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PubMed2004

Effects of monofunctional adducts of platinum(II) complexes on thermodynamic stability and energetics of DNA duplexes.

Effects of adducts of [PtCl(NH3)3]Cl or chlorodiethylenetriamineplatinum(II) on DNA stability were studied with emphasis on thermodynamic origins of that stability. Oligodeoxyribonucleotide duplexes (15-bp) containing the single, site-specific monofunctional adduct at G-residues of the central sequences TGT/ACA or 5'-AGT/5'-ACT were prepared and analyzed by differential scanning calorimetry, temperature-dependent ultraviolet absorption and circular dichroism. The unfolding of the platinated duplexes was accompanied by relatively small unfavorable free energy terms. This destabilization was enthalpic in origin. On the other hand, a relatively large reduction of melting temperature (T(m)) was observed as a consequence of the monofunctional adduct in the TGT sequence, whereas T(m) due to the adduct in the AGT sequence was reduced only slightly. We also examined the efficiency of the mammalian nucleotide excision repair system to remove from DNA the monofunctional adducts and found that these lesions were not recognized by this repair system. Thus, rather thermodynamic than thermal characterization of DNA adducts of monofunctional platinum compounds is a property implicated in the modulation of downstream effects such as protein recognition and repair.

DNA↗
PubMed2005

The conformational stability and thermodynamics of Fur A (ferric uptake regulator) from Anabaena sp. PCC 7119.

Fur (ferric uptake regulator) is a key bacterial protein that regulates iron acquisition and its storage, and modulates the expression of genes involved in the response to different environmental stresses. Although the protein is involved in several regulation mechanisms, and members of the Fur family have been identified in pathogen organisms, the stability and thermodynamic characterization of a Fur protein have not been described. In this work, the stability, thermodynamics and structure of the functional dimeric Fur A from Anabaena sp. PCC 7119 were studied by using computational methods and different biophysical techniques, namely, circular dichroism, fluorescence, Fourier-transform infrared, and nuclear magnetic resonance spectroscopies. The structure, as monitored by circular dichroism and Fourier-transform infrared, was composed of a 40% of alpha-helix. Chemical-denaturation experiments indicated that Fur A folded via a two-state mechanism, but its conformational stability was small with a value of DeltaG = 5.3 +/- 0.3 kcal mol(-1) at 298 K. Conversely, Fur A was thermally a highly stable protein. The high melting temperature (Tm = 352 +/- 5 K), despite its moderate conformational stability, can be ascribed to its low heat capacity change upon unfolding, DeltaCp, which had a value of 0.8 +/- 0.1 kcal mol(-1) K(-1). This small value is probably due to burial of polar residues in the Fur A structure. This feature can be used for the design of mutants of Fur A with impaired DNA-binding properties.

Anabaena↗
PubMed2005

Temperature dependence and thermodynamic properties of Ca2+ sparks in rat cardiomyocytes.

To elucidate the temperature dependence and underlying thermodynamic determinants of the elementary Ca2+ release from the sarcoplasmic reticulum, we characterized Ca2+ sparks originating from ryanodine receptors (RyRs) in rat cardiomyocytes over a wide range of temperature. From 35 degrees C to 10 degrees C, the normalized fluo-3 fluorescence of Ca2+ sparks decreased monotonically, but the Delta[Ca2+]i were relatively unchanged due to increased resting [Ca2+]i. The time-to-peak of Ca2+ sparks, which represents the RyR Ca2+ release duration, was prolonged by 37% from 35 degrees C to 10 degrees C. An Arrhenius plot of the data identified a jump of apparent activation energy from 5.2 to 14.6 kJ/mol at 24.8 degrees C, which presumably reflects a transition of sarcoplasmic reticulum lipids. Thermodynamic analysis of the decay kinetics showed that active transport plays little role in early recovery but a significant role in late recovery of local Ca2+ concentration. These results provided a basis for quantitative interpretation of intracellular Ca2+ signaling under various thermal conditions. The relative temperature insensitivity above the transitional 25 degrees C led to the notion that Ca2+ sparks measured at a "warm room" temperature are basically acceptable in elucidating mammalian heart function.

Animals↗
PubMed2005

Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA.

