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PubMed2006

Thermodynamics for single-molecule stretching experiments.

We show how to construct nonequilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a nonequilibrium ensemble of many replicas of the system which can be viewed as a large thermodynamic system, we discuss the validity of nonequilibrium thermodynamics relations and analyze the nature of dissipation in small systems through the entropy production rate. We show in particular that the Gibbs equation, when formulated in terms of average values of the extensive quantities, is still valid, whereas the Gibbs-Duhem equation differs from the equation obtained for large systems due to the lack of the thermodynamic limit. Single-molecule stretching experiments are interpreted under the prism of this theory. The potentials of mean force and mean position, now introduced in these experiments in substitution of the thermodynamic potentials, correspond respectively to our Helmholtz and Gibbs energies. These results show that a thermodynamic formalism can indeed be applied at the single-molecule level.

Journal Article↗
PubMed2005

Thermodynamics in solid mechanics: a commentary.

This commentary on thermodynamics in solid mechanics aims to provide an overview of the main concepts of thermodynamic processes as they apply to, and may be exploited for, studies in nonlinear solid mechanics. We give a descriptive commentary on the (physical) interpretation of these concepts, and relate these where appropriate to behaviour of solids under thermo-mechanical conditions. The motivation is firstly that students of solid mechanics have often had less exposure to thermodynamics than those in other branches of science and engineering, yet there is great value in analytical formulations of material behaviour derived from the principles of thermodynamics. It also sets the contributions in this Theme Issue in context. Along with the deliberately descriptive treatment of thermodynamics, we do outline the main mathematical statements that define the subject, knowing that full details are provided by the authors in their corresponding contributions to this issue. The commentary ends on a lighter note. In order to aid understanding and to stimulate discussion of thermodynamics in solid mechanics, we have invented a number of very basic and completely fictitious materials. These have strange and extreme behaviours that describe certain thermodynamics concepts, such as entropy, in isolation from the complexities of real material behaviour.

Journal Article↗
PubMed2004

Thermodynamics of weight loss diets.

BACKGROUND: It is commonly held that "a calorie is a calorie", i.e. that diets of equal caloric content will result in identical weight change independent of macronutrient composition, and appeal is frequently made to the laws of thermodynamics. We have previously shown that thermodynamics does not support such a view and that diets of different macronutrient content may be expected to induce different changes in body mass. Low carbohydrate diets in particular have claimed a "metabolic advantage" meaning more weight loss than in isocaloric diets of higher carbohydrate content. In this review, for pedagogic clarity, we reframe the theoretical discussion to directly link thermodynamic inefficiency to weight change. The problem in outline: Is metabolic advantage theoretically possible? If so, what biochemical mechanisms might plausibly explain it? Finally, what experimental evidence exists to determine whether it does or does not occur? RESULTS: Reduced thermodynamic efficiency will result in increased weight loss. The laws of thermodynamics are silent on the existence of variable thermodynamic efficiency in metabolic processes. Therefore such variability is permitted and can be related to differences in weight lost. The existence of variable efficiency and metabolic advantage is therefore an empiric question rather than a theoretical one, confirmed by many experimental isocaloric studies, pending a properly performed meta-analysis. Mechanisms are as yet unknown, but plausible mechanisms at the metabolic level are proposed. CONCLUSIONS: Variable thermodynamic efficiency due to dietary manipulation is permitted by physical laws, is supported by much experimental data, and may be reasonably explained by plausible mechanisms.

Journal Article↗
PubMed1998

Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus.

