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At least 487 records · Page 27Linked to original sources
PubMed2003

Thermodynamic analysis of the increased stability of major histocompatibility complex class II molecule I-Ek complexed with an antigenic peptide at an acidic pH.

The differential scanning calorimetry analysis of the murine major histocompatibility complex class II molecule, I-E(k), in complex with an antigenic peptide derived from mouse hemoglobin, showed that the thermal stability at the mildly acidic pH is higher than that at the neutral pH. Although the thermal unfolding of I-E(k)-hemoglobin was irreversible, we extracted the equilibrium thermodynamic parameters from the kinetically controlled heat capacity curves. Both the denaturation temperatures and the enthalpy changes were almost independent of the heating rate over 1 degrees C per min. The linear relation between the denaturation temperature and the calorimetric enthalpy change provided the heat capacity changes, which are classified into one for the mildly acidic pH region and another for the neutral pH region. The equilibrium thermodynamic parameters showed that the increased stability at the mildly acidic pH is because of the entropic effect. These thermodynamic data provided new insight into the current structural model of a transition to an open conformation at the mildly acidic pH, which is critical for the peptide exchange function of major histocompatibility complex class II in the endosome.

Acids↗
PubMed2003

Atypical effect of salts on the thermodynamic stability of human prion protein.

Prion diseases are associated with the conversion of cellular prion protein, PrPC, into a misfolded oligomeric form, PrPSc. Previous studies indicate that salts promote conformational conversion of the recombinant prion protein into a PrPSc-like form. To gain insight into the mechanism of this effect, here we have studied the influence of a number of salts (sodium sulfate, sodium fluoride, sodium acetate, and sodium chloride) on the thermodynamic stability of the recombinant human prion protein. Chemical unfolding studies in urea show that at low concentrations (below approximately 50 mm), all salts tested significantly reduced the thermodynamic stability of the protein. This highly unusual response to salts was observed for both the full-length prion protein as well as the N-truncated fragments huPrP90-231 and huPrP122-231. At higher salt concentrations, the destabilizing effect was gradually reversed, and salts behaved according to their ranking in the Hofmeister series. The present data indicate that electrostatic interactions play an unusually important role in the stability of the prion protein. The abnormal effect of salts is likely because of the ion-induced destabilization of salt bridges (Asp144-Arg148 and/or Asp147-Arg151) in the extremely hydrophilic helix 1. Contrary to previous suggestions, this effect is not due to the interaction of ions with the glycine-rich flexible N-terminal region of the prion protein. The results of this study suggest that ionic species present in the cellular environment may control the PrPC to PrPSc conversion by modulating the thermodynamic stability of the native PrPC isoform.

Base Sequence↗
PubMed2003

Thermodynamic description of the effect of the mutation Y49F on human glutathione transferase P1-1 in binding with glutathione and the inhibitor S-hexylglutathione.

The thermodynamics of binding of both the substrate glutathione (GSH) and the competitive inhibitor S-hexylglutathione to the mutant Y49F of human glutathione S-transferase (hGST P1-1), a key residue at the dimer interface, has been investigated by isothermal titration calorimetry and fluorescence spectroscopy. Calorimetric measurements indicated that the binding of these ligands to both the Y49F mutant and wild-type enzyme is enthalpically favorable and entropically unfavorable over the temperature range studied. The affinity of these ligands for the Y49F mutant is lower than those for the wild-type enzyme due mainly to an entropy change. Therefore, the thermodynamic effect of this mutation is to decrease the entropy loss due to binding. Calorimetric titrations in several buffers with different ionization heat amounts indicate a release of protons when the mutant binds GSH, whereas protons are taken up in binding S-hexylglutathione at pH 6.5. This suggests that the thiol group of GSH releases protons to buffer media during binding and a group with low pKa (such as Asp98) is responsible for the uptake of protons. The temperature dependence of the free energy of binding, DeltaG0, is weak because of the enthalpy-entropy compensation caused by a large heat capacity change. The heat capacity change is -199.5 +/- 26.9 cal K-1 mol-1 for GSH binding and -333.6 +/- 28.8 cal K-1 mol-1 for S-hexylglutathione binding. The thermodynamic parameters are consistent with the mutation Tyr49 --> Phe, producing a slight conformational change in the active site.