DNA binding of Klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template DNA. The temperature dependence of the binding affinity exhibits distinct curvature, with tightest binding at 25-30 degrees C. Nonlinear temperature dependence indicates Klenow binds different primed-template constructs with large heat capacity (DeltaCp) values (-870 to -1220 cal/mole K) and thus exhibits large temperature dependent changes in enthalpy and entropy. Binding is entropy driven at lower temperatures and enthalpy driven at physiological temperatures. Large negative DeltaCp values have been proposed to be a 'signature' of site-specific DNA binding, but type I DNA polymerases do not exhibit significant DNA sequence specificity. We suggest that the binding of Klenow to a specific DNA structure, the primed-template junction, results in a correlated thermodynamic profile that mirrors what is commonly seen for DNA sequence-specific binding proteins. Klenow joins a small number of other DNA-sequence independent DNA binding proteins which exhibit unexpectedly large negative DeltaCp values. Spectroscopic measurements show small conformational rearrangements of both the DNA and Klenow upon binding, and small angle x-ray scattering shows a global induced fit conformational compaction of the protein upon binding. Calculations from both crystal structure and solution structural data indicate that Klenow DNA binding is an exception to the often observed correlation between DeltaCp and changes in accessible surface area. In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding.

Binding Sites↗
PubMed1999

Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches.

The use of thermodynamic parameters for the calculation of oligonucleotide duplex stability provides the best estimates of oligonucleotide melting temperatures (Tm). Such estimates can be used for evidence-based design of molecular biological experiments in which oligonucleotide melting behavior is a critical issue, such as temperature or denaturing gradient gel electrophoreses, Southern blotting or hybridization probe assays on the LightCycler. We have developed a user friendly program for Tm calculation of matched and mismatched probes using the spreadsheet software Microsoft Excel. The most recently published values for entropy and enthalpy of Watson-Crick paris are used, and salt and oligonucleotide concentrations are considered. The 5' and 3' end stability is calculated for the estimation of primer specificity. In addition, the influence of all possible mutations under a given probe can be calculated automatically. The experimental evaluation of predicted Tm with the LightCycler, based on 14 hybridization probes for different gene loci, showed an excellent fit between measured results and values predicted with the thermodynamic model in 14 matched, 25 single mismatched and 8 two-point mismatched assays (r = 0.98; Sy. x = 0.90; y = 1.01 x -0.38). This program is extremely useful for the design of oligonucleotide probes because the use of probes that do not discriminate with a reasonable Tm difference between wild-type and mutation can be avoided in advance.

Base Pair Mismatch↗
PubMed2006

Variable stoichiometry with thermodynamic control in ADM1.

The effect of a variable stoichiometry of the carbohydrate fermentation process in the IWA Anaerobic Digestion Model No.1 (ADM1) is investigated. Most existing anaerobic digestion models including ADM1 consider a fixed-stoichiometry for their conversion processes. The ADM1 model was first transformed into an only mol based model to remove some errors derived from the mixed COD-mol based standard model and to allow for implementation of the variable stoichiometry. Consequently, the values of the butyrate and acetate catabolic yields of carbohydrate fermentation are made dependent on the hydrogen concentration and the reactor pH according to the predictions of a recently developed mixed culture fermentation model based on thermodynamic considerations. The simulation results obtained showed no significantly different responses in terms of effluent quality and system robustness between the standard and the variable stoichiometry ADM1 under overload conditions, and for both single- and two-step anaerobic digestion configurations. This behaviour is explained by the non-limiting acetogenic activity that compensated for the changes in the acidogenic products, typical behaviour for serial processes close to equilibrium. Based on the results obtained, thermodynamic rather than kinetic control for these conversions is suggested. Depending on the objectives to be met, lumping of carbohydrate fermenters and oxidative acetogens into a single biomass group with a variable stoichiometry is proposed for further consideration.

Anaerobiosis↗
PubMed2001

Brain oxidative stress--analytical chemistry and thermodynamics of glutathione and NADPH.