We used isothermal titration calorimetry and fluorescence spectroscopy to investigate the thermodynamics of non-sequence-specific DNA-binding by the Sso7d protein from the archaeon Sulfolobus solfataricus. We report the Sso7d-poly(dGdC) binding thermodynamics as a function of buffer composition (Tris-HCl or phosphate), temperature (15 to 45 degrees C), pH (7.1 to 8.0), osmotic stress and solvent (H2O/2H2O), and compare it to poly (dAdT) binding; and we have previously also reported the salt concentration dependence. Binding isotherms can be represented by the McGhee-von Hippel model for non-cooperative binding, with a binding site size of four to five DNA base-pairs and binding free energies in the range DeltaG degrees approximately -7 to DeltaG degrees approximately -10 kcal mol-1, depending on experimental conditions. The non-specific nature of the binding is reflected in similar thermodynamics for binding to poly(dAdT) and poly(dGdC). The native lysine methylation of Sso7d has only minor effects on the binding thermodynamics. Sso7d binding to poly(dGdC) is endothermic at 25 degrees C with a binding enthalpy DeltaH degrees approximately 10 kcal mol-1 in both phosphate and Tris-HCl buffers at pH 7.6, indicating that DeltaH degrees does not include large contributions from coupled buffer ionization equilibria at this pH. The binding enthalpy is temperature dependent with a measured heat capacity change DeltaCp degrees=-0.25(+/-0.01) kcal mol-1 K-1 and extrapolations of thermodynamic data indicate that the complex is heat stable with exothermic binding close to the growth temperature (75 to 80 degreesC) of S. solfataricus. Addition of neutral solutes (osmotic stress) has minor effects on DeltaG degrees and the exchange of H2O for 2H2O has only a small effect on DeltaH degrees, consistent with the inference that complex formation is not accompanied by net changes in surface hydration. Thus, other mechanisms for the heat capacity change must be found. The observed thermodynamics is discussed in relation to the nature of non-sequence-specific DNA-binding by proteins.

Archaeal Proteins↗
PubMed1999

The application of thermodynamic principles to histochemical and morphometric tissue research: principles and practical outline with focus on the glycosciences.

Physicochemical terms such as entropy or current of entropy are commonly used to refer solely to the description of reactions in the realm of chemistry and physics. Since these thermodynamic terms have a predictive value for the further course of development of such reactions, e.g., extent of a chemical reaction or affinity of molecular interactions, it is tempting to introduce the respective algorithms to biological problems. By combining quantitative morphology with the histochemical visualization of distinct cellular and textural properties such as nuclear DNA contents or intensity of histochemical staining, equations from the general theory of thermodynamics can be adapted. They permit appropriate calculations to be performed which introduce the entropy concept to the processing of the information collected by analysis of structures formed by histochemically labeling cells. The theory of weighted graphs offers the appropriate mathematical tools. Nuclei are defined as vertices. Their DNA contents measured by the integrated optical density or additional cellular features (for example staining intensity of applied immuno-/ligandohistochemical probes) define the associated weights and the minimum spanning tree as a derivative from Voronoi's theorem for the definition of the geometrical neighborhood. This technique is equivalent to syntactic structure analysis as developed by Lu and Fu (1978), Sanfeliu et al. (1981), Kayser and Schlegel (1982), and Kayser (1988). Assuming that the texture of a healthy tissue is displayed in the energetically most efficient and stable manner to perform the required biological functions, i.e., to maintain the lowest level of entropy, deviations from this level are reflected in differences in distances and weights between neighboring nuclei or cells. The measure of textural differences in relation to the normal appearance of an organ or tissue is denoted as structural entropy. Since organisms or their compartments are thermodynamically open systems, they are insufficiently described by the (structural) entropy. This parameter only provides a snapshot, with no information about the status of entropy changes from a directed exchange with the environment. The current of entropy, which is equivalent to the amount of entropy exported or imported through a boundary, is an appropriate measure of the "thermodynamic distance" of the system under consideration from its environment, as is readily appreciated for tumors. A solid tumor is a biological system embedded in another one (healthy tissue). Its current of entropy can be calculated if its boundary and proliferative activity are known. This parameter can be measured by histochemical methods (Ki-67 antibody) or from the cytometric characteristics (percentage of S-phase-related tumor cells), and the boundary can be measured by the volume fraction of the internal vessels and the size of the external surface of the tumor. Since biochemical factors will contribute to the generation and establishment of these structural and thermodynamic features at the level of tissue organization, histochemical studies can uncover the correlation with these parameter alterations. Taking glycohistochemical determinants as an example for this hypothesis, the potential value of combining the results of immuno-/ligandohistochemistry with the data derived from the cytometric or syntactic structure analysis measurements and from the calculations based on thermodynamic theorems is illustrated.