Binding Sites↗
PubMed2006

Selection of representative congener for polychlorinated trans-azobenzenes (PCt-ABs) based on comprehensive thermodynamical and quantum-chemical characterization.

Thirty-one thermodynamical and quantum-chemical descriptors were used to characterize all 209 chloro trans-azobenzenes (Ct-ABs, PCt-ABs) in terms of their environmental stability and specific dioxin-like toxicity. Some of the PCt-ABs are produced as a by-side impurity during the manufacture of 3,4-dichloroaniline (DCA) and its derivatives and thus can be found in technical products of certain chloroaniline herbicides. A prepared basic thermodynamic and quantum-chemical property data matrix of PCt-ABs was interpreted using Principal Component Analysis (PCA). The PCA of the thermodynamic and quantum-chemical data matrix created a three-dimensional model that explained 78% (68% + 6% + 4%) of the total variance in the data set. The loading plot shows that the first Principal Component (PC) is influenced by variables describing molecular weight, polarizability and lipophilicity. The second PC was strongly influenced by the most positive partial charge on atoms and the most negative partial charge on atoms. The third PC depends on energy of the highest occupied molecular orbital. Next, factors extracted from PCA were used for selection of a representative set of eight trans-chloroazobenzene congeners, which seemed in the best way reflect a diverse property of all 209 PCt-ABs.

Chlorobenzenes↗
PubMed2002

Thermodynamic aspects of biopolymer functionality in biological systems, foods, and beverages.

Molecular mimicry and molecular symbiosis are proposed to be the main factors controlling thermodynamic activity and phase behavior of macromolecular compounds in foods, beverages, and chyme. Molecular mimicry implies a chemical resemblance of hydrophilic surfaces of globular proteins with their chemical information hidden in the hydrophobic interior and low excluded volume of the globules. The molecular mimicry contributes to the efficiency of enzymes. Molecular symbiosis means that interactions attraction or repulsion) between biopolymer molecules greatly differing in conformation (globular and rod-like) favor the biological efficiency of one of them at least. The symbiosis is based on excluded volume effects of macromolecules in mixed solutions. Association-dissociation of rod-like macromolecules can dictate thermodynamic activity of an enzyme in the mixed solution. Thermodynamic incompatibility is typical of food macromolecules, whose denaturation, association, complexing, and chemical modification reduce their mimicry and co-solubility. Foods are normally phase-separated systems with highly volume-occupied phases. The phase-separated nature of the gel-like chyme is important to the efficiency of digestion of mixed diets. Phase separation of biopolymer mixtures, presumably, underlies mechanisms of nonspecific immune defense. The phase behavior-functionality relationships is presented through concrete examples of some foods (such as milk products, low-fat spreads, ice cream, wheat and rye doughs, thermoplastic extrudates, etc.), beverages (tea and coffee), and chyme.

Animals↗
PubMed1983

Thermodynamics of drug-DNA interactions.

Batch calorimetry, differential scanning calorimetry (DSC), uv/vis absorption spectroscopy, fluorescence spectroscopy, and circular dichroism (CD), have been used to detect, monitor, and thermodynamically characterize the binding of daunomycin, dipyrandenium, dipyrandium, and netropsin to poly d(AT) and actinomycin D to salmon testes (ST) DNA. The following thermodynamic binding profiles have been obtained. (table; see text) All the poly d(AT) binding studies were done at 25 degrees C while actinomycin binding to ST DNA was performed at 1 degree C to enhance drug solubility. These thermodynamic parameters are interpreted in terms of specific interactions that have been proposed as part of models for the binding of each drug.

Animals↗
PubMed1996

Partial thermodynamic parameters for prediction stability and washing behavior of DNA duplexes immobilized on gel matrix.

