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PubMed1998

Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain.

The thermodynamics of the c-Myb DNA-binding domain (R2R3) interaction with its target DNA have been analyzed using isothermal titration calorimetry and amino acid mutagenesis. The enthalpy of association between the standard R2R3, the Cys130 mutant substituted with Ile, and the cognate DNA is -12.5 (+/- 0.1) kcal mol-1 at pH 7.5 and at 20 degrees C, and this interaction is enthalpically driven throughout the physiological temperature range. In order to understand the DNA recognition mechanism, several pairs of interactions were investigated using single and multiple-base alterations with single and multiple-amino acid substituted mutants. The interactions between the standard R2R3 and many non-cognate DNAs were accompanied by binding enthalpy changes and heat capacity changes, although their affinities were reduced. The roles of the electrostatic interactions in binding to the cognate and the non-cognate DNAs were also analyzed from the dependency of the thermodynamic parameters on the salt concentration. The heat capacity change was found to be significantly dependent upon the salt concentration. Several mutant proteins bound to the multiple-base altered DNA with very small enthalpy changes, although they bound to the cognate and the single-base altered DNAs with detectable enthalpy and heat capacity changes. From the thermodynamic cycles derived from the DNA binding of the amino acid substituted R2R3 to the base substituted DNA duplexes, the individual thermodynamic mechanisms of the specific DNA recognition of R2R3 were dissected. The local folding mechanism was highlighted by the substitution of Pro with either Gly or Ala at the linker between R2 and R3. The characteristic thermodynamic features of specific and non-specific DNA binding are discussed.

Amino Acid Substitution↗

PubMed2000

Thermodynamics and evolution.

The science of thermodynamics is concerned with understanding the properties of inanimate matter in so far as they are determined by changes in temperature. The Second Law asserts that in irreversible processes there is a uni-directional increase in thermodynamic entropy, a measure of the degree of uncertainty in the thermal energy state of a randomly chosen particle in the aggregate. The science of evolution is concerned with understanding the properties of populations of living matter in so far as they are regulated by changes in generation time. Directionality theory, a mathematical model of the evolutionary process, establishes that in populations subject to bounded growth constraints, there is a uni-directional increase in evolutionary entropy, a measure of the degree of uncertainty in the age of the immediate ancestor of a randomly chosen newborn. This article reviews the mathematical basis of directionality theory and analyses the relation between directionality theory and statistical thermodynamics. We exploit an analytic relation between temperature, and generation time, to show that the directionality principle for evolutionary entropy is a non-equilibrium extension of the principle of a uni-directional increase of thermodynamic entropy. The analytic relation between these directionality principles is consistent with the hypothesis of the equivalence of fundamental laws as one moves up the hierarchy, from a molecular ensemble where the thermodynamic laws apply, to a population of replicating entities (molecules, cells, higher organisms), where evolutionary principles prevail.

Animals↗

PubMed2003

Elucidating thermodynamic parameters for electron transfer proteins using isothermal titration calorimetry: application to the nitrogenase Fe protein.

Establishing thermodynamic parameters for electron transfer reactions involving redox proteins is essential for a complete description of these important reactions. While various methods have been developed for measuring the Gibbs free energy change (Delta G(HR) or E(m)) for the protein half-reactions, deconvolution of the respective contributions of enthalpy (Delta H(HR)) and entropy (Delta S(HR)) changes is much more challenging. In the present work, an approach is developed using isothermal titration calorimetry (ITC) that allows accurate determination of all of these thermodynamic parameters for protein electron transfer half-reactions. The approach was validated for essentially irreversible and reversible electron transfer reactions between well-characterized mediators and between mediators and the protein cytochrome c. In all cases, the measured thermodynamic parameters were in excellent agreement with parameters determined by electrochemical methods. Finally, the calorimetry approach was used to determine thermodynamic parameters for electron transfer reactions of the nitrogenase Fe protein [4Fe-4S](2+/+) couple in the absence or presence of MgADP or MgATP. The E(m) value was found to change from -290 mV in the absence of nucleotides to -381 mV with MgATP and -423 mV with MgADP, consistent with earlier values. For the first time, the enthalpy (Delta H(HR)) and entropy (Delta S(HR)) contributions for each case were established, revealing shifts in the contribution of each thermodynamic parameter induced by nucleotide binding. The results are discussed in the context of current models for electron transfer in nitrogenase.