Animals↗
PubMed1989

Thermodynamic analysis of the drug-receptor interaction.

Thermodynamic analysis of pharmacologic data potentially offers an insight into the molecular events underlying drug-receptor interactions not obtainable by other techniques. Embodied in thermodynamics are the laws governing the interconvertibility of heat and work and, hence, it is a particularly apt framework for the analysis of the transduction of information from ligand to biological tissue during the initiation of a drug effect. Implicit in thermodynamic analysis of pharmacologic data is quantitative measurement of the driving forces involved in the drug-receptor interaction (in place of less precise terms such as "affinity"). In addition, the cautious interpretation of thermodynamic analysis can give clues to the underlying mechanisms of the drug-receptor interaction that is beyond the resolving power of other parameters, such as the dissociation constant. The present review is an attempt to identify representative reports that have overtly analyzed pharmacologic data with thermodynamic analysis, to summarize the findings within and across studies (particularly regarding enthalpy- versus entropy-driven binding of agonists and antagonists), to point out and address some apparent inconsistencies that can arise, and to consider the application of thermodynamic analysis to data obtained using isolated tissue preparations.

Animals↗
PubMed2005

Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry.

Analysis of the stoichiometric structure of metabolic networks provides insights into the relationships between structure, function, and regulation of metabolic systems. Based on knowledge of only reaction stoichiometry, certain aspects of network functionality and robustness can be predicted. Current theories focus on breaking a metabolic network down into non-decomposable pathways able to operate in steady state. The physics underlying these theories is based on mass balance and the laws of thermodynamics. However, due to the inherent nonlinearity of the thermodynamic constraints on metabolic fluxes, computational analysis of large-scale biochemical systems can be expensive. In this study, it is shown how the feasible reaction directions may be determined by either computing the allowable ranges under the mass-balance and thermodynamic constraints or by analyzing the stoichiometric structure of the network. The computed reaction directions translate into a set of linear constraints necessary for thermodynamic feasibility. This set of necessary linear constraints is shown to be sufficient to guarantee feasibility in certain cases, thus translating the nonlinear thermodynamic constraints to linear. We show that for a reaction network of 44 internal reactions representing energy metabolism, the computed linear inequality constraints represent necessary and sufficient conditions for thermodynamic feasibility.

Cell Physiological Phenomena↗
PubMed1995

Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex.

As part of an overall program to characterize the impact of mutagenic lesions on the physiochemical properties of DNA, we report here the results of a comparative spectroscopic and calorimetric study on a family of DNA duplexes both with and without the oxidative lesion 2'-deoxy-7-hydro-8-oxoguanosine (8-oxodG). Specifically, we have studied a family of eight 13-mer duplexes of the form [5'-GCGTAC[G* or G]CATGCG-3'].[3'-CGCATG[C, A, T, or G]GTACGC-5'] in which G* is the 8-oxodG lesion. These eight duplexes, which we designate by the identity of the variable central base pair (e.g., G*C), reflect two subsets: four duplexes in which the modified guanine base is positioned opposite each of the four possible canonical residues (G*C, G*A, G*G, G*T) and the corresponding four "control" duplexes in which the guanine is not modified (GC, GA, GG, GT). The data derived from our spectroscopic and calorimetric measurements on these eight duplexes allow us to evaluate the influence of the 8-oxodG lesion, as well as the base opposite the lesion, on the conformation, the thermal and thermodynamic stability, and the melting thermodynamics of the host DNA duplex. We find that modification of dG to 8-oxodG (G*) does not change the global DNA duplex conformation as judged by circular dichroism spectra. Despite this structural similarity, our data reveal that the dG to dG* modification does influence duplex thermal and thermodynamic properties, some of which depend on the base opposite the lesion. Thus, apparent structural identity does not mean that two duplexes necessarily will exhibit equivalent thermal and/or thermodynamic properties. In general, we find that the thermodynamic effects induced by the lesion (e.g., GC vs G*C) or by mismatched base pairs (e.g., GC vs GG) can result in relatively large changes in enthalpy which are partially or wholly compensated entropically to produce relatively modest changes in free energy. Our data also suggest that the biologically observed differential recognition of 8-oxodG duplexes and the preferential nucleotide insertion opposite 8-oxodG residues cannot be rationalized simply in terms of large thermodynamic differences.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1998

Thermodynamics of membrane partitioning for a series of n-alcohols determined by titration calorimetry: role of hydrophobic effects.

