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PubMed2002

Thermodynamics and bioenergetics.

Bioenergetics is concerned with the energy conservation and conversion processes in a living cell, particularly in the inner membrane of the mitochondrion. This review summarizes the role of thermodynamics in understanding the coupling between the chemical reactions and the transport of substances in bioenergetics. Thermodynamics has the advantages of identifying possible pathways, providing a measure of the efficiency of energy conversion, and of the coupling between various processes without requiring a detailed knowledge of the underlying mechanisms. In the last five decades, various new approaches in thermodynamics, non-equilibrium thermodynamics and network thermodynamics have been developed to understand the transport and rate processes in physical and biological systems. For systems not far from equilibrium the theory of linear non-equilibrium thermodynamics is used, while extended non-equilibrium thermodynamics is used for systems far away from equilibrium. All these approaches are based on the irreversible character of flows and forces of an open system. Here, linear non-equilibrium thermodynamics is mostly discussed as it is the most advanced. We also review attempts to incorporate the mechanisms of a process into some formulations of non-equilibrium thermodynamics. The formulation of linear non-equilibrium thermodynamics for facilitated transport and active transport, which represent the key processes of coupled phenomena of transport and chemical reactions, is also presented. The purpose of this review is to present an overview of the application of non-equilibrium thermodynamics to bioenergetics, and introduce the basic methods and equations that are used. However, the reader will have to consult the literature reference to see the details of the specific applications.

Animals↗
PubMedDate not supplied

Thermodynamic databases for proteins and protein-nucleic acid interactions.

Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.

DNA↗
PubMed2003

Calculation of thermodynamic properties of species from binding of a ligand by a macromolecule.

In the absence of experimental methods for determining concentrations of species in protein-ligand binding, it is not possible to determine the thermodynamic properties of species directly. However, this article on a simple reaction system shows that measurements of the average number of oxygen molecules bound at various T, pH and concentrations of molecular oxygen can be used to calculate thermodynamic properties of species. The simple system considered has some of the characteristics of the binding of oxygen by hemoglobin, but it has been simplified so that the method for obtaining thermodynamic information can be clarified. A table of standard thermodynamic properties of species is the most efficient way to store thermodynamic information on a reaction system. All the standard further transformed thermodynamic properties at specified T, pH and concentrations of molecular oxygen, all the standard transformed thermodynamic properties at specified T and pH, and all the standard thermodynamic properties of species at a specified temperature can be calculated. These calculations are based on the fact that the mathematical function for the standard further transformed Gibbs energy of the system contains all the thermodynamic information on the system. These properties are all interrelated by Maxwell equations.

Hemoglobins↗
PubMed2001

Network thermodynamics and complexity: a transition to relational systems theory.

Most systems of interest in today's world are highly structured and highly interactive. They cannot be reduced to simple components without losing a great deal of their system identity. Network thermodynamics is a marriage of classical and non-equilibrium thermodynamics along with network theory and kinetics to provide a practical framework for handling these systems. The ultimate result of any network thermodynamic model is still a set of state vector equations. But these equations are built in a new informative way so that information about the organization of the system is identifiable in the structure of the equations. The domain of network thermodynamics is all of physical systems theory. By using the powerful circuit simulator, the Simulation Program with Integrated Circuit Emphasis (SPICE), as a general systems simulator, any highly non-linear stiff system can be simulated. Furthermore, the theoretical findings of network thermodynamics are important new contributions. The contribution of a metric structure to thermodynamics compliments and goes beyond other recent work in this area. The application of topological reasoning through Tellegen's theorem shows that a mathematical structure exists into which all physical systems can be represented canonically. The old results in non-equilibrium thermodynamics due to Onsager can be reinterpreted and extended using these new, more holistic concepts about systems. Some examples are given. These are but a few of the many applications of network thermodynamics that have been proven to extend our capacity for handling the highly interactive, non-linear systems that populate both biology and chemistry. The presentation is carried out in the context of the recent growth of the field of complexity science. In particular, the context used for this discussion derives from the work of the mathematical biologist, Robert Rosen.

Biological Transport↗
PubMed2006

Systematic assignment of thermodynamic constraints in metabolic network models.