Adenosine Diphosphate↗

PubMed1996

Thermodynamics of 5-HT3 receptor binding discriminates agonistic from antagonistic behaviour.

Thermodynamic parameters delta G degree, delta H degree and delta S degree of the binding equilibrium of eleven ligands (seven agonists and four antagonists) to the serotonin 5-HT3 receptor subtype have been determined by affinity measurements carried out on rat cortex membranes at six different temperatures (0, 10, 20, 25, 30, 35 degrees C) and van't Hoff plots. Affinity constants were obtained from saturation experiments of [3H]endo-N-(9-methyl-9-azabicyclo[3.3.1]non-3-yl)-1-methyl-1-H-indazole- 3- carboxamide ([3H]BRL 43694, a selective 5-HT3 ligand) or by its displacement in inhibition assays for the other compounds. Van't Hoff plots were essentially linear in the temperature range investigated, showing that the delta Cp degree of the binding equilibrium is nearly zero. Thermodynamic parameters are in the range 18 < or = delta H degree < or = 53 kJ mol-1 and 202 < or = delta S degree < or = 320 J K-1 mol-1 for agonists and -16 < or = delta H degree < or = 0 kJ mol-1 and 70 < or = delta S degree < or = 179 J K-1 mol-1 for antagonists indicating that agonistic binding is totally entropy-driven while antagonistic binding is relatively less entropy- and more enthalpy-driven in the -T delta S degree versus delta H degree plot the thermodynamic data are clearly arranged in separate clusters for agonists and antagonists, which, therefore, turn out to be thermodynamically discriminated. Experimental results are discussed according to the following main points: (i) the approximate linearity of the delta H degree versus delta S degree plot in terms of enthalpy-entropy compensation and (ii) the fact that delta Cp degree approximately equal to 0 for practically all membrane receptors at variance with most reactions involving biomacromolecules in solution. Finally, the phenomenon of thermodynamical discrimination is reviewed and found to occur in five distinct membrane receptorial systems.

Animals↗

PubMed1994

Biochemical thermodynamics.

Biochemists need two types of reaction equations, chemical equations in terms of species and biochemical equations in terms of reactants at specified pH and concentrations of free metal ions that are bound by reactant species. Both types of reaction equations have corresponding equilibrium constants, K for chemical reactions and K' for biochemical reactions. When the pH is specified you enter a whole new world of thermodynamics. There are new thermodynamic properties, new names (transformed thermodynamic properties), and new values, which are quite different, especially for the standard transformed Gibbs energy. This raises nomenclature problems because it is important to be able to distinguish between chemical equations and biochemical equations at a glance. It is also important to distinguish between the standard thermodynamic properties calculated from K and its temperature coefficient and the standard transformed thermodynamic properties calculated from K' and its temperature coefficient.

Biochemistry↗

PubMed1990

Allowance for thermodynamic nonideality and Donnan effects in binding studies. Activity coefficients of charged ligands in the presence of albumin.

A combination of ultrafiltration with either equilibrium dialysis or frontal gel chromatography has been used to evaluate the effects of thermodynamic nonideality in mixtures of bovine serum albumin and charged ligands. Studies with methyl orange, chlorpromazine and chromate as ligand all demonstrated inadequacy of the Donnan effect for description of the difference between the concentrations of free ligand in a mixture and the protein-free phase with which it is in dialysis equilibrium. On the basis of a quantitative relationship derived for the situation in which Donnan and thermodynamic nonideality effects both operate, values of the second virial coefficient for albumin and ligand have been determined. For albumin and either methyl orange or chlorpromazine the magnitude of this second virial coefficient has been rationalized on the statistical-mechanical basis of excluded volume. For the albumin-chromate system, however, the thermodynamic nonideality was manifested as a negative deviation from Raoult's Law, in keeping with the classical behaviour of electrolyte ions. From the viewpoint of the characterization of ligand binding a unique feature of the ultrafiltration/gel chromatography and ultrafiltration/equilibrium dialysis methods is their ability to define not only the binding function but also the activity coefficient of ligand for a given acceptor-ligand mixture. Consequently, irrespective of whether the ligand is charged or uncharged, the intrinsic binding constant that is determined is the thermodynamic parameter instead of the apparent value that is obtained from methods based on assumed thermodynamic ideality.