Recent studies have shown that the traditional paradigm relying on hydrophobic effects is not adequate to describe membrane partitioning of amphiphilic solutes. To elucidate the thermodynamics and determine the role of the hydrophobic effect in the partitioning of small amphiphilic molecules into lipid bilayers, we have used titration calorimetry to directly measure the enthalpy, partition coefficients, and heat capacity change for the partitioning of a series of n-alcohols into lipid bilayers of several lipid compositions. The incremental thermodynamic quantities have been compared with model compound data for partitioning into bulk hydrocarbon solvents. We have found that there is a large negative heat capacity change upon partitioning, indicating a major contribution from the dehydration of nonpolar solute moieties; however, these hydrophobic effects also involve changes in lipid interactions with water in the interfacial region of the bilayer. In addition, we have found that the enthalpy effects are large, indicating that the partitioning process is accompanied by significant changes in the intralipid interactions within the bilayer. Cholesterol has a large effect on partitioning thermodynamics, making both the enthalpy and entropy contributions significantly more positive, resulting in a relatively small net decrease in the negative free energy of partitioning. These results demonstrate that while hydrophobic interactions play a major role in partitioning, the process is considerably more complex than the partitioning of model compounds between water and bulk hydrocarbons, with major contributions coming from changes in the structure and thermodynamic state of the bilayer, including the interfacial region. The results are discussed in terms of both the thermodynamics of partitioning and the role of lipid properties in membrane function. Our results support a paradigm for membrane structure and function in which the thermodynamic state, which is a function of lipid composition, temperature, and dissolved solutes, is a critical membrane property.

1,2-Dipalmitoylphosphatidylcholine↗
PubMedDate not supplied

New global communication process in thermodynamics: impact on quality of published experimental data.

Thermodynamic data are a key resource in the search for new relationships between properties of chemical systems that constitutes the basis of the scientific discovery process. In addition, thermodynamic information is critical for development and improvement of all chemical process technologies. Historically, peer-reviewed journals are the major source of this information obtained by experimental measurement or prediction. Technological advances in measurement science have propelled enormous growth in the scale of published thermodynamic data (almost doubling every 10 years). This expansion has created new challenges in data validation at all stages of the data delivery process. Despite the peer-review process, problems in data validation have led, in many instances, to publication of data that are grossly erroneous and, at times, inconsistent with the fundamental laws of nature. This article describes a new global data communication process in thermodynamics and its impact in addressing these challenges as well as in streamlining the delivery of the thermodynamic data from "data producers" to "data users". We believe that the prolific growth of scientific data in numerous and diverse fields outside thermodynamics, together with the demonstrated effectiveness and versatility of the process described in this article, will foster development of such processes in other scientific fields.

Chemistry↗
PubMed2003

Dehalogenation potential of municipal waste incineration fly ash. II. Comparison of dehalogenation pathways of fly ash and model fly ash with thermodynamic calculations.

