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PubMed2003

Allowance for thermodynamic non-ideality in the characterization of protein self-association by frontal exclusion chromatography: hemoglobin revisited.

This investigation re-examines theoretical aspects of the allowance for effects of thermodynamic non-ideality on the characterization of protein self-association by frontal exclusion chromatography, and thereby provides methods of analysis with greater thermodynamic rigor than those used previously. Their application is illustrated by reappraisal of published exclusion chromatography data for hemoglobin on the controlled-pore-glass matrix CPG-120. The equilibrium constant of 100/M that is obtained for dimerization of the alpha(2)beta(2) species by this means is also deduced from re-examination of published studies of concentrated hemoglobin solutions by osmotic pressure and sedimentation equilibrium methods.

Chromatography, Gel↗

PubMed2003

Fundamental equation of thermodynamics for protein-ligand binding.

For the internal energy and every thermodynamic potential that can be defined by a Legendre transform, there is a fundamental equation that contains all the thermodynamic information about a system. For a system involving the binding of molecular oxygen and hydrogen ions by a protein, fundamental equations are given for the Gibbs energy G, the transformed Gibbs energy G' at specified pH, and the further transformed Gibbs energy G" at specified pH and specified concentration of molecular oxygen. The Maxwell equations for these various Gibbs energies are important because they provide the connection with experimentally determined properties and increase our understanding of these properties. Measurements of the average number of oxygen molecules bound as a function of T, pH and concentration of molecular oxygen make it possible to calculate Delta(f)G"(o) of the reactant. Maxwell equations make it possible to calculate the average number of hydrogen ions bound, Delta(f)S"(o), Delta(f)H"(o) and their partial derivatives. These relations are illustrated with numerical calculations on a simple reaction system.

Algorithms↗

PubMed2003

Thermodynamics of denaturation of complexes of barnase and binase with barstar.

Differential scanning calorimetry was used to study the thermodynamics of denaturation of protein complexes for which the free energy stabilizing the complexes varied between -8 and -16 kcal/mol. The proteins studied were the ribonucleases barnase and binase, their inhibitor barstar and mutants thereof, and complexes between the two. The results are in good agreement with the model developed by Brandts and Lin for studying the thermodynamics of denaturation for tight complexes between two proteins which undergo two-state thermal unfolding transitions.

Bacterial Proteins↗

PubMed1997

Thermodynamics, molecules and the Gibbs conference.

Molecular concepts have been gradually incorporated into chemical thermodynamics. This is done by applying standard thermodynamics manipulations to systems which are restricted by the assumption of a specific molecular model or mechanism. Here we trace the development of this procedure and its applications from Avogadro's hypothesis to modern work on site-directed mutagenesis.

Models, Chemical↗

PubMed1998

A thermodynamic investigation of reactions catalyzed by tryptophan synthase.

Microcalorimetry and high-performance liquid chromatography have been used to conduct a thermodynamic investigation of the following reactions catalyzed by the tryptophan synthase alpha 2 beta 2 complex (EC 4.2.1.20) and its subunits: indole(aq) + L-serine(aq) = L-tryptophan(aq) + H2O(1); L-serine(aq) = pyruvate(aq) + ammonia(aq); indole(aq) + D-glyceraldehyde 3-phosphate(aq) = 1-(indol-3-yl)glycerol 3-phosphate(aq); L-serine(aq) + 1-(indol-3-yl)glycerol 3-phosphate(aq) = L-tryptophan(aq) + D-glyceraldehyde 3-phosphate(aq) + H2O(1). The calorimetric measurements led to standard molar enthalpy changes for all four of these reactions. Direct measurements yielded an apparent equilibrium constant for the third reaction; equilibrium constants for the remaining three reactions were obtained by using thermochemical cycle calculations. The results of the calorimetric and equilibrium measurements were analyzed in terms of a chemical equilibrium model that accounted for the multiplicity of the ionic states of the reactants and products. Thermodynamic quantities for chemical reference reactions involving specific ionic forms have been obtained. These quantities permit the calculation of the position of equilibrium of the above four reactions as a function of temperature, pH, and ionic strength. Values of the apparent equilibrium constants and standard transformed Gibbs free energy changes delta r G'(m) degree under approximately physiological conditions are given. Le Châtelier's principle provides an explanation as to why, in the metabolic pathway leading to the synthesis of L-tryptophan, the third reaction proceeds in the direction of formation of indole and D-glyceraldehyde 3-phosphate even though the apparent equilibrium constant greatly favors the formation of 1-(indol-3-yl)glycerol 3-phosphate.

Amino Acids↗

PubMed1999

A thermodynamic analysis of a family of small globular proteins: SH3 domains.