Animals↗

PubMed1990

Thermodynamics of local linkage effects. Contracted partition functions and the analysis of site-specific energetics.

A thermodynamic theory is presented for the description of local, site-specific linkage effects in biological macromolecules. The theory is developed from a basic isomorphism involving the intensive quantities of a thermodynamic system at equilibrium. Local linkage effects can be cast within the same mathematical framework as the one used in the statistical thermodynamic theory of global linkage effects involving different ligands. In addition to this parallel, local linkage effects give rise to apparent violations of thermodynamic stability that can be of relevance in energy transduction phenomena. It is also shown that the canonical partition function for the macromolecule as a whole can be expressed in terms of contracted partition functions that greatly simplify calculations of the relevant thermodynamic properties of individual sites. Site-specific Hill plots, partition coefficients and free energies of linkage are introduced and their properties discussed in connection with those of analogous global quantities. Calculation of the free energies of linkage for human hemoglobin yields a minimal phenomenological scheme for the coupling among subunits.

Binding Sites↗

PubMed2004

Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability.

Here, we perform protein thermodynamic simulations within a set of boundary conditions, effectively blanketing the experimental data. The thermodynamic parameters, melting temperature (TG), enthalpy change at the melting temperature (DeltaHG) and heat capacity change (DeltaCp) were systematically varied over the experimentally observed ranges for small single domain reversible two-state proteins. Parameter sets that satisfy the Gibbs-Helmholtz equation and yield a temperature of maximal stability (TS) around room temperature were selected. The results were divided into three categories by arbitrarily chosen TG ranges. The TG ranges in these categories correspond to typical values of the melting temperatures observed for the majority of the proteins from mesophilic, thermophilic and hyperthermophilic organisms. As expected, DeltaCp values tend to be high in mesophiles and low in hyperthermophiles. An increase in TG is accompanied by an up-shift and broadening of the protein stability curves, however, with a large scatter. Furthermore, the simulations reveal that the average DeltaHG increases with TG up to approximately 360 K and becomes constant thereafter. DeltaCp decreases with TG with different rates before and after approximately 360 K. This provides further justification for the separate grouping of proteins into thermophiles and hyperthermophiles to assess their thermodynamic differences. This analysis of the Gibbs-Helmholtz equation has allowed us to study the interdependence of the thermodynamic parameters TG, DeltaHG and DeltaCp and their derivatives in a more rigorous way than possible by the limited experimental protein thermodynamics data available in the literature. The results provide new insights into protein thermostability and suggest potential strategies for its manipulation.

Computer Simulation↗

PubMed2004

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

Animals↗

PubMed2005

The difference between partitioning and distribution from a thermodynamic point of view: NSAIDs as an example.