Oxidative stress occurs in the brain due to stroke, Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, trauma, aging and other conditions. Analysis of the effects of oxidative stress can involve quantitation of brain GSH, GSSG, NADPH and NADP. Reliable and rapid assays have been developed for these compounds and will be presented in detail. The assays have been used to analyze the effects of brain oxidative stress. Thermodynamic calculations can be performed to find the observed electrochemical potentials of the GSSG/GSH and the NADP/NADPH couples during oxidative stress. The biochemical consequences of these thermodynamic changes in the cell will be discussed as well as the defense mechanisms available to the cell to recover from oxidative stress.

Animals↗
PubMed2004

Strategy for the development of a thermodynamically stable oral microemulsion.

Microemulsions, being thermodynamically stable systems, with low viscosity and elegant in appearance have attracted interest not only for the delivery of single drug substances with low water solubility but for the stabilization of drugs in combination due to their preferential solubility in either the water or oil phases. Microemulsion design involves the solubilisation of an optimum amount of the dispersed phase in the continuous phase, utilizing the minimum amount of surfactant/mixture of surfactants/cosurfactants. It is the choice of the surfactant/surfactant mixture and/or cosurfactants, which poses the greatest challenge in the design of a thermodynamically stable microemulsion formulation. This paper will present a strategy for choosing surfactants to achieve a stable, dilutable microemulsion formulation for oral administration. Ternary and pseudo-ternary phase diagrams were constructed by titrating a series of mixtures [lipid (miglyol 812): cosurfactant and/or surfactant (cremophor RH, imwitor 308/742, sorbitol, brij 97, crillet 3)] with water at room temperature, the phases formed visually assessed after each addition and classified as isotropic (ME), liquid crystalline (LC) or coarse emulsions (EM). Results indicate that the surfactant combination of imwitor 308 and crillet 3 proved most successful in incorporating 25 to 30% miglyol 812 into a microemulsion formulation utilizing an intermediate quantity of surfactant and maintaining homogeneity on dilution.

Anisotropy↗
PubMed1987

Control of the generation and reactions of free radicals in biological systems by kinetic and thermodynamic factors.

Quantifiable redox properties are useful predictors of substrate reactivity in enzyme-catalysed redox reactions of e.g. nitroreductases or peroxidases. Redox properties may also control the rates of electron-transfer reactions between radical products of reduction and oxidation, and endogenous oxidants and reductants respectively. However, in numerous instances prototropic properties of substrate or radical may have profound kinetic consequences, protonation of radicals frequently slowing down electron-transfer reactions. Further, reactions which are thermodynamically extremely unfavourable may still proceed if radical products are removed from the pre-equilibrium efficiently. Thus kinetic considerations often outweigh the purely thermodynamic viewpoint.

Computer Simulation↗
PubMedDate not supplied

Thermodynamic study of iodocyanopindolol beta-adrenoceptors interactions with rat lung and cerebral cortex.

(+/-)125 I-cyanopindolol ((+/-) I CYP) was used to characterize beta-adrenoceptors on rat lung and cerebral cortex membranes. The affinity of (+/-) ICYP was higher for lung (Kd = 64.3 pM) at 37 degrees C. The association reaction of (+/-) ICYP was faster with lung (k+1 = 1.52 X 10(9) M-1.min-1) than with cerebral cortex beta-adrenoceptors (k+1 = 1.75 X 10(8) M-1.min-1). In both tissues, the dissociation reaction followed a biphasic process with a fast (t 1/2 = 15.4 min and 5.6 min for lung and cerebral cortex respectively) and a slow component (t 1/2 = 474 min and 255 min for lung and cerebral cortex respectively). The thermodynamic parameters for (+/-) ICYP - beta-adrenoceptors binding have been determined from kinetics and equilibrium studies, for the two tissues, at several temperatures between 0 degrees and 44 degrees C. For lung and cerebral cortex, Arrhenius plots were linear with different energies of activation. Van't Hoff plot was not linear for lung and the standard enthalpy and entropy changes of (+/-) ICYP - beta-adrenoceptors interaction decreased linearly with temperature: the binding occurred with a negative heat capacity change (delta Cp degrees = -368.9 cal. moles-1.K-1) at 25 degrees C. Thermodynamic and kinetic results show that binding of (+/-) ICYP to lung beta-adrenoceptors could involve two successive equilibria with a conformational change of the beta-adrenergic receptor.