The stability and folding thermodynamics of two SH3-domains, belonging to Fyn and Abl proteins, have been studied by scanning calorimetry and urea-induced unfolding. They undergo an essentially two-state unfolding with parameters similar to those of the previously studied alpha-spectrin SH3 domain. The correlations between the thermodynamic parameters (heat capacity increment, delta Cp,U, the proportionality factor, m, and the Gibbs energy, delta Gw298) of unfolding and some integral structural parameters, such as polar and non-polar areas exposed upon domain denaturation, have been analyzed. The experimental data on delta Cp,U and the m-factor of the linear extrapolation model (LEM) obey the simple empirical correlations deduced elsewhere. The Gibbs energies calculated from the DSC data were compared with those found by fitting urea-unfolding curves to the LEM and the denaturant-binding model (DBM). The delta Gw298 values found with DBM correlate better with the DSC data, while those obtained with LEM are systematically smaller. The systematic difference between the parameters calculated with LEM and DBM are explained by an inherent imperfection of the LEM.

Amino Acid Sequence↗

PubMed1980

Thermodynamic properties of free and immobilized subtilopeptidase from Bacillus subtilis PR-70.

Thermodynamics of free and immobilized subtilopeptidase was studied over the temperature range from 30 degrees to 80 degrees C and from 30 degrees to 90 degrees C, respectively. The apparent optimum temperature of free enzyme was 50 degrees C and of the immobilized enzyme 60 degrees C. The heat of the reaction (delta E), accompanied by the process, was calculated from the slope of the Arrhenius equation to be 56 770 cal/mole for free enzyme and 36 640 cal/mole for immobilized enzyme. The standard free energy change (delta G) and the standard entropy change (delta S) were found to be + 241 cal/mole and + 186.6 cal/mole/degree at 30 degrees C for free enzyme and + 142 cal/mole and 120.5 cal/mole/degree at 30 degrees C for immobilized enzyme. The values of these thermodynamic quantities at other temperatures were also summarized. Studying the reaction order of heat inactivation showed that free and immobilized enzyme followed a first order reaction. The energy of inactivation was found to be 18 900 cal/mole and 24 400 cal/mole for free and immobilized enzyme, respectively.

Bacillus subtilis↗

PubMed1976

[Quantitative and thermodynamic study of weak A erythrocyte phenotypes].

The analysis of more than 140 "weak A" samples: A3, Ax, Aend, Am, Ay and Ael, support the classical distinction between each subgroup which has been established on serological and genetical data. Accordingly, a valuable classification of these rare phenotypes must take into account, (i) the mode of inheritance, (ii) the agglutination pattern of the RBC by anti-A reagents, (iii) the presence or absence of soluble A substances in the saliva of secretors. The question is then open to know if such related erythrocytic antigens, whose specificity appears to be very similar, could be described on a quantitative basis or on qualitative structural variations. Evidence for quantitative differences was first demonstrated by a gradual decrease in the standard agglutinability of "weak A" RBC with human anti-A (B) sera, from A3 red cells (63 +/- 10%) to Ax (33 +/- 10%), Aend (10 +/- 5%) then Am, Ay and Ael (0%), and secondly by direct measurement of A antigen site densities, the mean values being respectively 35.10(3) A sites/RBC (A3); 4.8 10(3) (Ax); 3.5 10(3) (Aend) and 0.7 10(3) (Am, Ael). Further investigation on A3, Ax and Aend RBC agglutinability lead also to the demonstration of a large heterogeneity in the A antigenic content of red cells inside one individual sample. The most striking result was obtained with Aend phenotypes which appeared like A + O transmitted mosaicisms. However, heterogeneity was also observed, but to a lesser extent, among A3 and Ax RBC. The significance of this heterogeneity is discussed and used to explained the typical picture of agglutinability commonly observed with such red cells and anti-A antibodies. Qualitative difference were also studied by estimation of equilibrium constants (Ko) and thermodynamic parameters (delta Fo, delta Ho and delta So) associated with the binding of rabbit 125I-IgG anti-A molecules onto A RBC determinants. Only small variations of thermodynamic parameters were observed between each subgroup, but the high Ko values (greater than 10(8)M-1) measured, strongly suggest that "weak A" RBC determinants would process a common antigenic structure of the type: alpha-GalNAc (1 leads to 3) [alphaLFuc (1 leads to 2) beta Gal. However, the small differences of reactivity observed from one sample to an other could be related to slight variations in tridimensional configurations of oligosaccharides chains bearing the A specificity, associated with their variable antigenic content.

ABO Blood-Group System↗

PubMed1978

[Thermodynamic study of the allohemagglutinins of the ABO system].