Solubility and solvation of some NSAIDs were studied in their non-ionic (aqueous buffers of pH 2.0) and ionic molecular form (pH 7.4) over a wide temperature interval. Absolute scale values for the thermodynamic terms (Gibbs energy, enthalpy and entropy) were obtained. Thermodynamic parameters of the transfer of the molecules from one buffer to the other (representing protonation/deprotonation) were derived. It has been found that the thermodynamic characteristics of solvation (hydration) of (+)- and (+/-)-IBP in the buffers show a difference, which is larger than the experimental error. This may be explained by differences in the association states of the molecules in solution. For the other NSAIDs studied, a correlation between the Gibbs energy of transfer, deltaG(tr) (pH 7.4-->pH 2.0) and the pK(a)-value, and a compensation effect between the enthalpic and entropic terms have been revealed. Thermodynamic aspects of the transfer process from the buffers to n-octanol were analysed. The two types of the transfer processes (non-dissociated molecule to octanol (partitioning), and dissociated form to octanol (distribution)) have essentially different driving forces: partitioning is enthalpy driven, whereas the transfer of the ionic form is entropy driven. The following points are discussed: (a) significance of using water-octanol systems (logP as a measure of drug lipophilicity) to describe biological membranes (lipid systems); (b) differences in thermodynamic aspects of the partitioning/distribution processes of these systems; (c) advantages of the present transfer method approach in comparison with temperature dependencies of logP to analyse the driving forces of partitioning/distribution.

1-Octanol↗

PubMed1989

Thermodynamic efficiency of bacterial growth calculated from growth yield of Pseudomonas oxalaticus OX1 in the chemostat.

In order to determine the thermodynamic efficiency of bacterial growth, Pseudomonas oxalaticus OX1 was grown in carbon-limited continuous cultures. 11 different carbon sources, ranging from oxalate (most oxidised component) to ethanol (most reduced component), were used as limiting substrate in these experiments. From the experimental yield values (expressed as C-mol dry weight produced per C-mol carbon substrate consumed) the thermodynamic efficiencies were calculated. On substrates more reduced than biomass (such as ethanol and glycerol) the thermodynamic efficiency of growth of P. oxalaticus was negative but it reached a maximum of 23 +/- 3% with substrates with a degree of reduction of 3 (citrate) and lower. The actual concentrations of the components involved were incorporated into the calculations but this affected the overall thermodynamic efficiency only to a small extent. This result strengthens the conclusion of Westerhoff et al. (Westerhoff, H.V., Hellingwerf, K.J. and Van Dam, K. (1983) Proc. Natl. Acad. Sci. 80, 305-309) that bacteria have been optimised towards a theoretical thermodynamic efficiency of 24%, corresponding with maximisation of growth rate at optimal efficiency, with highly oxidised substrates.

Bicarbonates↗

PubMed2000

Can thermodynamic measurements of receptor binding yield information on drug affinity and efficacy?

The present commentary surveys the methods for obtaining the thermodynamic parameters of the drug-receptor binding equilibrium, DeltaG degrees, DeltaH degrees, DeltaS degrees, and DeltaC degrees (p) (standard free energy, enthalpy, entropy, and heat capacity, respectively). Moreover, it reviews the available thermodynamic data for the binding of agonists and antagonists to several G-protein coupled receptors (GPCRs) and ligand-gated ion channel receptors (LGICRs). In particular, thermodynamic data for five GPCRs (beta-adrenergic, adenosine A(1), adenosine A(2A), dopamine D(2), and 5-HT(1A)) and four LGICRs (glycine, GABA(A), 5-HT(3), and nicotinic) have been collected and analyzed. Among these receptor systems, seven (three GPCRs and all LGICRs) show "thermodynamic agonist-antagonist discrimination": when the agonist binding to a given receptor is entropy-driven, the binding of its antagonist is enthalpy-driven, or vice versa. A scatter plot of all entropy versus enthalpy values of the database gives a regression line with the equation TDeltaS degrees (kJ mol(-1); T = 298.15 K) = 40.3 (+/- 0.7) + 1.00 (+/-0.01) DeltaH degrees (kJ mol(-1)); N = 184; r = 0.981; P < 0.0001 - which is of the form DeltaH degrees = beta. DeltaS degrees, revealing the presence of the "enthalpy-entropy compensation" phenomenon. This means that any decrease of binding enthalpy is compensated for by a parallel decrease of binding entropy, and vice versa, in such a manner that affinity constant values (K(A)) of drug-receptor equilibrium (DeltaG degrees = -RT ln K(A) = DeltaH degrees - TDeltaS degrees ) cannot be greater than 10(11) M(-1). According to the most recent hypotheses concerning drug-receptor interaction mechanisms, these thermodynamic phenomena appear to be a consequence of the rearrangement of solvent molecules that occurs during the binding.

