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PubMed2004

Effects of temperature acclimation on lactate dehydrogenase of cod (Gadus morhua): genetic, kinetic and thermodynamic aspects.

The aim of this study was to determine the effects of seasonal temperature variation on the functional properties of lactate dehydrogenase (LDH) from white muscle and liver of Norwegian coastal cod (Gadus morhua) and the possible relevance of LDH allelic variability for thermal acclimation. Two groups of fishes were acclimated to 4 degrees C or 12 degrees C for one year. Polymorphism was observed in only one (Ldh-B) of the three Ldh loci expressed in cod liver and/or muscle. Isozyme expression remained unchanged regardless of acclimation temperature (T(A)). The products of locus Ldh-B comprise only 14-19% (depending on the tissue) of total LDH activities and, consequently, differences between phenotypes are negligible in terms of their effect on LDH total performance. No kinetic (, V(max)) or thermodynamic (E(a), DeltaG) differences were found among Ldh-B phenotypes. Clear kinetic differences were observed between LDH isoforms in the two tissues. However, the Arrhenius activation energy (E(a)) for pyruvate reduction was the same for both tissues (E(a)=47 kJ mol(-1)) at T(A)=12 degrees C. Factors T(A), tissue and phenotype did not reveal a significant effect on the Gibbs free energy change (DeltaG) of the reaction (55.5 kJ mol(-1)). However, at T(A)=4 degrees C, the E(a) was increased (E(a)=53-56 kJ mol(-1)) and the temperature dependence of the constant of substrate inhibition for pyruvate () decreased in both muscle and liver. In conclusion, the strategies of LDH adjustment to seasonal temperature variations in cod involve changes in LDH concentration (quantitative), adjustment of thermodynamic (E(a)) and kinetic () properties of the LDH (modulative) but not the expression of alternative isoforms (qualitative). We assume that the observed increase in E(a) and the decrease of temperature dependence of at low T(A) is the result of structural changes of the LDH molecule (temperature-driven protein folding). We propose a new mechanism of metabolic compensation of seasonal temperature variations - cold acclimation results in changes in the kinetic and thermodynamic properties of LDH in a way that favours aerobic metabolism through reduction of the competition of LDH for pyruvate in normoxic conditions.

Acclimatization↗
PubMed1997

Analysis of water sorption behavior of native and denatured proteins by solution thermodynamics.

Water sorption isotherms of native and denatured ovalbumin samples were measured, and their affinity for water was quantitatively analyzed by solution thermodynamics. The structural change of the proteins was evaluated by several methods. Water activity above 0.9 was measured by adding a specific amount of water to a sample, while that elbow 0.9 was measured with apparatus for water sorption isotherms. Thus, water sorption isotherms for native and denatured ovalbumin samples were obtained up to a water activity of 0.99. The water sorption behavior of ovalbumin was affected not by its hydrophobicity but by its prominent conformational change. It was confirmed that parameter delta Gs calculated by solution thermodynamics was more suitable for evaluating the affinity for water from water sorption isotherms than delta Gws calculated by conventional adsorption thermodynamics.

Adsorption↗
PubMed2000

Thermodynamic molecular switch in macromolecular interactions.

It is known that most living systems can live and operate optimally only at a sharply defined temperature, or over a limited temperature range, at best, which implies that many basic biochemical interactions exhibit a well-defined Gibbs free energy minimum as a function of temperature. The Gibbs free energy change, deltaG(o) (T), for biological systems shows a complicated behavior, in which deltaG(o)(T) changes from positive to negative, then reaches a negative value of maximum magnitude (favorable), and finally becomes positive as temperature increases. The critical factor in this complicated thermodynamic behavior is a temperature-dependent heat capacity change (deltaCp(o)(T) of reaction, which is positive at low temperature, but switches to a negative value at a temperature well below the ambient range. Thus, the thermodynamic molecular switch determines the behavior patterns of the Gibbs free energy change, and hence a change in the equilibrium constant, Keq, and/or spontaneity. The subsequent, mathematically predictable changes in deltaH(o)(T), deltaS(o)(T), deltaW(o)(T), and deltaG(o)(T) give rise to the classically observed behavior patterns in biological reactivity, as demonstrated in three interacting protein systems: the acid dimerization reaction of alpha-chymotrypsin at low pH, interaction of chromogranin A with the intraluminal loop peptide of the inositol 1,4,5-triphosphate receptor at pH 5.5, and the binding of L-arabinose and D-galactose to the L-arabinose binding protein of Escherichia coli. In cases of protein unfolding of four mutants of phage T4 lysozyme, no thermodynamic molecular switch is observed.

