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PubMed2000

Thermodynamic analysis of diffusion of non-electrolytes across plant cuticles in the presence and absence of the plasticiser tributyl phosphate.

Solute mobility in cuticular membranes (CMs) of 14 plant species (Citrus aurantiumn L., Citrus grandis L., Hedera helix L., Ilex aquifolium L., Ilex paraguariensis St.-Hil., Malus domestica Borkh. cv. Golden Delicious, Populus alba L., Prunus laurocerasus L., Pyrus communis L. cv. Bartlett, Conference and Gellerts Butterbirne, Pyrus pyrifolia (Burm. f.) Nakai, Schefflera actinophylla (Endl.) Harms and Strophanthus gratus Baill.) was measured over the temperature range 25-55 degrees C. The five organic model compounds differed in size (130-349 cm3 mol(-1)) and cuticle/water partition coefficient (18-10(8)). For all individual CMs (n = 297), the data were plotted according to the thermodynamic relationship between the preexponential factor (which is proportional to entropy) of the Arrhenius equation and the activation energy (enthalpy) of diffusion (ED). A strict linear correlation was obtained, providing evidence that the five compounds diffused along the same lipophilic diffusion path in all plant species tested. Extracting cuticular waxes from CMs of four plant species (Hedera, Pyrus, Schefflera and Strophanthus) had no effect on the slope of the plot but a parallel displacement towards higher entropy was observed with these polymer matrix (MX) membranes. This displacement is interpreted as a temperature-independent tortuosity factor directly related to entropy. The influence of the plasticiser tributyl phosphate on solute mobility at various temperatures was measured for CM and MX membranes. The plasticiser increased solute mobility and ED was reduced drastically for both membrane types. This plasticiser effect was almost completely reversible, when tributyl phosphate was desorbed from the membranes. For both, plasticised CM and MX, the thermodynamic correlation exists whereby all data points lie on the same line. The data are used to characterise the lipophilic pathway across plant cuticles in terms of the free-volume theory.

Diffusion↗
PubMed2005

Reduction thermodynamics of the T1 Cu site in plant and fungal laccases.

The thermodynamic parameters for reduction of the type-1 (T1) copper site in Rhus vernicifera and Trametes versicolor laccases and for the derivative of the former protein from which the type-2 copper has been selectively removed (T2D) have been determined with UV-vis spectroelectrochemistry. In all cases, the enthalpic term turns out to be the main determinant of the Eo' of the T1 site. Also the difference between the reduction potentials of the two laccases is enthalpy-based and reflects differences in the coordination features of the T1 sites and their protein environment. The T1 sites in native R. vernicifera laccase and its T2D derivative show the same Eo', as a result of compensatory differences in the reduction thermodynamics. This suggests that removal of the type-2 (T2) copper results in modification of the reduction-induced solvent reorganization effects, with no influence in the structure of the multicopper protein site. This conclusion is supported by NMR data recorded on the native, the T2D, and Hg-substituted T1 derivatives of R. vernicifera laccase, which show that the T1 and T2/T3 sites are largely noninteracting.

Copper↗
PubMed2000

Redox thermodynamics of low-potential iron-sulfur proteins.

The enthalpy and entropy changes associated with protein reduction (deltaHdegrees,(rc), deltaSdegrees,(rc)) were determined for a number of low-potential iron-sulfur proteins through variable temperature direct electrochemical experiments. These data add to previous estimates making available, overall, the reduction thermodynamics for twenty species from various sources containing all the different types of metal centers. These parameters are discussed with reference to structural data and calculated electrostatic metal-environment interaction energies, and redox properties of model complexes. This work, which is the first systematic investigation on the reduction thermodynamics of Fe-S proteins, contributes to the comprehension of the determinants of the differences in reduction potential among different protein families within a novel perspective. Moreover, comparison with analogous data obtained previously for electron transport (ET) metalloproteins with positive reduction potentials, i.e., cytochromes c, blue copper proteins, and HiPIPs, helps our understanding of the factors controlling the reduction potential in ET species containing different metal cofactors. The main results of this work can be summarized as follows.

Desulfovibrio↗
PubMed2004

Nonlinear viscoelastic, thermodynamically consistent, models for biological soft tissue.