Earlier we showed that reported in literature nearest-neighbor thermodynamic parameters describe poorly the thermal-induced behavior of DNA duplexes immobilized in gel. Here we present a complete set of partial thermodynamic parameters for all 10 nearest-neighbor interactions specially developed for duplexes immobilized in gel. This thermodynamic library allows to predict dissociation enthalpy and free energy of DNA duplex immobilized in gel matrix from its base sequence. The predicted values are in good agreement with the experimental ones. Dissociation enthalpy and free energy are needed for such application as (i) predicting relative stability of duplexes formed by DNA with oligonucleotides immobilized in cells of gel matrix; (ii) selecting optimal conditions for hybridization experiment; (iii) predicting washing curves and washing temperatures at irreversible temperature-stepped wash of DNA out of oligonucleotide gel matrix; (iv) selecting optimal conditions for washing gel matrix.

Acrylic Resins↗
PubMed1997

Mg2+ dependence of the structure and thermodynamics of wheat germ and lupin seeds 5S rRNA.

The formation and stability of structural elements in two 5S rRNA molecules from wheat germ (WG) and lupin seeds (LS) as a function of Mg2+ concentration in solution was determined using the adiabatic differential scanning microcalorimetry (DSC). The experimentally determined thermodynamic parameters are compared with calculations using thermodynamic databases used for prediction of RNA structure. The 5S rRNA molecules which show minor differences in the nucleotide sequence display very different thermal unfolding profiles (DSC profiles). Numerical deconvolution of DSC profiles provided information about structural transformations that take place in both 5S rRNA molecules. A comparative analysis of DSC data and the theoretical thermodynamic models of the structure was used to establish a relationship between the constituting transitions found in the melting profiles and the unfolding of structural domains of the 5S rRNA and stability of its particular helical elements. Increased concentrations of Mg2+ ions induces additional internal interactions stabilising 5S rRNA structures found at low Na+ concentrations. Observed conformational transitions suggest a structural model in which the extension of helical region E dominates over the postulated tertiary interaction between hairpin loops. We propose that helix E is stabilised by a sequence of non-standard pairings extending this helix by the formation of tetra loop e and an almost total reduction of loop d between helices E and D. Two hairpin structures in both 5S rRNA molecules: the extended C-C' and the extended E-E'-E" hairpins appear as the most stable elements of the structure. The cooperativity of the unfolding of helixes in these 5S rRNA molecules changes already at 2 mM Mg2+.

Base Sequence↗
PubMed1997

Thermodynamic cycle between DNA and RNA constituents for conformation of the sugar ring from nuclear magnetic resonance study.

The effect of a structural change of ribose to deoxyribose, by replacement of 2'-OH by 2'-H, on the conformational equilibrium of the sugar ring is described in terms of one thermodynamic cycle. The method is based on the observation that conformational correlations of the sugar ring--side chain ensemble in DNA and RNA components show one general pattern, reflecting an intrinsic physical property of this ensemble. The pattern determines a choice of model systems to study. The systems consist of pairs of DNA and RNA components, nucleosides and nucleotides in aqueous solution, where all conformational factors are fully controlled. This approach allowed us to describe the thermodynamic cycle and measure its fundamental parameters, equilibrium constants and free energy differences, delta delta G, from a nuclear magnetic resonance study. The delta delta G values as determined for pairs of ribo- and deoxyribo-nucleosides in classes of syn-constrained and anti-preferred models, are comparable and lie in a narrow range, delta delta G = 1.7 +/- 0.1 [kJ/mol]. For pairs of ribo- and deoxyribo-nucleotides, the delta delta G values also lie in narrow ranges, delta delta G = 1.7 +/- 0.1 [kJ/mol] for 5'-phosphate nucleotides and delta delta G = 1.9 +/- 0.1 [kJ/mol] for 3'-phosphate nucleotides, i.e. similar to those observed for nucleosides. The measured quantity, delta delta G, is generally observed in a relatively narrow range, delta delta G = 1.75 +/- 0.15 [kJ/mol], irrespective of the class of the model system. This quantity represents a "pure" constant contribution, pe one sugar moiety, as a "driving force" for the N-->S shift in the sugar ring conformational equilibrium, when one compares RNA and DNA. This important thermodynamic quantity, delta delta G, has not hitherto been determined for nucleic acids. Ultimately the delta delta G quantity is revealed in the tendency to adopt S(C2'endo) sugar puckering domain by the majority of DNA structures, whereas RNA generally adopt an N(C3'endo) puckering domain. A possible biological significance of the delta delta G quantity may include evolutionary aspects of nucleic acids.