Arabinose↗
PubMed2004

Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity.

Given the three-dimensional structure of a protein, its thermodynamic properties are calculated using a recently introduced distance constraint model (DCM) within a mean-field treatment. The DCM is constructed from a free energy decomposition that partitions microscopic interactions into a variety of constraint types, i.e., covalent bonds, salt-bridges, hydrogen-bonds, and torsional-forces, each associated with an enthalpy and entropy contribution. A Gibbs ensemble of accessible microstates is defined by a set of topologically distinct mechanical frameworks generated by perturbing away from the native constraint topology. The total enthalpy of a given framework is calculated as a linear sum of enthalpy components over all constraints present. Total entropy is generally a nonadditive property of free energy decompositions. Here, we calculate total entropy as a linear sum of entropy components over a set of independent constraints determined by a graph algorithm that builds up a mechanical framework one constraint at a time, placing constraints with lower entropy before those with greater entropy. This procedure provides a natural mechanism for enthalpy-entropy compensation. A minimal DCM with five phenomenological parameters is found to capture the essential physics relating thermodynamic response to network rigidity. Moreover, two parameters are fixed by simultaneously fitting to heat capacity curves for histidine binding protein and ubiquitin at five different pH conditions. The three free parameter DCM provides a quantitative characterization of conformational flexibility consistent with thermodynamic stability. It is found that native hydrogen bond topology provides a key signature in governing molecular cooperativity and the folding-unfolding transition.

Computer Simulation↗
PubMed2006

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

Constraint-based modeling has proven to be a useful tool in the analysis of biochemical networks. To date, most studies in this field have focused on the use of linear constraints, resulting from mass balance and capacity constraints, which lead to the definition of convex solution spaces. One additional constraint arising out of thermodynamics is known as the "loop law" for reaction fluxes, which states that the net flux around a closed biochemical loop must be zero because no net thermodynamic driving force exists. The imposition of the loop-law can lead to nonconvex solution spaces making the analysis of the consequences of its imposition challenging. A four-step approach is developed here to apply the loop-law to study metabolic network properties: 1), determine linear equality constraints that are necessary (but not necessarily sufficient) for thermodynamic feasibility; 2), tighten V(max) and V(min) constraints to enclose the remaining nonconvex space; 3), uniformly sample the convex space that encloses the nonconvex space using standard Monte Carlo techniques; and 4), eliminate from the resulting set all solutions that violate the loop-law, leaving a subset of steady-state solutions. This subset of solutions represents a uniform random sample of the space that is defined by the additional imposition of the loop-law. This approach is used to evaluate the effect of imposing the loop-law on predicted candidate states of the genome-scale metabolic network of Helicobacter pylori.

Algorithms↗
PubMed2005

Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study.

The binding of aminoglycoside antibiotics to a broad range of macromolecular targets is coupled to protonation of one or more of the amino groups that typify this class of drugs. Determining how and to what extent this linkage influences the energetics of the aminoglycoside-macromolecule binding reaction requires a detailed understanding of the thermodynamics associated with the protonation equilibria of the aminoglycoside amino groups. In recognition of this need, a calorimetric- and NMR-based approach for obtaining the requisite thermodynamic information is presented using paromomycin as the model aminoglycoside. Temperature- and pH-dependent 15N NMR studies provide pK(a) values for the five paromomycin amino groups, as well as the temperature dependence of these pK(a) values. These studies also indicate that the observed pK(a) values associated with the free base form of paromomycin are lower in magnitude than the corresponding values associated with the sulfate salt form of the drug. This difference in pK(a) is due to drug interactions with the sulfate counterions at the high drug concentrations (> or = 812 mM) used in the 15N NMR studies. Isothermal titration calorimetry studies conducted at drug concentrations < or = 45 microM reveal that the extent of paromomycin protonation linked to the binding of the drug to its pharmacologically relevant target, the 16 S rRNA A-site, is consistent with the pK(a) values of the free base and not the sulfate salt form of the drug. Temperature- and pH-dependent isothermal titration calorimetry studies yield exothermic enthalpy changes (deltaH) for protonation of the five paromomycin amino groups, as well as positive heat capacity changes (deltaC(p)) for three of the five amino groups. Regarded as a whole, the results presented here represent an important first step toward establishing a thermodynamic database that can be used to predict how aminoglycoside-macromolecule binding energetics will be influenced by conditions such as temperature, pH, and ionic strength. Such a predictive capability is a critical component of any drug design strategy.