BACKGROUND, AIMS AND SCOPE: In the first part of this paper the main principles which control the dehalogenation of polychlorinated aromatic compounds on municipal waste incineration fly ash (MWI-FA) have been discussed and the model fly ash of similar dehalogenation activity has been proposed. Even if both systems show comparable dehalogenation properties, the main question concerning the postulated identical reaction mechanism in both cases is left unanswered. The other very important point is to what extent is this dechlorination mechanism thermodynamically controlled. The same problem is often discussed in the literature also for the de novo synthetic reactions. From the data it is clear that metallic copper plays a decisive role in the mechanism of the dehalogenation reaction. Although the results reported in the first part strongly support the idea that copper acts in this dechlorination as the reaction component, in contrast to its generally accepted catalytic behaviour, we believed that additional support for this conclusion can be obtained with the help of a thermodynamic interpretation of the mechanism of the reaction. RESULTS AND DISCUSSION: The pathways of hexachlorobenzene dechlorination on MWI-FA and model fly ash were studied in a closed system at 260-300 degrees C under nitrogen atmosphere. These pathways were the same for both systems, with the following prevailing sequences: hexachlorobenzene --> pentachlorobenzene --> 1,2,3,5-tetrachlorobenzene --> 1,3,5-trichlorobenzene --> 1,3-dichlorobenzene. Thermodynamic calculations were carried out by using the method of minimization total Gibbs energy of the whole system. In the calculations, the following reaction components were taken into account: all gaseous chlorinated benzenes, benzene, hydrogen chloride, a gaseous trimer Cu3Cl3, and also Cu2O and CuCl2 as solid components. The effect of the reaction temperature and the amount of copper and water vapour were considered as well. The effect of reaction temperature was determined from the data calculated for the 500 to 750 K temperature region. The effect of the initial composition was determined for the molar amounts of copper = 0.01-3 moles and water vapour = 0.2 to 3 moles per mole of chlorobenzene isomer CONCLUSIONS: The results of hexachlorobenzene dechlorination by MWI-FA and model fly ash under comparable reaction conditions allow us to conclude that both dechlorinations proceed via the same dechlorination pathways, which can be taken as an evidence of the identical dehalogenation mechanism for both systems. The relative percentual distribution of the dehalogenated products depends on the temperature, but not on the initial amount of water vapour or copper metal. On the other hand, the initial amount of copper substantially affects the conversion of the dehalogenation as well as the molar ratio of Cu3Cl3 to HCl in the equilibrium mixture. Comparison of the experimental with thermodynamic results supports the idea that dehalogenation reactions are thermodynamically controlled. RECOMMENDATIONS AND OUTLOOK: Thermodynamic analysis of the dehalogenation reactions may prove useful for a wide range of pollutants. The calculations concerning polychlorinated biphenyls and phenols are under study.

Carbon↗
PubMed2002

Thermal unfolding of soybean peroxidase. Appropriate high denaturant concentrations induce cooperativity allowing the correct measurement of thermodynamic parameters.

We have earlier reported that both guanidine hydrochloride (GdnHCl)-induced and heat-induced unfolding of seed coat soybean peroxidase (SBP), monitored by far UV CD, show single step transition. However, although GdnHCl-induced unfolding follows a two-state pathway, the heat-induced denaturation proceeds through intermediates as indicated by the very low cooperativity of transition. In the former case, analysis of the data based on the two-state model gives true thermodynamic parameters, whereas underestimated values are obtained in the latter case. Available complex equations also cannot be applied for the analysis of the thermal unfolding of SBP due to the absence of separate transitions for the intermediates. In the present study, we report a method to obtain true thermodynamic parameters from thermal transition curves of SBP using the two-state model. When SBP is subjected to thermal unfolding at high GdnHCl concentrations (5.8-6.9 M), cooperative behavior is observed, which allowed the analysis by the two-state model to determine their thermodynamic parameters. We then obtained the thermodynamic parameters in the absence of GdnHCl by extrapolating the graph of linear dependence of DeltaH(m) on T(m) to the T(m) corresponding to 0 m GdnHCl. Another key point for checking the validity of our method was the fact that the unfolded state of SBP generated by either heat or GdnHCl is the same by which we could cross-check our results with that obtained from GdnHCl unfolding. Having obtained the true thermodynamic parameters, we report a detailed thermodynamic study of SBP. Further we address the effect of heme in the thermal unfolding mechanism of SBP.

Circular Dichroism↗
PubMed1980

The thermodynamic-buffer enzymes.