Animals↗
PubMed1986

The binding of agonists and antagonists to rat lung beta-adrenergic receptors as investigated by thermodynamics and structure-activity relationships.

Interaction of several agonists and antagonists with the relevant beta receptor were studied in vitro using rat lung membranes as beta-adrenergic receptor source. The influence of temperature, between 4 degrees C and 37 degrees C, on the ability of beta-adrenergic agonists and antagonists to displace (-)-[125I]iodocyanopindolol from beta-adrenergic receptors was checked. Thermodynamic parameters were calculated from the Kj values thus obtained. Lipophilicity of the twenty molecules was also measured using a RP-HPLC method. The results obtained show: the density of receptors was not affected by the temperature but their affinity for the twenty agonists and antagonists increased with decreasing temperature; the binding of agonists is enthalpy driven while that of antagonists is entropy driven, with the exception of the lipophilic agonist dobutamine; a single relationship between entropy and lipophilicity exists for all twenty compounds and would suggest that molecular structure and physicochemical properties account for the thermodynamics of binding.

Adrenergic beta-Agonists↗
PubMed1998

Thermodynamics of propylparaben/beta-cyclodextrin inclusion complexes.

The aim of this study was to develop models for rigorous analysis of phase solubility diagrams, particularly the descending portion, in order to obtain individual thermodynamic complex formation and solubility product constants. Additionally, the effect of varying the initial solute concentration St, in excess of the optimal solubility Sm, on the general shape of the plateau and descending portions of the solubility diagram was investigated. The solubilities of propylpapraben (Seq) were measured against initial beta-cyclodextrin concentrations (Lt) at different temperatures and different St. Equilibrium concentrations (Leq) were also measured. The only effect observed was a broadening of the plateau region with increase in St with no discernible effect on Sm. Simultaneous rigorous analysis of the rising as well as the descending portions of the phase diagram could only be interpreted in terms of formation of two soluble complexes: SL and S2L. Rigorous analysis of the descending portion allowed the determination of individual formation constants K11 (SL) and K21 (S2L) in addition to the solubility product of the less soluble complex KS11 (SL). Thermodynamic analysis of the individual solubility of propylparaben and beta-cyclodextrin was carried out in water at different temperatures. In aqueous beta-cyclodextrin solutions, however, the solubility of propylparaben is enhanced due to the formation of both SL (delta G11(0) = -26.4 kJ/mol) and S2L (delta G21(0) = -46.4 kJ/mol) soluble complexes. Formation of the SL-complex is favored both by enthalpy (delta H11(0) = -20.7 kJ/mol) and a slight increase in entropy (delta S11(0) = 18.6 J/mol.K). Formation of S2L from SL apparently involves stronger solute-SL binding (delta H21(0) = -45.9 kJ/mol) yet is retarded by a net decrease in entropy (delta S21(0) = -86.3 J/mol.K). The solubility of the SL-complex is highly endothermic (delta HS11(0) = 55.8 kJ/mol), and although is accompanied by much randomization (delta SS11(0) = 101.8 J/mol.K), its solubility remains quite low (delta GS11(0) = 25.5 kJ/mol). Molecular mechanical modeling of propylparaben/beta-cyclodextrin interactions in water revealed that the S2L-complex formation is energetically more favored.

Cyclodextrins↗
PubMed1990

Binding of the bovine basic pancreatic trypsin inhibitor (Kunitz) to the 33,000 Mr and 54,000 Mr species of human urokinase: thermodynamic study.

