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PubMed2001

Prediction of metal precipitates in tannery sludge leachate based on thermodynamic calculations.

Thermodynamic calculations were performed in order to predict the formation of metal precipitates during the tannery sludge leaching. Gibbs free energy deltaG=RTln(Qc/Kc) of precipitation reaction was used to examine the formation of precipitates during the leaching process. The values of activity equilibrium constant (Ka) of various precipitation reactions were adopted from the literature. The Ka values were corrected to obtain the corresponding values of concentration product (Qc) and concentration equilibrium constant (Kc) using the activity coefficients (gamma) of the ions. The activity coefficients (gamma) of the ions was calculated using Davies equation Lngammai=-1.172Zi2((I0.5/(1+I0.5))-0.3I) (aqueous solution, 25 degrees C, 1 atm, I>0.3 mol x l(-1)). The values of ionic strength (I) at different sludge solids concentration and leaching pH were obtained by measuring the concentration of all ionic species in the leachate. The thermodynamic calculations indicated that the possible metal precipitates formed during the leaching process were (am)Cr(OH)3, (am)CrPO4, (am)Fe(OH)3, alpha-FeOOH(goethite), FePO4.2H2O, (am)AIPO4-2H2O, CaSO4.2H2O(gypsum). The solubility of these precipitates was found to decrease with the increase in the ionic strength (or sludge solids concentration). The results of computations were supported by the experimental observations.

Chemical Precipitation↗
PubMed1996

Thermal unfolding of beta-lactoglobulin, alpha-lactalbumin, and bovine serum albumin. A thermodynamic approach.

Heat-treatment is one of the most commonly used processes in food preparation technology. An understanding of the thermodynamics of protein stability and of conformational changes of proteins, acquired through the measurement of the denaturation temperature, is therefore of particular importance. This paper attempts to shed light on the interpretation of recent calorimetric data on the thermal denaturation of bovine beta-lactoglobulin, alpha-lactalbumin, and bovine serum albumin by showing that thermodynamic parameters of heat-induced unfolding, measured by differential scanning calorimetry, are closely related to the prevailing chemical conditions such as pH, concentration of ions, protein purity, and protein concentration.

Hot Temperature↗
PubMed2006

R104H may suppress transthyretin amyloidogenesis by thermodynamic stabilization, but not by the kinetic mechanism characterizing T119 interallelic trans-suppression.

The tetrameric protein transthyretin (TTR) forms amyloid fibrils upon dissociation and subsequent monomer misfolding, enabling misassembly. Remarkably, the aggregation of one of over 100 destabilized TTR variants leads to familial amyloid disease. It is known that trans-suppression mediated by the incorporation of T119M subunits into tetramers otherwise composed of the most common familial variant V30M, ameliorates disease by substantially slowing the rate of tetramer dissociation, a mechanism referred to as kinetic stabilization of the native state. R104H TTR has been reported to be non-pathogenic, and recently, this variant has been invoked as a trans-suppressor of amyloid fibril formation. Here, we demonstrate that the trans-suppression mechanism of R104H does not involve kinetic stabilization of the tetrameric structure, instead its modest trans-suppression most likely results from the thermodynamic stabilization of the tetrameric TTR structure. Thermodynamic stabilization increases the fraction of tetramer at the expense of the misfolding competent monomer decreasing the ability of TTR to aggregate into amyloid fibrils. As a consequence of this stabilization mechanism, R104H may be capable of protecting patients with modestly destabilizing mutations against amyloidosis by slightly lowering the overall population of monomeric protein that can misfold and form amyloid.

Amino Acid Substitution↗
PubMed2004

A novel thermodynamic relationship based on Kramers Theory for studying enzyme kinetics under high viscosity.

In most studies of enzyme kinetics it has been found sufficient to use the classical Transition State Theory (TST) of Eyring and others. This theory was based on the solvent being an ideal dilute substance treated as a heat bath. However, enzymes found in organisms adapted to very low (psychrophiles) and very high (thermophiles) temperatures are also subjected to variable solute concentrations and viscosities. Therefore, the TST may not always be applicable to enzyme reactions carried out in various solvents with viscosities ranging from moderate to very high. There have been numerous advances in the theory of chemical reactions in realistic non-ideal solvents such as Kramers Theory. In this paper we wish to propose a modified thermodynamic equation, which have contributions from kcat, Km and the viscosity of the medium in which the enzyme reaction is occurring. These could be very useful for determining the thermodynamics of enzymes catalyzing reactions at temperature extremes in the presence of substrate solutions of different compositions and viscosities.

Catalysis↗
PubMed2001

Thermodynamic analysis of water interaction with excipient films.