DNA↗
PubMed2006

Thermodynamics constrains the evolution of insect population growth rates: "warmer is better".

Diverse biochemical and physiological adaptations enable different species of ectotherms to survive and reproduce in very different temperature regimes, but whether these adaptations fully compensate for the thermodynamically depressing effects of low temperature on rates of biological processes is debated. If such adaptations are fully compensatory, then temperature-dependent processes (e.g., digestion rate, population growth rate) of cold-adapted species will match those of warm-adapted species when each is measured at its own optimal temperature. Here we show that cold-adapted insect species have much lower maximum rates of population growth than do warm-adapted species, even when we control for phylogenetic relatedness. This pattern also holds when we use a structural-equation model to analyze alternative hypotheses that might otherwise explain this correlation. Thus, although physiological adaptations enable some insects to survive and reproduce at low temperatures, these adaptations do not overcome the "tyranny" of thermodynamics, at least for rates of population increase. Indeed, the sensitivity of population growth rates of insects to temperature is even greater than predicted by a recent thermodynamic model. Our findings suggest that adaptation to temperature inevitably alters the population dynamics of insects. This result has broad evolutionary and ecological consequences.

Adaptation, Physiological↗
PubMed2006

On chemical medicine, thermodynamics, and homeopathy.

The author indicates why homeopathic medicine is an example of future information medicine, a member of the more general psychophysiologic medicine group. Using standard chemical thermodynamics, it is readily shown that the driving force for all chemical reactions involves the logarithm of chemical activities for the different species involved. Because chemical activity is given by the product of concentration and thermodynamic activity coefficient, such reaction driving forces involve the sum of ln gamma ( j ) and ln c(j) for the j-species. Homeopathy involves the dilution of cj and succussion, which can increase gamma (j) ; thus, when c(j) goes to the ultradilution state, the thermodynamic driving force for change does not disappear as is assumed by many and, in fact, can even increase through the ln gamma ( j ) terms. Going to a more complex reference frame for viewing nature, one can, at least, qualitatively show how oscillating and decaying properties in time can occur for homeopathic remedies.

Biochemical Phenomena↗
PubMed2006

New t-gap insertion-deletion-like metrics for DNA hybridization thermodynamic modeling.

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. Thermodynamic distance functions are important components in the construction of DNA codes, and DNA codes are important components in biomolecular computing, nanotechnology, and other biotechnical applications that employ DNA hybridization assays. We show how our new distances can be calculated by using a dynamic programming method, and we derive a Varshamov-Gilbert-like lower bound on the size of some of codes using these distance functions as constraints. We also discuss software implementation of our DNA code design methods.

Base Sequence↗
PubMed2004

Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry.

UNLABELLED: The Thermodynamics of Enzyme-catalyzed Reactions Database (TECRDB) is a comprehensive collection of thermodynamic data on enzyme-catalyzed reactions. The data, which consist of apparent equilibrium constants and calorimetrically determined molar enthalpies of reaction, are the primary experimental results obtained from thermodynamic studies of biochemical reactions. The results from approximately 1000 published papers containing data on approximately 400 different enzyme-catalyzed reactions constitute the essential information in the database. The information is managed using Oracle and is available on the Web. AVAILABILITY: http://xpdb.nist.gov/enzyme_thermodynamics/

Biochemistry↗
PubMed2003

Mathematical models of solute retention in gas chromatography as sources of thermodynamic data. Part III. Alkylbenzenes as the test analytes.