Aminoglycosides↗
PubMed2006

Thermodynamics of lipid membrane solubilization by sodium dodecyl sulfate.

We provide a comprehensive thermodynamic description of lipid membrane dissolution by a charged detergent. To this end, we have studied the interactions between the anionic detergent sodium dodecyl sulfate (SDS) and the zwitterionic phospholipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in dilute aqueous solution (10 mM phosphate buffer, 154 mM NaCl, pH 7.4). Thermodynamic parameters of vesicle solubilization and reconstitution, membrane partitioning, and micelle formation were assessed by right-angle light scattering and isothermal titration calorimetry. Membrane translocation and dissolution proceed very slowly at 25 degrees C but are considerably accelerated at 65 degrees C. At this temperature, a simple SDS/POPC phase diagram (comprising vesicular, coexistence, and micellar ranges) and a complete set of partition coefficients and transfer enthalpies were obtained. Electrostatic repulsion effects at the membrane surface were implemented by combining Gouy-Chapman theory with a Langmuir adsorption isotherm to account for Na+ binding to membrane-incorporated DS-. This approach offered a quantitative understanding of solubilization and reconstitution processes, which were interpreted in terms of partition equilibria between and ideal mixing in all phases. More than any other property, the transbilayer flip-flop rate under given experimental conditions hence appears to dictate a detergent's suitability for thermodynamically controlled lipid membrane solubilization and reconstitution.

Lipid Bilayers↗
PubMed2006

Thermodynamic equilibrium of domains in a two-component Langmuir monolayer.

This [corrected] article outlines the results from a combined experimental and theoretical study on the properties of circular domains in a mixed Langmuir monolayer at thermodynamic equilibrium. The mixed monolayer consisted of a binary mixture of dimyristoyl-phosphatidyl-choline and dihydrocholesterol. A long-term fluorescence microscopy study of these domains was carried out over the course of approximately 60 h. Image analysis of the domains over time revealed that the domains ripened slowly with an [corrected] increase in mean domain radius and a [corrected] decrease in domain number density. At the end of the measurement, the domains remained polydisperse, and true thermodynamic equilibrium was not reached. Theoretically, collective thermodynamic equilibrium properties such as mean domain size and size distribution were calculated by combining micelle self-assembly theory and the "equivalent dipole" model for the self-energy of two-dimensional domains. The calculations predicted existence of finite-sized circular domains at equilibrium. This suggests that equilibrium circular monolayer domains of single- or multicomponent lipids with a finite size distribution should form only at very limited experimental conditions. Both the predicted mean domain size and size distribution are strongly affected by line tension and dipole moment density difference. A comparison between the theoretical and experimental results is made.

Cholestanol↗
PubMed2005

Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design.

All biological phenomena depend on molecular recognition, which is either intermolecular like in ligand binding to a macromolecule or intramolecular like in protein folding. As a result, understanding the relationship between the structure of proteins and the energetics of their stability and binding with others (bio)molecules is a very interesting point in biochemistry and biotechnology. It is essential to the engineering of stable proteins and to the structure-based design of pharmaceutical ligands. The parameter generally used to characterize the stability of a system (the folded and unfolded state of the protein for example) is the equilibrium constant (K) or the free energy (deltaG(o)), which is the sum of enthalpic (deltaH(o)) and entropic (deltaS(o)) terms. These parameters are temperature dependent through the heat capacity change (deltaCp). The thermodynamic parameters deltaH(o) and deltaCp can be derived from spectroscopic experiments, using the van't Hoff method, or measured directly using calorimetry. Along with isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) is a powerful method, less described than ITC, for measuring directly the thermodynamic parameters which characterize biomolecules. In this article, we summarize the principal thermodynamics parameters, describe the DSC approach and review some systems to which it has been applied. DSC is much used for the study of the stability and the folding of biomolecules, but it can also be applied in order to understand biomolecular interactions and can thus be an interesting technique in the process of drug design.

Calorimetry, Differential Scanning↗
PubMed1983

Hierarchial thermodynamic approach to the brain.

A thermodynamic approach to understanding the brain is presented. Thermodynamics may be extended to "higher than molecule" levels. The role of the concept of entropy in thermodynamic-based nonthermodynamic systems has been discussed. Static and dynamic structures, cooperative and competitive mechanisms and some of their neurobiological applications are discussed. Postsynaptic membrane noises, dynamic synaptic activity, synaptogenesis, plasticity, retinotopy and perception have been considered as self-organizing neural structures appearing at different hierarchical levels.

Animals↗
PubMed1980

The thermodynamics of nucleotide binding to proteins.