The interaction of water with excipients that can form moisture-protective coatings was examined earlier by the application of theoretical models. In this study, thermodynamic analysis of water-excipient film systems has been performed to elucidate the mechanistic details of the water-excipient interaction. Partial molal free energies, enthalpies, and entropies were computed for films of lipidic (glyceryl behenate, GB) and polymeric (polyvinyl alcohol, PVA) coating excipients using the temperature dependence of the adsorption process. The analysis of free energy changes showed that excipient films were not inert participants in the water sorption process. The isoteric heats of adsorption confirmed that water formed hydrogen bonds with the excipient films and allowed estimation of number of hydrogen bonds per water molecule. This result also provided the reason for hysteresis during drying. A comparative evaluation of the application of theoretical models and thermodynamic analysis revealed that results obtained from both approaches were not always complementary. An exponential relationship was found to exist between sorption microrate constants and water activity for the PVA films at all temperatures.

Adsorption↗
PubMed2002

Daunomycin binding to deoxypolynucleotides with alternating sequences: complete thermodynamic profiles of heterogeneous binding sites.

Complete thermodynamic binding profiles for the interaction of the anticancer drug, daunomycin with natural DNA and synthetic deoxypolynucleotides were described. Fluorescence titration method was used to estimate the equilibrium binding constants. Binding isotherms were found to be surprisingly complex in some cases, presumably because there were heterogeneous sites even in simple deoxypolynucleotides of repeating sequence. Some polynucleotides consisting of alternating sequence contain at least two different binding sites for daunomycin. The binding affinity of the primary binding sites of alternating and non-alternating sequences was found to differ by two orders of magnitude. An isothermal microtitration calorimeter was used to directly measure the binding enthalpy at 25 degrees C with a high sensitivity. The binding enthalpy of poly[d(A-T)] was found to be -5.5 Kcal/mol, which was much lower than any other polynucleotides, while the binding constant of the high affinity sites, was similar. In this report, the complete thermodynamic profiles of daunomycin binding to deoxypolynucleotides were reliably shown for the first time.

Antibiotics, Antineoplastic↗
PubMed2001

Interaction of [D-Trp6, Des-Gly10] LHRH ethylamide and hydroxy propyl beta-cyclodextrin (HPbetaCD): thermodynamics of interaction and protection from degradation by alpha-chymotrypsin.

PURPOSE: The purpose of this study is to investigate the mechanisms and thermodynamics of the interaction between hydroxypropyl beta-cyclodextrin (HPdetaCD) and [D-Trp6, des-Gly10] LHRH ethylamide (deslorelin), a peptide drug. METHODS: We used UV and fluorescence spectroscopy to study the interaction of HPbetaCD and deslorelin. Circular dichroism was used to study the conformational changes induced in deslorelin upon interaction with HP beta CD. The thermodynamics of the interaction of deslorelin and HPbetaCD was studied using isothermal titration calorimetry (ITC). We also determined the effect of HPbetaCD on the degradation of deslorelin by alpha-chymotrypsin. RESULTS: UV and fluorescence spectroscopy indicated that HPbetaD induced a change in polarity of the environment surrounding the chromophores of deslorelin. Wavelength selective fluorescence indicated an increase in the fluorescence polarization of deslorelin with an increase in excitation wavelength in the presence of HPbetaCD suggesting that tryptophan is present in a media of reduced mobility. Circular dichroism studies indicated that HPbetaCD stabilizes the conformation of deslorelin. In addition, ITC indicated an exothermic reaction between deslorelin and HPbetaCD with a low enthalpy of binding of approximately -600 cal/mol and a binding affinity of approximately -1.25 x 10(2) M-1. Finally, the rate of degradation of deslorelin by alpha-chymotrypsin was decreased by 33% in the presence of HPbetaCD. CONCLUSIONS: These results indicate that there is an interaction between HPbetaCD and deslorelin, which involves the inclusion of aromatic amino acids of deslorelin into the hydrophobic cavity of the cyclodextrin. This inclusion, providing steric hindrance, may be one of the mechanisms by which HPbetaCD reduces enzymatic hydrolysis of deslorelin.

2-Hydroxypropyl-beta-cyclodextrin↗
PubMed2006

Thermodynamics of CFTR channel gating: a spreading conformational change initiates an irreversible gating cycle.