The mechanical behavior of most biological soft tissue is nonlinear viscoelastic rather than elastic. Many of the models previously proposed for soft tissue involve ad hoc systems of springs and dashpots or require measurement of time-dependent constitutive coefficient functions. The model proposed here is a system of evolution differential equations, which are determined by the long-term behavior of the material as represented by an energy function of the type used for elasticity. The necessary empirical data is time independent and therefore easier to obtain. These evolution equations, which represent non-equilibrium, transient responses such as creep, stress relaxation, or variable loading, are derived from a maximum energy dissipation principle, which supplements the second law of thermodynamics. The evolution model can represent both creep and stress relaxation, depending on the choice of control variables, because of the assumption that a unique long-term manifold exists for both processes. It succeeds, with one set of material constants, in reproducing the loading-unloading hysteresis for soft tissue. The models are thermodynamically consistent so that, given data, they may be extended to the temperature-dependent behavior of biological tissue, such as the change in temperature during uniaxial loading. The Holzapfel et al. three-dimensional two-layer elastic model for healthy artery tissue is shown to generate evolution equations by this construction for biaxial loading of a flat specimen. A simplified version of the Shah-Humphrey model for the elastodynamical behavior of a saccular aneurysm is extended to viscoelastic behavior.

Animals↗
PubMed2006

Thermodynamic and kinetic analysis of the H2 threshold for Methanobacterium bryantii M.o.H.

H2 thresholds, concentrations below which H2 consumption by a microbial group stops, have been associated with microbial respiratory processes such as dechlorination, denitrification, sulfate reduction, and methanogenesis. Researchers have proposed that observed H2 thresholds occur when the available Gibbs free energy is minimal (DeltaG approximately 0) for a specific respiratory reaction. Others suggest that microbial kinetics also may play a role in controlling the thresholds. Here, we comprehensively evaluate H2 thresholds in light of microbial thermodynamic and kinetic principles. We show that a thermodynamic H2 threshold for Methanobacterium bryantii M.o.H. is not controlled by DeltaG for methane production from H2 + HCO3-. We repeatedly attain a H2 threshold near 0.4 nM, with a range of 0.2-1 nM, and DeltaG for methanogenesis from H2 + HCO3- is positive, +5 to +7 kJ/mol-H2, at the threshold in most cases. We postulate that the H2 threshold is controlled by a separate reaction other than methane production. The electrons from H2 oxidation are transferred to an electron sink that is a solid-phase component of the cells. We also show that a kinetic threshold (S(min)) occurs at a theoretically computed H2 concentration of about 2400 nM at which biomass growth shifts from positive to negative.

Hydrogen↗
PubMed2005

Thermodynamic characteristics of plasminogen activation by indirect activators.

Several indirect plasminogen (Pg) activators are known including streptokinase and the monoclonal antibody IV-Ic, whose mechanism of activation is well studied. To characterize thermodynamically the activation of Pg by streptokinase (SK) and the monoclonal antibody (mAB) IV-Ic, the activation energies were calculated for various reaction stages. Activation energy of 7.4 kcal/mol was determined for the interaction of the chromogenic substrate S-2251 with plasmin (Pm) and activated equimolar complexes Pm-SK and Pg*SK at the steady-state reaction stage, and 18.7 kcal/mol with the complexes Pg*IV-Ic. A 2.5-fold increase in the energy of activation for the Pg*IV-Ic complex suggests a more intricate mechanism of its interaction with the substrate. At the stage of increasing active center concentrations and the formation of activated complexes Pg*SK and Pg*mAB IV-Ic, the activation energy was found to be 10.5 and 38 kcal/mol, respectively. At this reaction stage the conformational rearrangement of Pg molecule with the formation of active center is the limiting stage determining the reaction rate. Unexpectedly high energy of activation at the second stage of interaction between mAB IV-Ic and Pg suggests several simultaneous reactions and complexity of conformation rearrangement in the Pg molecule in activated complexes, thus requiring large energy expense. Formation of the active center is probably accompanied by its transition within a narrow temperature range into another conformation state with the change in activation parameters of the reaction. Quantitative evaluation of the studied reactions from the perspective of thermodynamics of the enzymatic reactions gives more comprehensive characteristics of the activation mechanism.

