a partition function of degree n. Again these properties are the consequence of the postulates of structural kinetics associated with simple ideas derived from statistical thermodynamics.

Enzymes↗
PubMed2001

Thermodynamic pressure in nonlinear nonequilibrium thermodynamics of dilute nonviscous gases.

In this paper, using extended thermodynamics, we build up a nonlinear theory for a dilute nonviscous gas under heat flux. The fundamental fields are the density, the velocity, the internal energy density, and the heat flux. The constitutive theory is builtup without approximations. We single out the nonlinear complete expressions of the Gibbs equation and of the nonequilibrium pressure. In particular, we determine the complete expressions furnished by the theory for the nonequilibrium pressure tensor and thermodynamic pressure, i.e., the derivative of the nonequilibrium internal specific entropy with respect to the specific volume, times the nonequilibrium temperature. In a second-order approximation these expressions are identical with those obtained in Phys. Rev. E 51, 158 (1995), using information theory.

Journal Article↗
PubMed1985

Thermodynamic compatibility of proteins in aqueous media. Part 2. The effect of some physicochemical factors on thermodynamic compatibility of casein and soybean globulin fraction.

A study has been made on the effect of temperature, sodium chloride, pH and cysteine on the thermodynamic compatibility of casein and soybean globulin fraction in aqueous medium. The section of miscibility gap characterizing the influence of the indicated factors on the compatibility of proteins has been determined. Assessment has been made of the influence of pH and cysteine on a) the effective molecular weights of casein and soybean globulin fraction and b) the difference in the intensity of interaction between each protein and a solvent. The experimental data obtained on the compatibility of proteins were found in good agreement with the theoretical concepts which establish the dependence of the compatibility of polymers on the ratio of their molecular weights, the intensity of interactions between polymers, as well as on the difference in the intensities of interaction between each of them and a solvent, i.e. on the difference of protein hydrophilicities.

Caseins↗
PubMed1986

Thermodynamic compatibility of proteins in aqueous media. Part 3. Studies on the role of intermolecular interactions in the thermodynamics of compatibility of proteins according to the data of dilution enthalpies.

The flow microcalorimetric method was used to determine the enthalpies of diluting solutions of ovalbumin, bovine serum albumin, casein, soybean globulin fraction, thermotropic aggregates of ovalbumin, mixtures of ovalbumin-bovine serum albumin, casein-soybean globulin fraction, and ovalbumin-thermotropic aggregates of ovalbumin in water. The calorimetric data obtained were compared with the data on phase equilibrium in the systems Water-Ovalbumin-Bovine serum albumin, Water-Casein-Soybean globulin fraction, Water-Ovalbumin-Thermotropic aggregates of ovalbumin. Intermolecular interactions have been shown to play a significant role in the thermodynamics of protein compatibility.

Animals↗
PubMed1992

Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions.