The effect of pH and temperature on the apparent association equilibrium constant (Ka) for the binding of the bovine basic pancreatic trypsin inhibitor (BPTI, Kunitz inhibitor) to the 33,000 Mr and 54,000 Mr species of human urokinase (EC 3.4.21.31) has been investigated. Under all the experimental conditions, values of Ka for BPTI binding to the 33,000 Mr and 54,000 Mr species of human urokinase are identical. On lowering the pH from 9.5 to 4.5, values of Ka (at 21.0 degrees C) for BPTI binding to human urokinase (33,000 Mr and 54,000 Mr species) decrease thus reflecting the acidic pK-shift of the His-57 catalytic residue from 6.9, in the free enzyme, to 5.1, in the proteinase:inhibitor complex. At pH 8.0, values of the apparent thermodynamic parameters for BPTI binding to human urokinase (33,000 Mr and 54,000 Mr species) are: Ka = 4.9 x 10(4) M-1, delta G degree = -6.3 kcal/mol, and delta S degree = -37 entropy units (all at 21.0 degrees C); and delta H degree = +4.6 kcal/mol (temperature independent over the explored range, from 5.0 degrees C to 45.0 degrees C). Thermodynamics of BPTI binding to human urokinase (33,000 Mr and 54,000 Mr species) have been analyzed in parallel with those of related serine (pro)enzyme Kazal- and /Kunitz-type inhibitor systems. Considering the known molecular models, the observed binding behaviour of BPTI to human urokinase (33,000 Mr and 54,000 Mr species) was related to the inferred stereochemistry of the proteinase/inhibitor contact region.

Animals↗
PubMed1991

Binding of the bovine and porcine pancreatic secretory trypsin inhibitor (Kazal) to human leukocyte elastase: a thermodynamic study.

The effect of pH and temperature on the apparent association equilibrium constant (Ka) for the binding of the bovine and porcine pancreatic secretory trypsin inhibitor (Kazal-type inhibitor, PSTI) to human leukocyte elastase has been investigated. At pH 8.0, values of the apparent thermodynamic parameters for human leukocyte elastase: Kazal-type inhibitor complex formation are: bovine PSTI--Ka = 6.3 x 10(4) M-1, delta G degree = -26.9 kJ/mol, delta H degree = +11.7 kJ/mol, and delta S degree = +1.3 x 10(2) entropy units; porcine PSTI--Ka = 7.0 x 10(3) M-1, delta G degree = -21.5 kJ/mol, delta H degree = +13.0 kJ/mol, and delta S degree = +1.2 x 10(2) entropy units (values of Ka, delta G degree and delta S degree were obtained at 21.0 degrees C; values of delta H degree were temperature independent over the range (between 5.0 degrees C and 45.0 degrees C) explored). On increasing the pH from 4.5 to 9.5, values of Ka for bovine and porcine PSTI binding to human leukocyte elastase increase thus reflecting the acidic pK-shift of the His57 catalytic residue from congruent to 7.0, in the free enzyme, to congruent to 5.1, in the serine proteinase: inhibitor complexes. Thermodynamics of bovine and porcine PSTI binding to human leukocyte elastase has been analyzed in parallel with that of related serine (pro)enzyme/Kazal-type inhibitor systems. Considering the known molecular models, the observed binding behaviour of bovine and porcine PSTI to human leukocyte elastase was related to the inferred stereochemistry of the serine proteinase/inhibitor contact region(s).

Animals↗
PubMed2000

B cell responses to a peptide epitope. X. Epitope selection in a primary response is thermodynamically regulated.

We examine the etiological basis of hierarchical immunodominance of B cell epitopes on a multideterminant Ag. A model T-dependent immunogen, containing a single immunodominant B cell epitope, was used. The primary IgM response to this peptide included Abs directed against diverse determinants presented by the peptide. Interestingly, affinity of individual monomeric IgM Abs segregated around epitope recognized and was independent of their clonal origins. Furthermore, affinity of Abs directed against the immunodominant epitope were markedly higher than that of the alternate specificities. These studies suggested that the affinity of an epitope-specific primary response, and variations therein, may be determined by the chemical composition of epitope. This inference was supported by thermodynamic analyses of monomer IgM binding to Ag, which revealed that this interaction occurs at the expense of unfavorable entropy changes. Permissible binding required compensation by net enthalpic changes. Finally, the correlation between chemical composition of an epitope, the resultant affinity of the early primary humoral response, and its eventual influence on relative immunogenicity could be experimentally verified. This was achieved by examining the effect of various amino-terminal substitutions on immunogenicity of a, hitherto cryptic, amino-terminal determinant. Such experiments permitted delineation of a hierarchy of individual amino acid residues based on their influence; which correlated well with calculated Gibbs-free energy changes that individual residue side chains were expected to contribute in a binding interaction. Thus, maturation of a T-dependent humoral response is initiated by a step that is under thermodynamic control.