CFTR is the only ABC (ATP-binding cassette) ATPase known to be an ion channel. Studies of CFTR channel function, feasible with single-molecule resolution, therefore provide a unique glimpse of ABC transporter mechanism. CFTR channel opening and closing (after regulatory-domain phosphorylation) follows an irreversible cycle, driven by ATP binding/hydrolysis at the nucleotide-binding domains (NBD1, NBD2). Recent work suggests that formation of an NBD1/NBD2 dimer drives channel opening, and disruption of the dimer after ATP hydrolysis drives closure, but how NBD events are translated into gate movements is unclear. To elucidate conformational properties of channels on their way to opening or closing, we performed non-equilibrium thermodynamic analysis. Human CFTR channel currents were recorded at temperatures from 15 to 35 degrees C in inside-out patches excised from Xenopus oocytes. Activation enthalpies(DeltaH(double dagger)) were determined from Eyring plots. DeltaH(double dagger) was 117 +/- 6 and 69 +/- 4 kJ/mol, respectively, for opening and closure of partially phosphorylated, and 96 +/- 6 and 73 +/- 5 kJ/mol for opening and closure of highly phosphorylated wild-type (WT) channels. DeltaH(double dagger) for reversal of the channel opening step, estimated from closure of ATP hydrolysis-deficient NBD2 mutant K1250R and K1250A channels, and from unlocking of WT channels locked open with ATP+AMPPNP, was 43 +/- 2, 39 +/- 4, and 37 +/- 6 kJ/mol, respectively. Calculated upper estimates of activation free energies yielded minimum estimates of activation entropies (DeltaS(double dagger)), allowing reconstruction of the thermodynamic profile of gating, which was qualitatively similar for partially and highly phosphorylated CFTR. DeltaS(double dagger) appears large for opening but small for normal closure. The large DeltaH(double dagger) and DeltaS(double dagger) (TDeltaS(double dagger) >/= 41 kJ/mol) for opening suggest that the transition state is a strained channel molecule in which the NBDs have already dimerized, while the pore is still closed. The small DeltaS(double dagger) for normal closure is appropriate for cleavage of a single bond (ATP's beta-gamma phosphate bond), and suggests that this transition state does not require large-scale protein motion and hence precedes rehydration (disruption) of the dimer interface.

ATP-Binding Cassette Transporters↗
PubMed1980

Thermodynamic and kinetic studies of the gating behavior of a K+-selective channel from the sarcoplasmic reticulum membrane.

A voltage-dependent, K+-selective ionic channel from sarcoplasmic reticulum of rabbit skeletal muscle has been studied in a planar phospholipid bilayer membrane. The purpose [corrected] of this work is to study the mechanism by which the channel undergoes transitions between its conducting and nonconducting states. Thermodynamic studies show that the "open" and "closed" states of the channel exist in a voltage-dependent equilibrium, and that the channel displays only a single open state; the channel conductance is 120 pmho in 0.1 M K+. The channel's gating process follows single exponential kinetics at all voltages tested, and the individual opening and closing rate constants are exponentially dependent on voltage. The individual rate constants may also be determined from a stochastic analysis of channel fluctuations among multiple conductance levels. Neither the thermodynamic nor the kinetic parameters of gating depend on the absolute concentration of channels in the bilayer. The results are taken as evidence that the channel gates by an unusually simple two-state conformational mechanism in which the equivalent of 1.1 net charges are moved across the membrane during the formation of the open channel.

Animals↗
PubMed2005

Thermodynamics and information in aging: why aging is not a mystery and how we will be able to make rational interventions.

Currently, the aging research field lacks consensus in its focus and methodology. Foundational principles, such as the evolutionary origins and physiological definition of aging, remain controversial. The aim of this paper is to resolve these issues. By applying the concepts of thermodynamics and information in an evolutionary context, the aging phenotype can be derived from first principles. Life uses information storage to maintain its distance from thermodynamic equilibrium. Since it is impossible to make any process 100% efficient, a selective force (i.e., natural selection) is needed to maintain the information's viability. Natural selection operates upon generations, and for reasons discussed subsequently, the somatic body cannot implement an analogous selective process. The aging phenotype we see can be derived from this model along with a number of insights that will enhance our ability to make intelligent and rational interventions.

Aging↗
PubMed2001

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

MOTIVATION: Protein-nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein-nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have developed a Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT). RESULTS: We have collected experimentally observed binding data from the literature. ProNIT contains several important thermodynamic data for protein-nucleic acid binding, such as dissociation constant (K(d)), association constant (K(a)), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), heat capacity change (DeltaC(p)), experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data are integrated into a relational database system together with structural and functional information to provide flexible searching facilities by using combinations of various terms and parameters. A www interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. AVAILABILITY: ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.

Amino Acid Sequence↗
PubMed2004

Thermodynamic binding studies of bivalent oligosaccharides to galectin-1, galectin-3, and the carbohydrate recognition domain of galectin-3.

