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PubMed1999

Antibody variable region binding by Staphylococcal protein A: thermodynamic analysis and location of the Fv binding site on E-domain.

Immunoglobulins of human heavy chain subgroup III have a binding site for Staphylococcal protein A on the heavy chain variable domain (V(H)), in addition to the well-known binding site on the Fc portion of the antibody. Thermodynamic characterization of this binding event and localization of the Fv-binding site on a domain of protein A is described. Isothermal titration calorimetry (ITC) was used to characterize the interaction between protein A or fragments of protein A and variants of the hu4D5 antibody Fab fragment. Analysis of binding isotherms obtained for titration of hu4D5 Fab with intact protein A suggests that 3-4 of the five immunoglobulin binding domains of full length protein A can bind simultaneously to Fab with a Ka of 5.5+/-0.5 x 10(5) M(-1). A synthetic single immunoglobulin binding domain, Z-domain, does not bind appreciably to hu4D5 Fab, but both the E and D domains are functional for hu4D5 Fab binding. Thermodynamic parameters for titration of the E-domain with hu4D5 Fab are n = 1.0+/-0.1, Ka = 2.0+/-0.3 x 10(5) M(-1), and deltaH = -7.1+/-0.4 kcal mol(-1). Similar binding thermodynamics are obtained for titration of the isolated V(H) domain with E-domain indicating that the E-domain binding site on Fab resides within V(H). E-domain binding to an IgG1 Fc yields a higher affinity interaction with thermodynamic parameters n = 2.2+/-0.1, Ka > 1.0 x 10(7) M(-1), and deltaH = -24.6+/-0.6 kcal mol(-1). Fc does not compete with Fab for binding to E-domain indicating that the two antibody fragments bind to different sites. Amide 1H and 15N resonances that undergo large changes in NMR chemical shift upon Fv binding map to a surface defined by helix-2 and helix-3 of E-domain, distinct from the Fc-binding site observed in the crystal structure of the B-domain/Fc complex. The Fv-binding region contains negatively charged residues and a small hydrophobic patch which complements the basic surface of the region of the V(H) domain implicated previously in protein A binding.

Binding Sites↗
PubMed1998

Halogenation of aromatic compounds: thermodynamic, mechanistic and ecological aspects.

Biological halogenation of aromatic compounds implies the generation of reducing equivalents in the form of e.g. NADH. Thermodynamic calculations show that coupling the halogenation step to a step in which the reducing equivalents are oxidized with a potent oxidant such as O2 or N2O makes the halogenation reaction thermodynamically feasible without the input of additional energy in the form of e.g. NADH. In a current model on the halogenation of tryptophan to 7-chloro-L-tryptophan NADH and O2 are proposed as co-substrates in a reaction in which the aromatic compound is oxidized via an epoxide as intermediate. The thermodynamic calculations thus indicate that such a route hinges on mechanistic insights but has no thermodynamic necessity. Furthermore the calculations suggest that halogenation of tryptophan and other aromatic compounds should be possible with N2O, and possibly even with nitrate replacing O2 as the oxidant.

Antifungal Agents↗
PubMed1977

A field and circuit thermodynamics for integrative physiology. I. Introduction to the general notions.

In this first of three articles on a physical basis for integrative physiology, statistical mechanical concepts are developed into a field thermodynamics. The development begins by comparing the different ways change is viewed in biology compared to physics. The Hamiltonian field concept unites the two. The requirements of a thermostatic description are introduced; then those of nonequilibrium thermodynamics are added. Conditions suitable for continuum, near-equilibrium analysis of systems are given; then the role of physical forces in organization is discussed. The development returns to statistical mechanics, and introduces conservation principles and equations of change for ensembles of interacting units. A general notion of systems and thermodynamic engines is discussed next, and a narrative account of the explanatory scope of field thermodynamics is given. Its applications to living systems are the subject of the subsequent two articles of this series.

Biophysical Phenomena↗
PubMed1978

A field and circuit thermodynamics for integrative physiology. II. Power and communicational spectroscopy in biology.

This paper continues the development begun in Part I (15), to show in what way it is meaningful to reduce biological phenomena to physical theory at any level of organization. The appropriate level-independent physics is comprised of thermostatics, thermodynamics of irreversible processes, statistical mechanics, and nonlinear mechanics. Generalized, these approaches lead to a spectroscopic description of the constellation of periodic processes that constitute the living states. The spectroscopic description is here applied also to the inputs received by living systems, from lethal, high-energy, nuclear particles and radiation to low-energy communicational signals that make up languages understandable at the various levels in an hierarchical system. The concept of language is then itself generalized, showing how the empirical relation discovered by Zipf can be derived from a thermodynamic basis. It is demonstrated that certain linguistic and statistical-mechanical distribution functions can be related. Applications of the field thermodynamic approach to two problems in transport phenomena are given in APPENDIX I; applications of field thermodynamics to language and communication are given in APPENDIX II.

Biological Transport↗
PubMed2005

Thermodynamics of phenanthrene partition into solid organic matter from water.