BACKGROUND: The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of such models. For this, several computational tools have been developed that particularly assist in identifying and compiling the organism-specific lists of metabolic reactions. In contrast, the last step of the model reconstruction process, which is the definition of the thermodynamic constraints in terms of reaction directionalities, still needs to be done manually. No computational method exists that allows for an automated and systematic assignment of reaction directions in genome-scale models. RESULTS: We present an algorithm that - based on thermodynamics, network topology and heuristic rules - automatically assigns reaction directions in metabolic models such that the reaction network is thermodynamically feasible with respect to the production of energy equivalents. It first exploits all available experimentally derived Gibbs energies of formation to identify irreversible reactions. As these thermodynamic data are not available for all metabolites, in a next step, further reaction directions are assigned on the basis of network topology considerations and thermodynamics-based heuristic rules. Briefly, the algorithm identifies reaction subsets from the metabolic network that are able to convert low-energy co-substrates into their high-energy counterparts and thus net produce energy. Our algorithm aims at disabling such thermodynamically infeasible cyclic operation of reaction subnetworks by assigning reaction directions based on a set of thermodynamics-derived heuristic rules. We demonstrate our algorithm on a genome-scale metabolic model of E. coli. The introduced systematic direction assignment yielded 130 irreversible reactions (out of 920 total reactions), which corresponds to about 70% of all irreversible reactions that are required to disable thermodynamically infeasible energy production. CONCLUSION: Although not being fully comprehensive, our algorithm for systematic reaction direction assignment could define a significant number of irreversible reactions automatically with low computational effort. We envision that the presented algorithm is a valuable part of a computational framework that assists the automated reconstruction of genome-scale metabolic models.

Algorithms↗
PubMed2005

Thermodynamic stability of ecosystems.

The stability of ecosystems during periods of stasis in their macro-evolutionary trajectory is studied from a non-equilibrium thermodynamic perspective. Individuals of the species are considered as units of entropy production and entropy exchange in an open thermodynamic system. Within the framework of the classical theory of irreversible thermodynamics, and under the condition of constant external constraints, such a system will naturally evolve toward a globally stable thermodynamic stationary state. It is thus suggested that the ecological steady state, or stasis, is a particular case of the thermodynamic stationary state, and that the evolution of community stability through natural selection is a manifestation of non-equilibrium thermodynamic directives. Furthermore, it is argued that punctuation of stasis leading to ecosystem succession, may be a manifestation of non-equilibrium "phase transitions" brought on by a change of external constraints through a thermodynamic critical point.

Animals↗
PubMed2003

Relating single-molecule measurements to thermodynamics.

Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and which are allowed to fluctuate. Thus an experiment in which the end-to-end distance of the polymer molecule is fixed and the tension fluctuates yields a different result than an experiment where the force is fixed and the end-to-end distance fluctuates. It is further shown that this difference is due to asymmetry in the distribution of end-to-end distances for a single molecule, and that the difference vanishes in the appropriate thermodynamic limit; that is, as the polymer molecule becomes long compared to its persistence length. Despite these differences, much of the thermodynamic formalism still applies on the single-molecule level if the thermodynamic free energies are replaced with appropriate potentials of mean force. The primary remaining differences are consequences of the fact that unlike the free energies, the potentials of mean force are not in general homogeneous functions of their variables. The basic thermodynamic concepts of an intensive or extensive quantity, and the thermodynamic relationships that follow from them, are therefore less useful for interpreting single-molecule experiments.

Anisotropy↗
PubMed1998

Receptor binding thermodynamics as a tool for linking drug efficacy and affinity.

Determination of drug-receptor binding constants (association, KA, or dissociation, KD = l/KA) by radiochemical specific binding assays has proved to be an invaluable tool for screening of potential active drugs. Simple determination of KA (or KD) values makes it possible, however, to calculate the standard free energy delta G degree = -RTln KA = RTln KD (T = 298.15 K) of the binding equilibrium but not that of its two components as defined by the Gibbs equation delta G degree = delta H degree - T delta S degree, where delta H degree and delta S degree are the equilibrium standard enthalpy and entropy, respectively. This incomplete knowledge is highly inconvenient from a pure thermodynamic point of view as delta H degree and delta S degree carry much information on the details of the drug-receptor interaction and the interplay of both reaction partners with the solvent. In recent times it has been shown that the relative delta H degree and delta S degree 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. The first case of thermodynamic discrimination was reported for the beta-adrenergic G-protein coupled receptor (GPCR) and only recently has it been confirmed for adenosine A1 and A2a receptors. Only very recently has the binding thermodynamics of ligand-gated ion channel receptors (LGICR) been investigated and data for four receptors have been reported showing that all of them are thermodynamically discriminated. While it seems difficult at present to find a reasonable explanation for the thermodynamic discrimination phenomenon in GPCR, some hypotheses can be suggested for LGICR. Since global delta H degree and delta S degree values of the binding process are expected to be heavily affected by rearrangements occurring in the solvent, thermodynamic discrimination in LGICR is at least logically understandable admitting that the observed delta H degree (and then delta S degree) values are determined by both specific binding and abrupt variation of water-accessible receptor surfaces consequent to the setting up of the channel opening.