Antibodies, Monoclonal↗
PubMed2005

The first thermodynamic characterization of beta-1,3-xylanase from a marine bacterium.

Sequence analysis of beta-1,3-xylanase (TxyA) from a marine bacterium, Alcaligenes sp. strain XY-234 implied that an xylan-binding module belonging to carbohydrate-binding module family 31 (TxyA-CBM) is separated from a catalytic module belonging to glycosyl hydrolase family 26 (TxyA-CM) by a putative glycine-rich linker [Okazaki, F., et al. (2002) J. Bacteriol. 184: 2399-2403]. In order to reveal the role of these structural features of TxyA, two modules, TxyA-CBM and TxyA-CM, were constructed, and those modules and full-length TxyA were characterized by thermodynamic studies. TxyA-CBM and TxyA-CM showed full reversible folding from denaturant-induced unfolded forms, exhibited higher thermodynamic stabilities. The conformational stability of both truncated modules is industrially desirable, as well as aiding the understanding of the enzymatic characterization of the two modules of beta-1,3-xylanase separated by a long linker.

Alcaligenes↗
PubMed2005

The thermodynamics of the partitioning of ionizing molecules between aqueous buffers and phospholipid membranes.

PURPOSE: To study the thermodynamics of partitioning of eight ionising dual D2-recepto beta2-adrenoceptor agonists between vesicles of L-alpha-dimyristoylphosphatidylcholine (DMPC) and aqueous buffers. METHODS: The thermodynamics of partitioning have been studied by isothermal titration calorimetry (ITC). RESULTS: Compounds which are predominantly cationic at pH 7.4 (designated as class 1 compounds) have a more exothermic partitioning than those which are predominantly in the electronically neutral form (designated as class 2 compounds) at pH 7.4, and less positive standard entropies of partitioning. Under acidic conditions (pH 4.0), class compounds 2 (predominantly electronically neutral at pH 7.4) are almost completely cationic and accordingly have a more exothermic partitioning than at pH 7.4. The standard entropies of partitioning also depend on the pH. When the compounds are predominantly cationic, the standard entropy change is less positive (less favourable) than under conditions where the compounds are predominantly electronically neutral. CONCLUSIONS: The observations are consistent with the notion of there being a favourable electrostatic interaction (enthalpically) between the positively charged amino-group of predominantly cationic compounds and the negatively charged phosphate group of the vesicle.

Adrenergic Agonists↗
PubMed1985

Relative abilities of phosphagens with different thermodynamic or kinetic properties to help sustain ATP and total adenylate pools in heart during ischemia.

Hearts of chicks fed the creatine analog, 1-carboxymethyl-2-iminoimidazolidine (cyclocreatine), accumulated 15 mumol/g wet wt of the synthetic phosphagen, cyclocreatine-3-P; had total creatine levels reduced from the normal 6 mumol/g to only 1.8 mumol/g; and had their glycogen levels tripled. During total ischemia in vitro these hearts utilized the cyclocreatine-P for synthesis of ATP, had greatly prolonged glycolysis, and exhibited a two- to fivefold delay in depletion of both ATP and the total adenylate pool, relative to controls. Accumulation from the diet of comparable levels of the closely related 1-carboxyethyl-2-imino-3-phosphonoimidazolidine (homocyclocreatine-P) by heart was accompanied by only slight lowering of total creatine to 4.2 mumol/g, and a tripling of glycogen levels. During ischemia these hearts exhibited prolonged glycolysis, but they did not utilize the very stable homocyclocreatine-P (200,000-fold less reactive than creatine-P) and thus formed less Pi; most significantly, there was no delay in depletion of ATP levels relative to controls. Feeding of creatine doubled total creatine levels in heart, but had no marked effect on ATP depletion during ischemia; in all dietary groups creatine-P pools had fallen to less than or equal to 1.2 mumol/g by first tissue sampling. Although adaptive responses were also involved, maximal conservation of ATP and total adenylate pools in heart during ischemia apparently required, in addition to adequate glycogen reserves, substantial levels of a kinetically competent phosphagen that is thermodynamically poised to continue to assist glycolysis in buffering decreases and oscillations in the [ATP]/[free ADP] ratio at the lower phosphorylation potentials and more acid pH characteristic of later stages of ischemia. Decreases and oscillations in the [ATP]/[free ADP] ratio cannot be buffered effectively late in ischemia by the creatine-P system for thermodynamic reasons, or by the homocyclocreatine-P system because of kinetic limitations.