Many thermodynamic assays on natural allohemagglutinins ABO were undertaken by different authors. Our experiment concerns anti-A and anti-B. The allohemagglutinins level was determined by the Probit Method, using bromelin red blood cells and methyl cellulose, with an autoanalyser. This thermodynamic assay was carried out in almost the same conditions as those used by Wurmser. The data reveal an intraphenotypic (anti-A) or intra genotypic heterogeneity (anti-B) in the repartition of affinities. Average enthalpy changes are, in this methodology, interphenotypic (anti-A) and intergenotypic (anti-B) features. For Wurmser every genotype has a typical feature: so this author concludes a natural agglutinin homogeneity. Heterogeneity showed by our experimentation seems bound to the specific IgM and IgG repartition of each serum. Specific anti-A or anti-B IgM are more exothermic than specific IgG. The apparent disagreement must be interpreted owing to the fact that in N4 Wurmser's method, the only agglutinins determined are specific IgM.

ABO Blood-Group System↗

PubMed2000

Thermodynamic analysis of compact formation; compaction, unloading, and ejection. I. Design and development of a compaction calorimeter and mechanical and thermal energy determinations of powder compaction.

The aim of this investigation was to determine and evaluate the thermodynamic properties, i.e. heat, work, and internal energy change, of the compaction process by developing a 'Compaction Calorimeter'. Compaction of common excipients and acetaminophen was performed by a double-ended, constant-strain tableting waveform utilizing an instrumented 'Compaction Simulator.' A constant-strain waveform provides a specific quantity of applied compaction work. A calorimeter, built around the dies, used a metal oxide thermistor to measure the temperature of the system. A resolution of 0.0001 degrees C with a sampling time of 5 s was used to monitor the temperature. An aluminum die within a plastic insulating die, in conjunction with fiberglass punches, comprised the calorimeter. Mechanical (work) and thermal (heat) calibrations of the elastic punch deformation were performed. An energy correction method was outlined to account for system heat effects and mechanical work of the punches. Compaction simulator transducers measured upper and lower punch forces and displacements. Measurements of the effective heat capacity of the samples were performed utilizing an electrical resistance heater. Specific heat capacities of the samples were determined by differential scanning calorimetry. The calibration techniques were utilized to determine heat, work, and the change in internal energies of powder compaction. Future publications will address the thermodynamic evaluation of the tablet sub-processes of unloading and ejection.

Calibration↗

PubMed2002

Thermodynamics in [Mn(II)-antibiotics-bacitracin] mixed system: a polarographic approach.

Polarographic technique was used to determine the kinetic parameters, thermodynamic parameters and stability constants (log(beta)) of Mn(II) complexes with neomycin, chlortetracycline, oxytetracycline, tetracycline, penicillin V and penicillin G as primary ligands and bacitracin as the secondary ligand, at pH 7.3+/-0.01 and an ionic strength mu=1.0 M (NaClO(4)) at 25 degrees C. The study was also carried out at 35 degrees C to determine the stability constants and thermodynamic parameters viz. enthalpy change (DeltaH), entropy change (DeltaS) and free energy change (DeltaG) of complexes.

Anti-Bacterial Agents↗

PubMed2002

Thermodynamic assessment in heavy metal migration at El-Akader landfill site, North Jordan.

Thermodynamic analysis of subsoil pore water indicates that Fe, Cu, Zn, and Pb exist as a metal hydroxy complex of the forms [Me OH] + and [Me(OH2)]o, although a complex of [PbCl]+ is also significant, but not predominant. The analysis also demonstrates that the dissolved transition metal concentration of the subsoil pore waters are controlled at carbonate minerals saturation levels, whereas Fe concentration in leachate solutions associated with waters are controlled at FeS2 saturation levels. Thermodynamic calculations and Eh-pH diagrams suggest that Fe(OH)2, Zn(OH)2 and Pb(OH)2 are not stable phases in the solids of the subsoil.

Environmental Monitoring↗

PubMed1996

Thermodynamics of base pairing.

The study of the thermodynamics of base pairing is a rapidly expanding field due to its importance for taking advantage of opportunities presented by the growing database of nucleic acid sequences. Both natural and unnatural nucleic acids are being studied. The determination of nearest-neighbor parameters from optical melting data for RNA-DNA and DNA-DNA duplexes with Watson-Crick base pairs is particularly noteworthy. The foundations are also being laid for a theoretical understanding of these thermodynamics.

Base Composition↗

PubMedDate not supplied

A thermodynamic model describing the nature of the crista junction: a structural motif in the mitochondrion.