Amino Acid Sequence↗
PubMed2004

Hydrodynamic consequences of glycolysis: thermodynamic basis and clinical relevance.

Since Warburg's original description of aerobic and anaerobic glycolysis in 1924, the biochemical and molecular bases of glucose metabolism in cells have been characterized. However, its thermodynamic implications have found little attention. Van't Hoff's law of thermodynamics was applied here to describe how glucose metabolism affects intracellular osmotic pressure, hence revealing how glucose metabolism provides cells with osmotic energy as well as chemical energy. Ensuing osmosis-driven movement of free water across membranes affects cell volume and shape, hydration of intracellular components, and interactions of cells with their environment. Comparative analysis of extant data revealed strong evidence for clinically relevant glycolysis-driven effects under hypoxic conditions known to occur in cancer, vascular disease as well as intensive care, including critical and preventable ones affecting treatment effectiveness and thus, clinical outcome. These findings provide the first evidence confirming the existence of glycolysis-driven hydrodynamic effects and suggest that high levels of aerobic and anaerobic glycolysis provide a common biophysical basis in seemingly unrelated medical conditions.

Cell Hypoxia↗
PubMed1988

Human monoclonal cryoimmunoglobulins. III. Analysis of thermodynamic properties of Jir (IgG3 kappa) protein by fluorescence polarization measurement.

In order to characterize the thermodynamic property of cryoimmunoglobulin which is related to the temperature-dependent solubility change in aqueous solution, the fluorescence polarization measurement of 1-dimethylaminonaphthalene-5-sulfonyl (DNS) conjugated cryoimmunoglobulin (Jir) and monoclonal immunoglobulins in various solvent conditions were comparatively carried out using the steady state excitation method by altering temperatures from nearly 10 to 40 degrees C, and the rotational relaxation times (rho h) for these molecules were calculated according to the Perrin-Weber's equation using the values of polarization (P). The results indicated that the rho h value of DNS-Jir (170 nsec) was almost twice that obtained by myeloma protein (90 nsec) belonging to the same subclass with Jir, but was considerably shorter than that obtained by a soluble immune complex with a molecular weight equivalent to Jir dimer. These results suggested that the molecular structure of Jir protein was thermodynamically less-flexible than that of the myeloma proteins, and that the restricted intra-molecular flexibility might be responsible for the unusual property of cryoimmunoglobulin.

Animals↗
PubMed1999

A predictive thermodynamic model for the bioreduction of acetophenone to phenethyl alcohol using resting cells of Saccharomyces cerevisiae.

Equilibrium conversions were observed in the range of 60.2-76.0% with different initial compositions of reaction media for the bioreduction of acetophenone using resting cells of Saccharomyces cerevisiae in aqueous solutions at 30 degrees C. The reduction of acetophenone in the cells under anaerobic conditions is considered to be coupled with the oxidation of ethanol to acetate in the cytoplasm. A biphasic thermodynamic model is proposed which includes a nonuniform distribution of reagents across the cell membrane, a transmembrane pH gradient, ideal and nonideal solution models, and a basic reaction stoichiometry (ACP + (1/2) EtOH + (1/2)H2O <--> PEA + (1/2)Ac- + (1/2)H+). The intracellular activity coefficients were based on the Lewis-Randall rule for acetophenone, phenethyl alcohol, and H2O and Henry's law for ethanol, acetate anion, and H+. The overall standard Gibbs free energy was estimated to be -0.11 kcal/mol at a pH 7, 25 degrees C, and 1 atm. The intracellular thermodynamic activity coefficients of acetophenone and phenethyl alcohol were predicted to be 471.2 and 866.4, respectively, using the measured initial distribution coefficients and calculated extracellular activity coefficients. The model reflected a zero Gibbs free energy change at calculated conversions within 4% of the measured equilibrium conversions. The analysis verified the effect of the concentration ratio of the substrate acetophenone to the co-substrate ethanol on the conversion efficiency and suggested that the intracellular pH and the pH gradient across the cell transmembrane significantly affect the predicted equilibrium conversion. The intracellular pH of resting, viable cells of Bakers' yeast at the bioconversion conditions was determined experimentally to be 5.77.

Acetophenones↗