Adenine Nucleotides↗
PubMed1988

Substrate as a source of thermodynamic nonideality in enzyme kinetic studies: invertase-catalyzed hydrolysis of sucrose.

Expressions for the effects of thermodynamic nonideality arising from the use of high concentrations of small substrate in enzyme kinetic studies are derived. Their application to experimental results for the hydrolysis of sucrose by yeast invertase (pH 4.9, 37 degrees C) signifies that the progressive decrease in initial velocity at high sucrose concentration is consistent with the occurrence of isomeric expansion during the transition of an enzyme-substrate complex to its activated state. Ultracentrifuge studies on the yeast enzyme preparation are then used to establish the physical acceptability of the volume change required to account for the kinetic effects in these terms: the postulated expansion of 1.3 liter/mol would represent a mere 0.16% increase in hydrated volume (or a corresponding increase in extent of asymmetry). Finally, although originally interpreted to signify an effect of sucrose on water concentration, published results for the invertase-sucrose system [J. M. Nelson and M. P. Schubert (1928) J. Amer. Chem. Soc. 50, 2188-2193] also find a rational explanation in terms of the present analysis based on effects of thermodynamic nonideality in enzyme kinetic studies.

Catalysis↗
PubMed1989

Effects of thermodynamic nonideality on the kinetics of ester hydrolysis by alpha-chymotrypsin: a model system with preexistence of the isomerization equilibrium.

The effects of a small inert solute, sucrose, on the kinetics of hydrolysis of N-acetyl-tryptophan ethyl ester by bovine alpha-chymotrypsin have been investigated. In studies at pH 7 and 20 degrees C the presence of 0.5 M sucrose in assay mixtures caused no discernible change in kinetic parameters, a result consistent with existence of the enzyme in a single conformational state under those conditions. However, at pH 3.5 and 50 degrees C, conditions under which the enzyme comprises an equilibrium mixture of compact and expanded isomeric states, inclusion of the inert solute led to a considerable decrease in Michaelis constant (0.84 to 0.61 mM) but no significant change in maximal velocity. These results were shown to be amenable to quantitative interpretation in terms of thermodynamic nonideality effects on catalysis by an enzyme undergoing reversible isomerization in the absence of substrate. For that analysis, which required experimental estimates of the equilibrium constant for preexisting isomerization of enzyme and the activity coefficient of substrate, the magnitude of the former (0.3) was obtained by difference spectroscopy: liquid-liquid partition studies with bromobenzene as organic phase were used to determine the effect of sucrose on the activity coefficient of N-acetyltryptophan ethyl ester. Such agreement between experimental kinetic findings and theoretical predictions based on considerations of excluded volume points to the possible use of the space-filling effects of small solutes for delineating the gross extent of conformational changes associated with reversible isomerization of proteins, and hence to the potential of thermodynamic nonideality as a probe for studying protein denaturation mechanisms as well as substrate-mediated changes associated with enzyme reaction mechanisms.

Chymotrypsin↗
PubMed1990

Thermodynamic nonideality as a probe of reversible protein unfolding effected by variations in pH and temperature: studies of ribonuclease.

Thermodynamic nonideality arising from the space-filling effect of added sucrose is employed to confirm that the reversible unfolding of ribonuclease A effected by acid may be described as an equilibrium between native and unfolded states of the enzyme. However, the extent of the volume change is far too small for the larger isomer to be the fully expanded state, a result signifying that the acid-mediated unfolding of ribonuclease does not conform with the two-state equilibrium model of protein denaturation. Although the thermal denaturation of ribonuclease A is characterized by a larger increase in volume, quantitative reappraisal of published results on the effects of glycerol on this transition at pH 2.8 (Gekko, K., and Timasheff, S. N., 1981 Biochemistry 20, 4677-4686) leads to an estimated volume increase that is much smaller than that inferred from hydrodynamic studies--a disparity attributed to the dual actions of glycerol as a space-filling solute and as a ligand that binds preferentially to the thermally unfolded form of the enzyme. Even in this unfavorable circumstance the fact that glycerol exerts a net excluded volume effect at least confirms that the thermal unfolding of ribonuclease A is an equilibrium transition between two discrete states. The strengths and limitations of using thermodynamic nonideality as a probe of the two-state equilibrium model of protein denaturation are discussed in the light of these findings.