Galectins are a growing family of animal lectins with common consensus sequences that bind beta-Gal and LacNAc residues. There are at present 14 members of the galectin family; however, certain galectins possess different structures as well as biological properties. Galectin-1 is a dimer of two homologous carbohydrate recognition domains (CRDs) and possesses apoptotic and proinvasive activities. Galectin-3 consists of a C-terminal CRD and an N-terminal nonlectin domain implicated in the oligomerization of the protein and is often associated with antiapoptotic activity. Because many cellular oligosaccharide receptors are multivalent, it is important to characterize the interactions of multivalent carbohydrates with galectins-1 and -3. In the present study, binding of bovine heart galectin-1 and recombinant murine galectin-3 to a series of synthetic analogs containing two LacNAc residues separated by a varying number of methylene groups, as well as biantennary analogs possessing two LacNAc residues, were examined using isothermal titration microcalorimetry (ITC) and hemagglutination inhibition measurements. The thermodynamics of binding of the multivalent carbohydrates to the C-terminal CRD domain of galectin-3 was also investigated. ITC results showed that each bivalent analog bound by both LacNAc residues to the two galectins. However, galectin-1 shows a lack of enhanced affinity for the bivalent straight chain and branched chain analogs, whereas galectin-3 shows enhanced affinity for only lacto-N-hexaose, a naturally occurring branched chain carbohydrate. The CRD domain of galectin-3 was shown to possess similar thermodynamic binding properties as the intact molecule. The results of this study have important implications for the design of carbohydrate inhibitors of the two galectins.

Binding Sites↗
PubMed1982

Correlation of thermodynamic and genetic properties in the Tn10 encoded TET gene control region.

The thermal stability of the Tn10 encoded tetracycline resistance (TET) gene control region is investigated by melting studies using purified DNA restriction fragments containing various amounts of flanking sequences. In order to study the thermodynamic properties of this control region under conditions, where enough flanking DNA is present to mimic the situation in the chromosome, the five step melting process of a 1450-bp DNA fragment is analyzed. Because most of the sequence of this DNA is not known, the assignment of the melting transitions to segments of the DNA is done by an experimental method. This employs the preparation of subfragments from the 1450-bp DNA and comparison of their denaturation profiles with the one of the intact sequence. This approach results in the complete assignment of the five denaturation steps. Rather than from the ends, the unwinding starts from the TET gene control region in the middle of the 1450-bp sequence. A clear correlation between the thermodynamic and genetic properties of this DNA is observed. The regulatory sequence forms a small cooperative unit with the lowest stability in the entire fragment. The thermal denaturation of the TET repressor. TET operator complex reveals, that the TET repressor specifically recognizes the double stranded TET operator DNA and stabilizes this structure by 2.4 degrees C. This results is also discussed as an example of the possible action of denaturing or stabilizing proteins on this genetic control region.

DNA Restriction Enzymes↗
PubMed1985

Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T).

Thermodynamic parameters for double strand formation have been measured for the sixteen double helices of the sequence dCA3XA3G.dCT3YT3G, with each of the bases A, C, G and T at the positions labelled X and Y. The results are analyzed in terms of nearest-neighbors and are compared with thermodynamic parameters for RNA secondary structure. At room temperature the sequence (Formula: see text) is more stable than (Formula: see text) and is similar in stability to (Formula: see text) and (Formula: see text) are least stable. At higher temperatures the sequences containing a G.C base pair become more stable than those containing only A.T. All molecules containing mismatches are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. At room temperature the most stable mismatches are those containing guanine (G.T, G.G, G.A); the least stable contain cytosine (C.A, C.C). At higher temperatures pyrimidine-pyrimidine mismatches become the least stable.

Base Composition↗
PubMed1989

Thermodynamics of the interactions of m-AMSA and o-AMSA with nucleic acids: influence of ionic strength and DNA base composition.

The equilibrium binding of the antitumor agent m-AMSA and its biologically inactive analog o-AMSA to native and synthetic DNAs are compared over a wide range of ionic strengths and temperatures. Although o-AMSA binds DNA with a higher affinity than m-AMSA it is not effective as an antitumor agent. Both m-AMSA and o-AMSA bind DNA in an intercalative manner. Indepth investigations into the thermodynamic parameters of these interactions reveal the interaction of m-AMSA with DNA to be an enthalpy driven process. In contrast, the structurally similar but biologically inactive o-AMSA binds DNA through an entropy driven process. The differences in thermodynamic mechanisms of binding between the two isomers reveal that the electronic and/or steric factors resulting from the position of the methoxy substituent group on the anilino ring directs the DNA binding properties of these compounds and ultimately the biological effectiveness as an antitumor agent.