Direct determination of thermodynamic data has always been a complicated and troublesome experimental task. Gas chromatography is among long-established working tools well suited to performing this particular task indirectly. Our own results were first presented in the papers by Ciazynska-Halarewicz and Kowalska (1,2), and this article is Part III in the series. Present experiments are carried out on low- and medium-polarity stationary phases at five different temperatures ranging from 323K to 423K. They enable determination of two thermodynamic properties of the alkylbenzenes, molar enthalpy of vaporization (DeltaH(vap)), and the chemical potential of partitioning of the methylene group between the two phases of the chromatographic system (Delta micro (p(-CH2-))). These properties are obtained from eight nonempirical models and, as is apparent from their derivation (3-7), the terms of the models have clearly defined physical meaning, which enables calculation of thermodynamic properties.

Benzene Derivatives↗
PubMed1991

Thermodynamics and living systems: problems and paradigms.

The utility of thermodynamic laws in biological systems is reviewed. The joint historical development of thermodynamics and of respiratory physiology in the 19th century is surveyed. From first principles of thermodynamics, problems are noted in their application to physiological calorimetry.

Calorimetry↗
PubMed1989

Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments.

NMR studies were carried out on various equimolar mixtures consisting of a combination of oligomers: d(ACGGCT) (I). d(pACGGCT) (Ia), d(TGCAGT) (II), d(AGCCGTACTGCA) (III), d(TGCAGTACGGCT) (IV). It is shown that I + II + III (MI) and Ia + II + III (M2) form stable duplexes with nicks in the centre of the respective double helices. A close analysis of the NOESY experiments of M1 and M2 revealed that these fragments form B-DNA type duplex structures. A comparison of the chemical-shift data of the nicked duplexes with those of the intact duplex of III + IV (M3) demonstrated that only small local distortions occur when a nick is introduced. The chemical-shift profiles of M1 and M3 were used to obtain the thermodynamic data for the duplex/coil transitions. The profiles of M1 were analysed by means of a new thermodynamic model (TRIDUP). From the calculated thermodynamic data of M1 and M3 it is concluded that the melting behaviour of M1 occurs cooperatively. A ligation experiment demonstrated that the relatively small substrate (M2) was almost completely joined after an overnight incubation at 14 degrees C.

Base Sequence↗
PubMed1992

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.

We determined the melting temperatures (Tm) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCl, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C.G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C.G, or G.C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37 degrees C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with delta G degrees 37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C.G to G.C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures.

Base Sequence↗
PubMed1993

Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding.

A combination of calorimetric and spectroscopic techniques was used to evaluate the thermodynamic behavior of a set of DNA hairpins with the sequence d(GCGCTnGCGC), where n = 3, 5 and 7, and the interaction of each hairpin with ethidium. All three hairpins melt in two-state monomolecular transitions, with tm's ranging from 79.1 degrees C (T3) to 57.5 degrees C (T7), and transition enthalpies of approximately 38.5 kcal mol-1. Standard thermodynamic profiles at 20 degrees C reveal that the lower stability of the T5 and T7 hairpins corresponds to a delta G degree term of +0.5 kcal mol-1 per thymine residue, due to the entropic ordering of the thymine loops and uptake of counterions. Deconvolution of the ethidium-hairpin calorimetric titration curves indicate two sets of binding sites that correspond to one ligand in the stem with binding affinity, Kb, of approximately 1.8 x 10(6) M-1, and two ligands in the loops with Kb of approximately 4.3 x 10(4) M-1. However, the binding enthalpy, delta Hb, ranges from -8.6 (T3) to -11.6 kcal mol-1 (T7) for the stem site, and -6.6 (T3) to -12.7 kcal mol-1 (T7) for the loop site. Relative to the T3 hairpin, we obtained an overall thermodynamic contribution (per dT residue) of delta delta Hb = delta(T delta Sb) = -0.7(5) kcal mol-1 for the stem sites and delta delta Hb = delta(T delta Sb) = -1.5 kcal mol-1 for the loop sites. Therefore, the induced structural perturbations of ethidium binding results in a differential compensation of favorable stacking interactions with the unfavorable ordering of the ligands.

Base Sequence↗