Animals↗

PubMed1996

Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein.

Two complementary aspects of the thermodynamics of the photoactive yellow protein (PYP), a new type of photoreceptor that has been isolated from Ectothiorhodospira halophila, have been investigated. First, the thermal denaturation of PYP at pH 3.4 has been examined by global analysis of the temperature-induced changes in the UV-VIS absorbance spectrum of this chromophoric protein. Subsequently, a thermodynamic model for protein (un)folding processes, incorporating heat capacity changes, has been applied to these data. The second aspect of PYP that has been studied is the temperature dependence of its photocycle kinetics, which have been reported to display an unexplained deviation from normal Arrhenius behavior. We have extended these measurements in two solvents with different hydrophobicities and have analyzed the number of rate constants needed to describe these data. Here we show that the resulting temperature dependence of the rate constants can be quantitatively explained by the application of a thermodynamic model which assumes that heat capacity changes are associated with the two transitions in the photocycle of PYP. This result is the first example of an enzyme catalytic cycle being described by a thermodynamic model including heat capacity changes. It is proposed that a strong link exists between the processes occurring during the photocycle of PYP and protein (un)folding processes. This permits a thermodynamic analysis of the light-induced, physiologically relevant, conformational changes occurring in this photoreceptor protein.

1-Butanol↗

PubMed1996

Understanding the thermodynamic stability of an RNA hairpin and its mutant.

The thermodynamic stability of RNA hairpin loops has been a subject of considerable interest in the recent past (Wimberly et al., 1991). There have been experimental reports indicating that the hairpins with a C(UUCG)G loop sequence are thermodynamically very stable (Wimberly et al., 1991). We used the solution structure of GGAC(UUCG)GUCC (Cheong et al., 1990; Varani et al., 1991) as the starting conformation in our attempt to understand its thermodynamic stability. We carried out molecular dynamics/free energy simulations to understand the basis for the destabilization of the C(UUCG)G loop by mutating cytosine (C7)-->uracil. Because of the limited length of simulation and the presence of kinetic barriers (solvent intervention) to the uracil-->cytosine mutation, all of our computed free energy differences are based on multiple forward simulations. Based on these calculations we find that the cytosine-->uracil mutation in the loop destabilizes it by approximately 1.5kcal/mol relative to that of the reference state, an A-form RNA but with cytosine (C7) looped out. This is the same sign and magnitude as that observed in the thermodynamic studies carried out by Varani et al.(1991). We have carried out free energy component analysis to understand the effect of mutating the cytosine residue to uracil on the thermodynamic stability of the C(UUCG)G hairpin loops. Our calculations show that the most significant contribution to the stability is from the phosphate group linking U5 and U6, which favors the cytosine residue over uracil by about 6.0 kcal/mol. The residues U5, U6, and G8 in the loop region also contribute significantly to the stability. The contributions from the salt and solvent compensate each other, indicating the dynamic nature of interactions of the environment with the nucleic acid system and the coupling between these two components.

Base Sequence↗

PubMed2002

Thermodynamic and kinetic models for the extraction of essential oil from savory and polycyclic aromatic hydrocarbons from soil with hot (subcritical) water and supercritical CO2.