Oxidative phosphorylation operates at optimal efficiency if and only if the condition of conductance matching L33/L11 = square root 1-q2 is fulfilled. In this relation L11 is the phenomenological conductance of phosphorylation, L33 the phenomenological conductance of the load, i.e. the irreversible ATP-utilizing processes in the cell, and q the degree of coupling of oxidative phosphorylation driven by respiration. Since during short time intervals L11 and q are constant whereas L33 fluctuates in the cell, oxidative phosphorylation would only rarely operate at optimal efficiency due to violation of conductance matching. This paper demonstrates that the reversible ATP-utilizing reaction catalyzed by adenylate kinase can effectively compensate deviations from conductance matching in the presence of a fluctuating L33 and hence allows oxidative phosphorylation to operate at optimal efficiency in the cell. Since the adenylate kinase reaction was found to buffer a thermodynamic potential, i.e. the phosphate potential, this finding was generalized to the concept of thermodynamic buffering. The thermodynamic buffering ability of the adenylate kinase reaction was demonstrated by experiments with incubated rat-liver mitochondria. Considerations of changes introduced in the entropy production by the adenylate kinase reaction allowed to establish the theoretical framework for thermodynamic buffering. The ability of thermodynamic buffering to compensate deviations from conductance matching in the presence of fluctuating loads was demonstrated by computer simulations. The possibility of other reversible ATP-utilizing reactions, like the ones catalyzed by creatine kinase and arginine kinase, to contribute to thermodynamic buffering is discussed. Finally, the comparison of the theoretically calculated steady-stae cytosolic adenine nucleotide concentrations with experimental data from perfused livers demonstrated that in livers from fed rats conductance matching is fulfilled on a time average and that the degree of coupling corresponded to qpec = 0.97 permitting the most economic maintenance of a maximal output power of oxidative phosphorylation. For the case of livers from starved rats this analysis suggested that the degree of coupling corresponded to qfec = 0.95, permitting the most economic maintenance of a maximal net rate of ATP synthesis at optimal efficiency of oxidative phosphorylation.

Adenine Nucleotides↗
PubMed1996

Network thermodynamics: analysis and synthesis of membrane transport system.

The bond graph expression of network thermodynamics is a useful tool for modeling of biological systems [1, 8, 9, 13]. Epithelial transport systems, such as frog skin and the acinar cell of the salivary gland, have been modeled and simulated using this tool [8, 9]. However, thermodynamic description of a complex system has been considered difficult [1], and doubt has also been cast on the applicability of network thermodynamics to thermal or entropy relations [2]. In this review, I discussed the thermodynamic basis for network thermodynamics using the availability function and assuming local equilibrium [7]. I also showed the applicability of bond graphs to the analysis of nonisothermal systems which include thermal conduction, thermoosmotic and thermoelectric phenomena [13]. Thus, network thermodynamics is suitable for analysis of more complicated systems and for computer simulation.

Animals↗
PubMed2004

Receptor binding thermodynamics at the neuronal nicotinic receptor.

Simple determination of K(A) or K(D) values makes it possible to calculate the standard free energy DeltaG degrees = -RTlnK(A) = RT lnK(D)(T= 298.15 K) of the binding equilibrium but not that of its two components as defined by the Gibbs equation DeltaG degrees = DeltaH degrees - TDeltaS degrees where DeltaH degrees and DeltaS degrees are the equilibrium standard enthalpy and entropy, respectively. Recently, it has been shown that the relative DeltaH degrees and DeltaS degrees magnitudes can often give a simple "in vitro" way for discriminating "the effect", that is the manner in which the drug interferes with the signal transduction pathways. This particular effect, called "thermodynamic discrimination", results from the fact that binding of antagonists may be enthalpy-driven and that of agonists entropy-driven, or vice-versa. In the past, the thermodynamic discrimination was reported for the beta-adrenergic G-protein-coupled receptor (GPCR) and confirmed later for adenosine A(1), A(2A) and A(3) receptors. Moreover, it has been found that the binding of all ligand-gated ion-channel receptors (LGICR) investigated was thermodynamically discriminated. In particular, affinity constants for typical neuronal nicotinic receptor ligands were obtained by both saturation and inhibition experiments with the radioligand [(3)H]-cytisine, a ganglionic nicotinic agonist. Thermodynamic parameters indicated that agonistic binding was both enthalpy- and entropy-driven, while antagonistic binding was totally entropy-driven. These results have shown that neuronal nicotinic receptor agonists and antagonists were thermodynamically discriminated. On these grounds, the thermodynamic behaviour makes it possible to discriminate drug pharmacological profiles in vivo through binding experiments in vitro.