Animals↗
PubMed1992

Thermodynamic elucidation of solute-induced lipid interdigitation phase: lipid interactions with hydrophobic versus amphipathic species.

Comparative thermodynamic studies on the interactions of aqueous dispersions of dipalmitoyl phosphatidylcholine (DPPC) bilayer vesicles with hydrophobic and amphipathic species were conducted to elucidate the nature of the solute-induced interdigitated lipid phase. Cyclohexanol, a strong hydrophobic species, lowers the temperature (tm) of the lipid main phase transition from the gel to the liquid-crystalline phase. Unlike ethanol (an amphipathic species), as reported previously, cyclohexanol does not exert a biphasic effect on tm (lowering tm at lower concentrations and raising tm at higher concentrations). At cyclohexanol greater than or equal to 15.4 mg/ml or 0.154 M, the thermogram of DPPC vesicles exhibits a small transition adjacent to the main phase transition but at a lower temperature. In contrast, ethanol does not promote such a small transition. Furthermore, the enthalpy (delta H) of the transition is increased in the presence of cyclohexanol. The sign of the enthalpy change (delta H-delta Ho) is positive and that of the free energy change (delta G-delta Go) is negative, a characteristic of solute-solute hydrophobic interaction. In contrast, DPPC bilayer vesicles exhibit both (delta H-delta Ho) and (delta G-delta Go) greater than 0 in the presence of ethanol in a concentration range where lipid vesicles exist in an interdigitated phase. To support the above distinct thermodynamic observations, fluorescence steady-state polarization (P) measurements were also performed. At the temperature below tm, the value of P decreases as cyclohexanol concentration increases, while a biphasic effect on P was found in the presence of ethanol. These findings support the postulation that the solute-induced interdigitated lipid phase requires the solute molecule to be amphipathic in nature.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1979

Ubiquinone in Rhodopseudomonas sphaeroides. Some thermodynamic properties.

In Rhodopseudomonas sphaeroides chromatophores there are 25 +/- 3 ubiquinone (Q) molecules/reaction center protein. They comprise several thermodynamically and functionally different ubiquinone complements. There are approx. 19 ubiquinones (Em7 = 90 mV) in the main ubiquinone complement which, within experimental resolution, appears thermodynamically homogenous and follows the redox reaction Q + 2e + 2H+ in equilibrium with QH2 from pH 5--9. A method which takes advantage of the 2H+ bound/molecule of Q reduced is described for measuring the time course of light-activated reaction center-driven reduction and oxidation of the 19 Q complement. No stable semiquinones were detected in the constitutents of the 19 Q complement. There are approx. 6 ubiquinones of lower Em which are currently unaccounted for, although one or possibly two of these can be assigned to the quinones of the reaction center protein. The remainder may be associated with the NADH-ubiquinone oxidoreductase.

Aerobiosis↗
PubMed1975

A comparison of the effects of ouabain and 2-deoxy-D-glucose on the thermodynamic variables of the frog skin.

Previous studies support the validity of a linear thermodynamic formalism relating the rates of active Na-+ transport and oxygen consumption Jr to the electrical potential difference delta-psi and the affinity A (negative free energy) of the metabolic driving reaction. The formulation was further tested in paired control and experimental hemiskins by the use of two inhibitors of Na-+ transport. Ouabain, a specific inhibitor of the Na-+ pump, might be expected to diminish the dependence of Jr on delta-psi without affecting A, whereas 2-deoxy-D-glucose, a competitive inhibitor of glucose metabolism should be expected to diminish A. Both inhibitors were used at concentrations adequate to depress Na-+ transport (i.e. short-circuit current Io) to some 50% of control level. Measurements were made of Io and dJr/d(delat-psi), and the apparent value of the affinity Aapp was calculated according to the thermodynamic formulation. Ouabain depressed minus dJr/d(delta-psi) without affecting Aapp whereas 2-deoxy-D-glucose depressed Aapp without affecting minus dJr/d(delta-psi). The demonstration of these effects indicated the utility of the formalism.