The use of electron tomography has allowed the three-dimensional membrane topography of the mitochondrion to be better understood. The most striking feature of this topology is the crista junction, a structure that may serve to divide functionally the inner membrane and intermembrane spaces. In situ these junctions seem to have a preferred size and shape independent of the source of the mitochondrion with few exceptions. When mitochondria are isolated and have a condensed matrix the crista junctions enlarge and become nondiscrete. Upon permeation of the inner membrane and subsequent swelling of the matrix space, the uniform circular nature of the crista junction reappears. We examine the distribution of shapes and sizes of crista junctions and suggest a thermodynamic model that explains the distribution based on current theories of bilayer membrane shapes. The theory of spontaneous curvature shows the circular junction to be a thermodynamically stable structure whose size and shape is influenced by the relative volume of the matrix. We conclude that the crista junction exists predominantly as a circular junction, with other shapes as exceptions made possible by specific characteristics of the lipid bilayer.

Animals↗

PubMed1996

Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions.

Biomolecular interactions can be defined by combining thermodynamic data on the energetic properties of the interaction with high-resolution structural data. The development of high sensitivity isothermal titration calorimetric equipment provides a dramatic advance in the gathering of thermodynamic data, and the interactions between biological macromolecules can now be described with unprecedented accuracy.

Calorimetry↗

PubMed2002

Thermodynamic analysis of human serum albumin interactions with glucose: insights into the diabetic range of glucose concentration.

The interaction of proteins with glucose results in their non-enzymatic glycation and influences their structural and functional properties. Human serum albumin (HSA) interacts with glucose forming glycated HSA. However, the glucose binding sites and the thermodynamic characteristics of the glycated HSA require further delineation. Here, the binding properties of HSA and glucose were studied utilizing fluorescent techniques. HSA was incubated with glucose in the 0-300mM range at 27 or 37 degrees C. The interaction of HSA with glucose showed two sets of binding sites. The first set consists of two sites with positive cooperativity and the second set consists of nine identical non-cooperative sites. The percentage of glycated HSA (gly%) and the moles of glucose bound to moles of HSA (r) were utilized to obtain binding constants and thermodynamic parameters based on the Wyman binding potential. The enthalpy of binding, obtained by van't Hoff relation, presented exothermicity up to 7mM glucose (126mg/dl, normal range) and endothermic propensity at higher glucose concentrations (>7mM, diabetic range). The start of endothermic propensity was consistent with the diabetic range of glucose concentration and indicates unfolding of HSA. The Gibbs free energy and entropy of binding further supports the unfolding of HSA. Therefore, glucose interacts with multiple sites on HSA affecting its biochemical and biophysical properties. This may interfere with HSA normal function contributing to diabetic complications.

Binding Sites↗

PubMed1996

An analysis of large rRNA sequences folded by a thermodynamic method.

BACKGROUND: The secondary structure of RNA can be predicted by the thermodynamics-based method of Zuker and Turner. The accuracy of the method's secondary structure predictions for rRNA can be assessed by using as reference the currently available rRNA secondary structure models that have been derived from comparative analysis of rRNA sequence alignments. RESULTS: We folded 72 23S rRNA sequences with the Zuker-Turner method and scored the resulting secondary structure predictions against the comparative model. Empirically, trends in the score were observed as a function of the phylogenetic memberships of the sequences and as a function of the base pairs secondary structural contexts. Further, three parameters were found that (anti-)correlate with the score. CONCLUSIONS: Three semiquantitative predictors of score were found: % of noncanonical base pairs, % of hairpin loops that were stable tetraloops, and sequence %G + C. The folding of rRNA is a tractable problem and thermodynamics-based folding algorithms, in particular, are useful in the study of this folding problem even for large RNA molecules (e.g. 16S and 23S rRNA).

Animals↗

PubMed1997

Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold.

BACKGROUND: The problem of how a protein chain can find its most stable structure without exhaustive sorting of all its possible conformations is known as the 'Levinthal paradox'. The purpose of this paper is to elucidate this problem and to estimate the rate of folding to the most stable structure near the point of thermodynamic equilibrium between this structure and the coil. RESULTS: Folding is rapid when it occurs in the vicinity of a thermodynamic 'all-or-none' transition from the coil to the lowest-energy fold: here the misfolded and semifolded states cannot 'trap' the folding chain since, even taken together, all these states are less stable than both the initial coil and the final stable fold of the chain. A stable globular structure can be rapidly achieved via a 'nucleation-and-growth' folding pathway that provides a continuous entropy-by-energy compensation along the folding pathway and thus provides a low free energy of the transition state. CONCLUSIONS: At the point of transition of the coil to the lowest-energy fold, an N-residue chain folds normally in approximately exp(N2/3) ns. Therefore, a 100-residue chain finds its most stable fold within minutes rather than in 10(100) ps = 10(80) years, according to the famous paradoxical estimate of Levinthal.

Aprotinin↗