The objective of this study is to quantify the contributions of cations, anions and water to stability and specificity of the interaction of lac repressor (lac R) protein with the strong-binding symmetric lac operator (Osym) DNA site. To this end, binding constants Kobs and their power dependences on univalent salt (MX) concentration (SKobs = d log Kobs/d log[MX]) have been determined for the interactions of lac R with Osym operator and with non-operator DNA using filter binding and DNA cellulose chromatography, respectively. For both specific and non-specific binding of lac R, Kobs at fixed salt concentration [KX] increases when chloride (Cl-) is replaced by the physiological anion glutamate (Glu-). At 0.25 M-KX, the increase in Kobs for Osym is observed to be approximately 40-fold, whereas for non-operator DNA the increase in Kobs is estimated by extrapolation to be approximately 300-fold. For non-operator DNA, SKobsRD is independent of salt concentration within experimental uncertainty, and is similar in KCl (SKobs,RDKCl = -9.8(+/- 1.0) between 0.13 M and 0.18 M-KCl) and KGlu (SKobs,RDKGlu = -9.3(+/- 0.7) between 0.23 M and 0.36 M-KGlu). For Osym DNA, SKobsRO varies significantly with the nature of the anion, and, at least in KGlu appears to decrease in magnitude with increasing [KGlu]. Average magnitudes of SKobsRO are less than SKobsRD, and, for specific binding decrease in the order [SKobsRO,KCl[>[SKobsRO,KAc[>[SKobsRO,KGlu[ . Neither KobsRO nor SKobsRO is affected by the choice of univalent cation M+ (Na+, K+, NH4+, or mixtures thereof, all as the chloride salt), and SKobsRO is independent of [MCl] in the range examined (0.125 to 0.3 M). This behavior of SKobsRO is consistent with that expected for a binding process with a large contribution from the polyelectrolyte effect. However, the lack of an effect of the nature of the cation on the magnitude of KobsRO at a fixed [MX] is somewhat unexpected, in view of the order of preference of cations for the immediate vicinity of DNA (NH4+ > K+ > Na+) observed by 23Na nuclear magnetic resonance. For both specific and non-specific binding, the large stoichiometry of cation release from the DNA polyelectrolyte is the dominant contribution to SKobs. To interpret these data, we propose that Glu- is an inert anion, whereas Ac- and Cl- compete with DNA phosphate groups in binding to lac repressor. A thermodynamic estimate of the minimum stoichiometry of water release from lac repressor and Osym operator (210(+/- 30) H2O) is determined from analysis of the apparently significant reduction in [SKobsRO,KGlu[ with increasing [KGlu] in the range 0.25 to 0.9 M. According to this analysis, SKobs values of specific and non-specific binding in KGlu differ primarily because of the release of water in specific binding. In KAc and KCl, we deduce that anion competition affects Kobs and SKobs to an extent which differs for different anions and for the different binding modes.

Anions↗
PubMed1976

Thermodynamic investigations of proteins. III. Thermodynamic description of lysozyme.

Standard functions of enthalpy, entropy and the Gibbs energy of native and denatured lysozyme in the range of 0-100 degrees C and pH 1.5-7.0 are represented in three-dimensional projections. The denaturational Gibbs energy change reaches 16 kcal mol-1 at conditions of maximal protein stability (0 degrees C, pH 4.5-7.0) and equals 14.5 kcal mol-1 at 25 degrees C and neutral pH. This result was found to be in agreement with the data reported from guanidine hydrochloride denaturation studies. Partial thermodynamic functions of the conformational and ionizational changes of the protein are obtained from entropy and Gibbs-energy changes in denaturation. The conformational partial entropy and Gibbs-energy change are found to be independent of pH. The pH-dependent partial ionizational entropy and Gibbs-energy changes are induced by normalization of the ionization behaviour of buried groups and cause a decrease of protein stability.

Binding Sites↗
PubMed1987

Enhancement of transdermal delivery by superfluous thermodynamic potential. I. Thermodynamic analysis of nifedipine transport across the lipoidal barrier.

In vitro techniques were used to test certain concepts regarding the enhancement of the transdermal delivery of nifedipine from topical vehicles. Tested vehicles include the volatile solvent acetone, nonvolatile solvents such as propylene glycol and isopropyl myristate, volatile/nonvolatile mixtures, and those mixtures with a polymer additive. An ethylene-vinyl acetate (EVA) copolymer membrane was used as the lipoidal barrier for the diffusing drug. Not merely the rate of transport per unit area, but the activity coefficient and the diffusion coefficient of the penetrating agent in the barrier were obtained. Despite the 10,000-fold difference in the vehicle concentration, water and several hydrophilic vehicles containing finely ground suspensions of the drug produced nearly the same rate of penetration. Some lipophilic solvents affected the barrier function of the EVA membrane to promote penetration of the drug. It has been found that the activity coefficient in the EVA membrane is very susceptible to wide variations by imbibition of such solvents. From volatile/nonvolatile mixtures, a transient enhancement in the transport of nifedipine across the membrane was observed. The increase in the flux was accounted for by the increase in the thermodynamic activity of the drug in the nonvolatile vehicle caused by the evaporation of the volatile component. The eventual decrease in penetration was the result of the drug precipitation from the supersaturated solution. The precipitation was inhibited and/or retarded during the entire time course of the experiments when a polymer additive was present. The steady-state fluxes from mixtures with a polymer additive were higher by about 3 to 5 times than that of the control experiment.

Biological Transport↗