Models describing the interaction of a small molecule with a protein are typically couched in terms of the stoichiometry, cooperativity, and binding free-energy change. These parameters are readily available from equilibrium dialysis experiments (or appropriate variations). With the recent advent of extremely sensitive calorimeters, it is possible to obtain thermal data for the binding reaction and, thus, the entire set of thermodynamic parameters, delta G', delta H', delta S', delta C', become readily available. This review is limited to the binding of nucleotides and nucleotide analogs to proteins for which complete thermal data are available. While the majority of such systems have been characterized by calorimetry, we have not excluded, per se, van't Hoff enthalpy determinations. The systems we have considered include, but are not limited to, thymidylate synthetase, phosphorylase, several dehydrogenases, aldolase, glutamine synthetase, hemoglobin, asparate transcarbamylase, and ribonuclease. A variety of forces contribute to the total free-energy change upon ligand binding. These forces include ionic, van der Waals, hydrogen bond, and hydrophobic. In several cases, properly designed experiments have allowed a partial resolution of the individual contributions of these various forces. Variation of easily accessible conditions such as temperature, pH, ionic strength, or solvent third component produce changes in the set of thermodynamic parameters which lead to the resolution of the forces. The generality of heat effects makes this method very useful for studying the involvement of protons in binding reactions. The variation in the magnitude and direction (release or uptake) of the proton flux is readily studied by determining the apparent heat of reaction at constant pH, ionic strength, and temperature in two or more buffers of differing heat of ionization. This application has been exploited in several cases and is examined in great detail. An overview of the results in these systems to date suggests that several trends observed in the thermodynamic parameters need to be confirmed by further experimentation and, if they hold, an appropriate theoretical basis must be developed to aid in their interpretation.

Animals↗
PubMedDate not supplied

Thermodynamic parameters of opioid binding in the presence and absence of G-protein coupling.

We have investigated the thermodynamic parameters of various opioid ligands interacting with their receptors in rat brain membranes. Affinity constants (Ka), enthalpy and entropy values were obtained from homologous displacement experiments performed at 0, 24 and 33 degrees C. It was found that all the opioid agonists tested ([3H]dihydromorphine (DHM) mu alkaloid; [3H]DAMGO mu peptide; [3H]deltorphin-B delta peptide) display endothermic binding accompanied with a large entropy increase, regardless of their chemical structure (alkaloid or peptide), or of their mu or delta receptor selectivity. In contrast, binding of the antagonist naloxone is exothermic, mainly enthalpy driven. Na+ or Mg2+ results only in quantitative changes of the thermodynamic parameters. In the presence of the GTP-analog Gpp(NH)p; or Gpp(NH)p + Na+; or Gpp(NH)p + Na- + Mg2+ the affinity of DHM binding dramatically decreases which might reflect functional uncoupling of the receptor-ligand complex and G-proteins. This altered molecular interactions are also indicated by curvilinear van't Hoff plot and entropy increase. It is concluded that the thermodynamic analysis provides means of determining the underlying driving forces of ligand binding and helps to delineate its mechanism.

Animals↗
PubMed1982

The mechanics and thermodynamics of separation flow through porous, molecularly disperse, solid media - the Poiseuille Lecture 1981.

Steady flow of a multicomponent, incompressible fluid through a connected, solid-like network is considered. The network acquires a finite deformation, bears the extra stresses required for mechanical balance, but does not flow. It constitutes at least one thermodynamic component and, in terms of the thermodynamics of irreversible processes, the simplest case of the flow of a binary solution through the network creates a three-component system with three independent cross-coefficients to be determined. The number of coefficients to be determined in the case of more than three components tends to become prohibitive. Hence, the formalism, developed for three components, is often applied, justifiably and unjustifiably, to practical problems in biology, where the system is much more complex. The conditions under which this is permissible are given and discussed. For such a case, the questions of volume and separation flows is also considered. Relationships are given in terms of the friction coefficients between the components. The important biorheological and thermodynamic role of the matrix is stressed throughout.

Animals↗
PubMed2004

DNA . RNA heteroduplex containing 8-oxo-7,8-dihydroguanosine: base pairing, structures, and thermodynamic stability.

Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-O-methylguanosine (8-oxoG-Me) were synthesized. The base pairing properties of 8-oxoG and 8-oxoG-Me in oligoribonucleotide in cDNA synthesis by reverse transcriptases were studied. dCMP was preferentially incorporated into the site opposite 8-oxoG or 8-oxoG-Me than into other dNMPs. TMP and dCMP were inserted preferentially into sites opposite 8-oxoG or 8-oxoG by reverse transcriptases. HIV-RT did not incorporate TMP, but RAV2-RT incorporated 50% more TMP than dCMP into the site opposite 8-oxoG. In the site opposite 8-oxoG-Me TMP was substantially incorporated by HIV-RT or RAV2-RT. Thermodynamic analysis of the DNA.RNA heteroduplex containing 8-oxoG revealed that 8-oxoG and 8-oxoG-Me formed base pairs with cytidine and thymidine with similar stability. The thermodynamic parameter (DeltaG degrees ) demonstrated that the formation of duplexes between 8-oxoG or 8-oxoG-Me and cytidine or thymidine is more thermodynamically favorable than with adenosine and guanosine. However, differences in the melting temperature and DeltaG degrees 's of 8-oxoG/dC and 8-oxoG/T were much smaller than between G/dC and G/T. CD spectra showed that DNA . RNA containing 8-oxoG or 8-oxoG-Me duplexes showed similarities between the A-type RNA and B-type DNA conformations.

Base Pairing↗
PubMed1975

Muscle as a thermodynamic machine.

Three main problems in the energetics of muscular contraction confront us at the present time:- (1) Thermodynamics. This is a labyrinthine subject in the sense that there are often several equally correct ways (that may appear different) of arriving at the same result. The recent advances in the kinetics of the reactions of muscle proteins have increased still further the need for understanding among muscle physiologists-and other biologists-of those parts of thermodynamics that concern them directly, notably those relating work and chemical change. (2) Energy balance. Over the whole cycle of contraction, relaxation and oxidative recovery, the observed energy output (heat + work) can be accounted for by the chemical processes currently believed to operate in the cycle. In contrast, during contraction and relaxation alone, the energy output is greater than can be accounted for by the extent of known chemical reactions combined with their heats of reaction (measured calorimetrically). The physical and chemical methods cross-check one another-hence the usefulness of the method. The details of this discrepancy may vary from species to species but it is seen in all the experiments known at this time. The general problem will be resolved only when we know more about the chemical reactions that have occurred and reliable measurements have been made of their heats of reaction in vitro. (3) Work balance. Work and heat differ thermodynamically and, since the production of work is a primary function of muscles, the question naturally arises whether the observed splitting of ATP (combined with estimates of the change in free energy of this reaction) is sufficient to account for the work observed. On present information, which is imperfect in several respects, the chemical change is sufficient to account for the work. Estimates of the efficiency of transduction vary in different laboratories from 45 to 66%.

Adenosine Diphosphate↗
PubMed1999

Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs.

The determination of the structural and functional contributions of natural modified nucleosides to tRNA has been limited by lack of an approach that can systematically incorporate the modified units. We have produced a number of oligonucleotide analogs, of the anticodon of yeast tRNA(Phe) by, combining standard automated synthesis for the major nucleosides with specialty chemistries for the modified nucleosides. In this study, both naturally occurring and unnatural modified nucleotides were placed in native contexts. Each oligonucleotide was purified and the nucleoside composition determined to validate the chemistry. The RNAs were denatured and analyzed to determine the van't Hoff thermodynamic parameters. Here, we report the individual thermodynamic contributions for Cm, Gm, m1G, m5C, psi. In addition m5m6U, m1psi, and m3psi, were introduced to gain additional understanding of the physicochemical contribution of psi and m5C at an atomic level. These oligonucleotides demonstrate that modifications have measurable thermodynamic contributions and that loop modifications have global contributions.

Anticodon↗
PubMedDate not supplied

[Thermodynamic theory of biological evolution and aging. Experimental verification of the theory].

Experimental data confirming original thermodynamic theory of biological evolution and aging are presented. Biological evolution (phylogenesis) and ontogenesis can be easily described within the frames of equilibrium hierarchical thermodynamics on the basis of temporal hierarchies law and the second principle of thermodynamics. The theory explains many facts and suggests new practical proposals in medical and biological science, particularly, in dietology, gerontology, and geriatrics. Application of the temporal hierarchies model to studying living nature offers horizonless possibilities for its understanding.

Aging↗
PubMedDate not supplied

[Clinical forms of ischemic heart disease and natural evolution of live information-thermodynamic systems].

Clinical forms of myocardial ischemia are considered in terms of a new approach towards illness formation as a violation of information exchange in a human organism. The latter is suggested to be an open information-thermodynamic system developing to a closed equilibrium stationary thermodynamic system with information as a factor of system stability and direction of the evolution guided by the second thermodynamic law.

Angina Pectoris↗