Mechanisms that control the extraction rates of essential oil from savory (Satureja hortensis) and polycyclic aromatic hydrocarbons (PAHs) from historically-contaminated soil with hot water and supercritical carbon dioxide were studied. The extraction curves at different solvent flow-rates were used to determine whether the extractions were limited primarily by the near equilibrium partitioning of the analyte between the matrix and solvent (i.e. partitioning thermodynamics, or the "elution" step) or by the rate of analyte desorption from the matrix (i.e. kinetics, or the "initial desorption" step). Two simple models were applied to describe the extraction profiles obtained with hot water and with supercritical CO2: (1) a model based solely on the thermodynamic distribution coefficient KD, which assumes that analyte desorption from the matrix is rapid compared to elution. and (2) a two-site kinetic model which assumes that the extraction rate is limited by the analyte desorption rate from the matrix, and is not limited by the thermodynamic (KD) partitioning that occurs during elution. For hot water extraction, the thermodynamic elution of analytes from the matrix was the prevailing mechanism as evidenced by the fact that extraction rates increased proportionally with the hot water flow-rate. This was also confirmed by the fact that simple removal calculations based on a single KD (for each essential oil compound) gave good fits to experimental data for flow-rates from 0.25 to 4 ml/min. In contrast, supercritical CO2 extraction showed only minimal dependence on flow-rate, and the simple KD model could only describe the initial 20-50% of the extraction. However, a simple two-site kinetic model gave a good fit for all CO2 flow-rates tested. The results of these investigations demonstrated that very simple models can be used to determine and describe extractions which are limited primarily by partitioning thermodynamics, or primarily by desorption kinetics. Furthermore, these results show that the time required for the recovery of essential oil from savory with hot water can be minimized by increasing flow-rate, with little change in the total volume of water required. In contrast, raising the flow-rate of supercritical CO2 has little effect on the mass of essential oils recovered per unit of time, indicating that optimal recovery of these compounds with supercritical CO2 (amount recovered for the lowest amount of CO2) requires longer extraction times rather than faster flow-rates.

Carbon Dioxide↗

PubMedDate not supplied

Cell motility and thermodynamic fluctuations tailoring quantum mechanics for biology.

Cell motility underlying muscle contraction is an instance of thermodynamics tailoring quantum mechanics for biology. Thermodynamics is intrinsically multi-agential in admitting energy consumers in the form of energy-deficient thermodynamic fluctuations. The onset of sliding movement of an actin filament on myosin molecules in the presence of ATP molecules to be hydrolyzed demonstrates that thermodynamic fluctuations transform their nature so as to accommodate themselves to energy transduction subject to the first law of thermodynamics. The transition from transversal to longitudinal fluctuations of an actin filament with the increase of ATP concentration coincides with the change in the nature of energy consumers acting upon thermal energy in the light of the first law, eventually embodying a uniform sliding movement of an actin filament.

Actins↗

PubMed1999

Thermodynamics in the present progressive mode and its role in the context of the origin of life.

The origin and evolution of biological organizations proceeding on Earth are put in a nonequilibrium thermodynamic framework within a cosmological context. The dynamic process responsible for chemical evolution leading to the origin of biological being depends upon consumer-dominating thermodynamics, in which the heat sink is taken to be active in extracting heat energy from a body at a higher temperature. Consumer-dominating thermodynamics follows from the fact that when a small hot body contacts a cold heat sink, it decreases the temperature at the possible fastest rate. The fastest temperature drop, when applied to chemical products being synthesized through the energy supplied from an external heat source, is selective in keeping only those products that can decrease the temperature at the fastest rate among the available alternatives. Synthesis of small organic molecules in the small ice grains in interstellar diffuse clouds irradiated by ultraviolet radiation is a representative case of consumer-dominating thermodynamics, in which diffuse clouds serve as cold heat sinks in the cosmological context. Another case of consumer-dominating thermodynamics predominant on Earth especially in the perspective of the origin and evolution of life is with submarine hydrothermal vents, in which the surrounding cold seawater constantly serves as the cold heat sink.

Biological Evolution↗

PubMed2003

Microbial surface thermodynamics and applications.

Microbial surface thermodynamics is the reflection of microbial physicochemical and biological characteristics and it bridges micro-scale structures with macro-scale biological functions. Microbial surface thermodynamics is theoretically based on colloid surface thermodynamics using the classical theory of colloidal stability, Derjauin-Landau-Verwey-Overbeek (DLVO) theory. An extended DLVO theory is applied to for the hydration forces not considered in the classical DLVO theory. Herein, a review of current application of microbial surface thermodynamic theory is presented. Microbial surface thermodynamic theory is the fundamental theory in interpreting microbial hydrophilicity or hydrophobicity, microbial attachment, and microbial biofilm development.

Bacteria↗