Amsacrine↗
PubMed1991

Effect of 5-methylcytosine on the stability of triple-stranded DNA--a thermodynamic study.

We have previously shown that the pyrimidine oligonucleotide 5'CTTCCTCCTCT (Y11) recognizes the double-helical stem of hairpin 5'GAAGGAGGAGA-T4-TCTCCTCCTTC (h26) by triple-helix formation (1). In this paper, we report the effect on triplex formation of substituting the cytosine residues of Y11 with 5-methylcytosines (5meY11). In addition, we have studied the thermodynamics of the interaction between h26 and 5meY11. The results can be summarised as follows: (i) gel electrophoresis shows that at T = 5 degrees C and pH 5, both Y11 and 5meY11 form DNA triple helices with h26, whereas at pH 6.8 only the methylated strand binds to h26; (ii) pH-stability curves of the DNA triplexes formed from h26 + Y11 and h26 + 5meY11 show that Y11 and 5meY11 are semi-protonated at pH 5.7 and 6.7, respectively. Thus, it is concluded that cytosine methylation expands the pH range compatible with triplex formation by one pH unit; (iii) as the unmethylated triplex (h26:Y11), the methylated one (h26:5meY11) denatures in a biphasic manner, in which the low temperature transition results from the dissociation of 5meY11 from h26. The Tm of the triplex to h26 plus 5meY11 transition is strongly enhanced (about 10 degrees C) by cytosine methylation. A van 't Hoff analysis of denaturation curves is presented; (iv) DSC experiments show that triplex formation between 5meY11 and h26 is characterized by delta H = -237 +/- 25 kJ/mol and delta S = -758 +/- 75 J/Kmol, corresponding to an average delta H of -21 kJ/mol and delta S of -69 J/Kmol per Hoogsteen base pair; (v) the thermodynamic analysis indicates that the extra stability imparted to the triplex by methylcytosine is entropic in origin.

5-Methylcytosine↗
PubMed1997

Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2.

The thermodynamic stability of nine dodecamers (four DNA and five RNA) of the same base composition has been compared by UV-melting. TheDeltaG of stabilisation were in the order: r(GACUGAUCAGUC)2>r(CGCAAATTTGCG)2 approximately r(CGCAUAUAUGCG)2>d(CGCAAATTTGCG)2 approximately r(CGCAAAUUUGCG)2>d(CGCATATATGCG)2 approximately d(GACTGATCAGTC)2>r(CGCUUUAAAGCG)2 approximately d(CGCTTTAAAGCG)2. Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but d(AAATTT) is stabilising, which has been attributed to the formation of a special B'structure involving large propeller twists of the A-T base pairs. The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2has been determined using NMR and restrained molecular dynamics calculations to assess the conformational reasons for its stability in comparison with d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of 0.89+/-0.29 A. The nucleotide conformations are typical of the A family of structures. However, although the helix axis displacement is approximately 4.6 A into the major groove, the rise (3.0 A) and base inclination ( approximately 6 degrees ) are different from standard A form RNA. The extensive base-stacking found in the AAATTT tract of the DNA homologue that is largely responsible for the higher thermodynamic stability of the DNA duplex is reduced in the RNA structure, which may account for its low relative stability.

Base Composition↗
PubMed1997

The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick.

'Stacking hybridization reactions' wherein two or more short DNA oligomers hybridize in a contiguous tandem orientation onto a longer complementary DNA single strand have been employed to enhance a variety of analytical oligonucleotide hybridization schemes. If the short oligomers anneal in perfect head-to-tail register the resulting duplex contains a nick at every boundary between hybridized oligomers. Alternatively, if the short oligomers do not hybridize precisely in register, i.e. single strand regions on the longer strand are left unbound, gaps are formed between regions where short oligomers bind. The resulting gapped DNA duplexes are considerably less stable than their nicked duplex analogs. Formation of base pair stacking interactions between neighboring oligomers at the nicks that do not occur in gapped duplexes has been proposed as the source of the observed added stability. However, quantitative evidence supporting this hypothesis for DNA has not been reported. Until now, a direct comparison of the thermodynamics of DNA nicks versus DNA gaps has not been performed. In this communication we report such a comparison. Analysis of optical melting experiments in a well defined molecular context enabled quantitative evaluations of the relative thermodynamic difference between nicked and gapped DNA duplexes. Results of the analysis reveal that a nick may be energetically favored over a gap by at least 1.4 kcal/mol and perhaps as much as 2.4 kcal/mol. The presence of a 5'phosphate at a nick or gap fails to significantly affect their stabilities.

DNA↗