GTP-Binding Proteins↗
PubMed2006

Thermodynamics-based metabolic flux analysis.

A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to the mass balance constraints typically used in MFA. TMFA produces flux distributions that do not contain any thermodynamically infeasible reactions or pathways, and it provides information about the free energy change of reactions and the range of metabolite activities in addition to reaction fluxes. TMFA is applied to study the thermodynamically feasible ranges for the fluxes and the Gibbs free energy change, Delta(r)G', of the reactions and the activities of the metabolites in the genome-scale metabolic model of Escherichia coli developed by Palsson and co-workers. In the TMFA of the genome scale model, the metabolite activities and reaction Delta(r)G' are able to achieve a wide range of values at optimal growth. The reaction dihydroorotase is identified as a possible thermodynamic bottleneck in E. coli metabolism with a Delta(r)G' constrained close to zero while numerous reactions are identified throughout metabolism for which Delta(r)G' is always highly negative regardless of metabolite concentrations. As it has been proposed previously, these reactions with exclusively negative Delta(r)G' might be candidates for cell regulation, and we find that a significant number of these reactions appear to be the first steps in the linear portion of numerous biosynthesis pathways. The thermodynamically feasible ranges for the concentration ratios ATP/ADP, NAD(P)/NAD(P)H, and H(extracellular)(+)/H(intracellular)(+) are also determined and found to encompass the values observed experimentally in every case. Further, we find that the NAD/NADH and NADP/NADPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively.

Escherichia coli↗
PubMed2003

[Equilibrium thermodynamics of quasi-closed biological systems. Cell differentiation and development of organisms].

The law of temporal hierarchies makes it possible to identify quasi-closed systems in open biological systems and to use the approaches of hierarchical quasi-equilibrium thermodynamics to establish the direction of ontogenesis and evolutionary processes. A short review of the achievements in the field of evolution biological thermodynamics and the thermodynamics of aging are presented. Cell differentiation, the development of multicell organisms, and the emergence of the structures of the higher hierarchies of the biological world are assumed to be determined by the thermodynamic direction of these processes. Cell organisms contain identical genes. Only some of them, however, function in the course of differentiation and development. Gene induction and repression during differentiation are determined by the position of newly emerging cells, whose properties depend on their functional position. These properties are determined by thermodynamic parameters of the cells' environment (thermostat), whose components and physicochemical characteristics affect gene induction and repression. A holographic (three-dimensional) design of the future organism (higher structures of the biological world) is determined by the thermodynamic demand for certain genes. The latter's operation is stimulated by their environment. One of the well-known examples that corroborates the presented model is the change of gene transcription when the nature of lipids and other metabolites contained in cells are changed. Application of the principle of stability of matter to the structures of adjacent hierarchies constitutes additional proof that quasi-equilibrium thermodynamics can be applied to the biological systems of the real world.

Biological Evolution↗
PubMed1978

[Thermodynamics and electrophysiology of the nervous system].

This study expresses a theory designed to associate the fundamental thermodynamic concepts to the electrophysiology of the nervous system. An analogy is drawn between the thermodynamic and electrical events of the myocardial cell during its mechanical phases with those thermodynamic and electrical events of the nerve cell during conduction. Although the myocardial and nerve cells are designed to perform different functions, their processes of membrane potential activation and corresponding directions of thermodynamic and entropy changes are basically the same. A thermodynamic view of nerve cell "active" potential corresponds to a passive downhill process during which the entropy of the system (nerve cell) increases. In contrast, the so called "resting" membrane potential corresponds to an active uphill process. Thus, there is a paradox because the nerve cell is thermodynamically passive during the "active" membrane potential, whereas it is thermodynamically active during the "resting" membrane potential. It is suggested that inhibition in the nervous system may be considered a thermodinamically active process. If the negentropic process fails, the result is the malfunctioning or the final destruction of the system.

Energy Metabolism↗