Animals↗
PubMed2003

Thermodynamics of specific protein-RNA interactions.

Description of the recognition specificity between proteins and nucleic acids at the level of molecular interactions is one of the most challenging tasks in biophysics. It is key to understanding the course and control of gene expression and to the application of the thus acquired knowledge in chemotherapy. This review presents experimental results of thermodynamic studies and a discussion of the role of thermodynamics in formation and stability of functional protein-RNA complexes, with a special attention to the interactions involving mRNA 5' cap and cap-binding proteins in the initiation of protein biosynthesis in the eukaryotic cell. A theoretical framework for analysis of the thermodynamic parameters of protein-nucleic acid association is also briefly surveyed. Overshadowed by more spectacular achievements in structural studies, the thermodynamic investigations are of equal importance for full comprehension of biopolymers' activity in a quantitative way. In this regard, thermodynamics gives a direct insight into the energetic and entropic characteristics of complex macromolecular systems in their natural environment, aqueous solution, and thus complements the structural view derived from X-ray crystallography and multidimensional NMR. Further development of the thermodynamic approach toward interpretation of recognition and binding specificity in terms of molecular biophysics requires more profound contribution from statistical mechanics.

Animals↗
PubMed2003

Simulating structural and thermodynamic properties of carcinogen-damaged DNA.

A pair of stereoisomeric covalent adducts to guanine in double-stranded DNA, derived from the reaction of mutagenic and tumorigenic metabolites of benzo[a]pyrene, have been well characterized structurally and thermodynamically. Both high-resolution NMR solution structures and an array of thermodynamic data are available for these 10S (+)- and 10R (-)-trans-anti -[BP]-N(2)-dG adducts in double-stranded deoxyoligonucleotides. The availability of experimentally well-characterized duplexes containing these two stereoisomeric guanine adducts provides an opportunity for evaluating the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for computing thermodynamic properties from molecular dynamics ensembles. We have carried out 3-ns molecular dynamics simulations, using NMR solution structures as the starting models for the 10S (+)- and 10R (-)-trans-anti-dG adducts in a DNA duplex 11-mer using AMBER 6.0. We employed the MM-PBSA method to compute the free energies, enthalpies, and entropies of the two adducts. Our complete thermodynamic analysis agrees quite well with the full experimental thermodynamic characterization of these adducts, showing essentially equal stabilities of the two adducts. We also calculated the nuclear Overhauser effect (NOE) distances from the molecular dynamics trajectories, and compared them against the experimental NMR-derived NOE distances. Our results showed that the simulated structures are in good agreement with the NMR experimental NOE data. Furthermore, the molecular dynamics simulations provided new structural and biological insights. Specifically, the puzzling observation that the BP aromatic ring system in the 10S (+)-trans-anti-dG adduct is more exposed to the aqueous solvent than the 10R (-)-trans-anti-dG adduct, is rationalized in terms of the adduct structures. The structural and thermodynamic features of these stereoisomeric adducts are also discussed in relation to their reported low susceptibilities to nucleotide excision repair.

Base Sequence↗
PubMed2006

Thermodynamic aspects of ion intercalation in KhFek[Fe(CN)6]l*mH2O compounds: application to the Everit's Salt/Prussian blue transition.

The K(+) reversible processes for ion exchange in K(h)Fe(k)[Fe(CN)(6)](l)*mH(2)O host compounds (Prussian Blue) were thermodynamically analyzed. A thermodynamic approach was established and developed based on the consideration of a lattice-gas model where the electronic contribution to the chemical potential is neglected and the ion-host interaction is not considered. The occupation fraction of the intercalation process was calculated from the kinetic parameters obtained through ac-electrogravimetry in a previous paper. In this way, the mass potential transfer function introduces a new way to evaluate the thermodynamic aspect of intercalation. Finally, based on the thermodynamic approach, the energy used to put each K(+) ion into the host material was calculated. The values were shown to be in good agreement with the values obtained through transient techniques, for example, cyclic voltammetry. As a result, this agreement between theory and experimental data validates the thermodynamic approach considered here, and for the first time, the thermodynamic aspects of insertion were considered for mixed valence materials.

Journal Article↗