Animals↗
PubMed1976

A non-equilibrium thermodynamics analysis of active transport within the framework of the chemiosotic theory.

The proton circuit devised by Mitchell in the chemiosmotic theory was subjected to analysis using the formalism of irreversible thermodynamics. The phenomenological coefficients and the degree of coupling relating co-permeant flows were derived from anion/H+, substrate/H+, cation/H+ and anion/anion biporter models. Linearity and equality of the cross-coefficients in Onsager relations were always satisfied. Macroscopic flows leading to charges splitting, such as oxido-reduction, hydro-dehydratation and transhydrogenase, are driven by a composite thermodynamic force which includes the proton-motive component. Multiple coupling occurs in the circuit when it is assumed that the net inward flux of protons becomes zero, i.e. when the circulation of protons reaches a stationary state. Under these conditions, oxidative phosphorylation, ATPase- or respiration-linked transhydrogenase and uptake of anion or cation against their electrochemical gradient may be predicted, in agreement with known experimental evidence.

Biological Transport, Active↗
PubMed1984

The thermostatics and thermodynamics of cotransport.

The thermostatics of cotransport are reviewed. A static-head equilibrium state across a cotransport system, without leaks, is thought to occur when the electrochemical potential of the driven solute, B prevents net flow of the driving solute, A. For a symport this gives the relationship (formula: see text) Where n is the stoichiometric coefficient, namely the number of moles of A transported per mole of B. (2) If either a symporter with a 2:1 stoichiometric coefficient and a 1:1 symporter, or alternatively, a 1:1 symporter and a 1:1 antiporter are placed in a series membrane array, then the predicted static-head equilibrium across the entire array conflicts with the zeroth law of thermodynamics. (3) There are two major reasons for this failure of cotransport theory; these are: (A) the thermostatic relationships derived shown in Point 1 are based on the assumption that the cotransport process takes place within a closed system. However, the membrane and the external reservoirs are open to the cotransported ligands. It follows that A and B in the external reservoirs can vary independently of the changes within the cotransport process. As no chemical reaction between A and B occurs in the external solutions, reactions within the membrane phase do not affect the equilibrium between the transported ligands in the open reservoirs. (B) It is assumed that the law of mass action can be applied to the cotransport chemical reactions within the membrane phase, without any allowance for the fact that these reactions occur within a 'small thermodynamic system'. Any proper analysis of the chemical potential of the transported intermediate must consider the effects of lower order ligand-carrier forms, which coexist and compete for space with the higher order cotransported forms on the binding matrix. If account is taken of this necessity, then a simple extension of the work of Hill and Kedem (1966) J. Theor. Biol. 10, 399-441 shows that: (a) the static-head equilibrium state cannot exist; (b) the stoichiometry of cotransport, whether symport, or antiport, does not affect the static-head distribution of cotransported ligands; (c) the hypothetical net charge of the transported ligand-carrier complex does not affect static-head equilibrium; (d) the only equilibrium state where there is zero net flow of both driving and driven transported ligand is at true equilibrium when the ligands are uniformly distributed across the membrane. (4) It is deduced that cotransport is not entirely an affinity-driven, but is partially an entropy-driven process.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenosine Triphosphate↗
PubMed1988

Thermodynamic-geometric correlations for the morphology of self-assembled structures of glycosphingolipids and their mixtures with dipalmitoylphosphatidylcholine.

The morphology of aqueous dispersions of five neutral glycosphingolipids (GalCer, GlcCer, LacCer, asialo-GM2, asialo-GM1), sulfatide, and five gangliosides (GM3, GM2, GM1, GD1a and GT1b) and their mixtures with dipalmitoylphosphatidylcholine was studied by negative staining electron microscopy. The morphological features are interpreted on the basis of thermodynamic and geometric constraints previously studied in these systems (Maggio, B (1985) Biochim. Biophys. Acta 815, 245-258). The correlation between the theoretical predictions and the experimental findings are in reasonable agreement. Small changes in the molecular parameters of the individual glycosphingolipids or in their proportion in mixtures with dipalmitoylphosphatidylcholine bring about remarkable variations on the type of structure formed, its radius of curvature and thermodynamic stability.

1,2-Dipalmitoylphosphatidylcholine↗