The thermodynamic behavior of organic contaminants in soils is essential to develop remediation technologies and assess risk from alternative technologies. Thermodynamics of phenanthrene partition into four solids(three soils and a bentonite) from water were investigated. The thermodynamics parameters (deltaH, deltaG degrees, deltaS degrees) were calculated according to experimental data. The total sorption heats of phenanthrene to solids from water ranged from -7.93 to -17.1 kJ/mol, which were less exothermic than the condensation heat of phenanthrene-solid (i.e., -18.6 kJ/mol). The partition heats of phenanthrene dissolved into solid organic matter ranged from 23.1 to 32.2 kJ/mol, which were less endothermic than the aqueous dissolved heat of phenanthrene (i.e., 40.2 kJ/mol), and were more endothermic than the fusion heat of phenanthrene-solid (i.e., 18.6 kJ/mol). The standard free energy changes, deltaG degrees, are all negative which suggested that phenanthrene sorption into solid was a spontaneous process. The positive values of standard entropy changes, deltaS degrees, show a gain in entropy for the transfer of phenanthrene at the stated standard state. Due to solubility-enhancement of phenanthrene, the partition coefficients normalized by organic carbon contents decrease with increasing system temperature (i.e., ln Koc = -0.284 ln S + 9.82 (n = 4, r2 = 0.992)). The solubility of phenanthrene in solid organic matter increased with increasing temperatures. Transports of phenanthrene in different latitude locations and seasons would be predicted according to its sorption thermodynamics behavior.

Adsorption↗
PubMedDate not supplied

[Differentiation of cells and organs from the point of view of the second law of thermodynamics and the "protein-machine" concept].

Differentiation of cells and organs arises on the basis of excessiveness at thermodynamically stable process of DNA synthesis as a thermodynamic system with a great relaxation time and alternative number for degrees of freedom. Entropy normalization for DNA is controlled by the exterior effects for DNA causing a thermodynamic unstable (quick) process of protein synthesis. While DNA is interacting with the medium, this process is stabilized not by a priori information which, probably, presupposes this in DNA, but by the ecologic recess inside the cell. The chain of reverse effect assumes transmission of DNA degrees of freedom of controlling effects not only from its neighboring environment, but both from the cell and the organism as a whole. A possibility of accidental occurrence in the natural selection is defined both by the above and the specification of the state equations for DNA which determines relative limitation of variants synthesized with its participation of key reaction groups in proteins. Evolution has no aim, but the principle of filling the ecologic recess creates an apparent expediency that does not differ from the presupposed one. The question--why are the state equations for DNA of this type--ultimately resolves itself into the question why the inner structure of a nucleus is of the kind it exists, i.e., at present it is beyond the possibility of scientific analysis. But with the existing equations of state the leading reason of differentiation for cells and organs is the second thermodynamics principle as tending to maximal chaos limited by the internal and external conditions.

Cell Differentiation↗
PubMed1986

Thermodynamic properties of agonist interactions with the beta adrenergic receptor-coupled adenylate cyclase system. II. Agonist binding to soluble beta adrenergic receptors.

The thermodynamic parameters associated with the interactions of agonists and antagonists with digitonin-solubilized beta adrenergic receptors were determined. A rapid method for measuring the binding of [125I]iodopindolol to soluble receptors using glass-fiber filters was developed. The binding of [125I]iodopindolol, an antagonist with intrinsic sympathomimetic activity, to soluble receptors was temperature-sensitive as is the binding of the ligand to membrane-bound receptors. The interactions of propranolol and timolol with soluble receptors were independent of temperature. In contrast, the binding of agonists to soluble receptors was sensitive to temperature, although insensitive to GTP. Thermodynamically, the interactions of the antagonists timolol and propranolol with soluble beta adrenergic receptors were entropy-driven, with little contribution from changes in enthalpy. This is consistent with a hydrophobic interaction between the receptor and the antagonist. The binding of [125I]iodopindolol was enthalpy-driven. The binding of full agonists with soluble receptors was described thermodynamically by changes in enthalpy and entropy that were negative relative to the values for propranolol and timolol, suggesting that the guanine nucleotide-binding protein required for stimulation of adenylate cyclase activity and an intact lipid environment are not involved in the thermodynamics of formation of the low-affinity component of agonist binding. These results are consistent with an agonist-induced change in the conformation of the receptor.

Adenylyl Cyclases↗
PubMedDate not supplied

[Thermodynamics of the state of a multicomponent CO2-CO-H2O-H2-N2 gas mixture in an electrolyzer with a solid electrolyte].

The thermodynamic state of the gas mixture CO2 = CO = H2O = H2 = N2 in the cathode space of the electrolyzer containing a solid electrolyte is investigated. Calculation of the thermodynamic state makes it possible to determine the theoretical voltage of decomposition and concentration of individual components of this mixture at the outlet of the electrolyzer or each electrolytic cell as applied to various modes of operation. Knowledge of these parameters is important to build a technological scheme of a gas mixture regeneration system. Equations of four independent reactions are used to describe thermodynamic equilibrium reactions are used to describe thermodynamic equilibrium of the gas mixture. Particular cases that occur, when one, two or more conditions of the technological process are not satisfied, are considered.

Carbon Dioxide↗
PubMed1996

[Hierarchical thermodynamics and gerontology].

The phenomenon of ageing of living creatures may be studied in the context of hierarchic thermodynamics. Ageing (ontogenesis) is regarded as a process of formation of the body's submolecular structure. A concept of the degree of ageing (the completion of ontogenesis) which is evaluated from changes in the Gibbs specific function of formation of the submolecular structure of the body's biological tissues is introduced. Quantitative criteria are proposed to find differences between the chronological and thermodynamic age of biological objects. The experimentally based thermodynamic approach reveals the impact of environmental parameters on longevity. The new discipline thermodynamic gerontology which will, in terms of the physical theory, substantially affect human longevity may be hoped to be formed in the coming years.

Aging↗
PubMed1977

A thermodynamic assessment of possible substrates for sulphate-reducing bacteria.

A thermodynamic feasibility study was applied as a means of predicting suitable energy-yielding substrates for growth of sulphate-reducing microorganisms. The average free energy release per electron pair for a substrate-sulphate oxidoreduction may be more or less than the energy requirement for ATP synthesis from ADP and Pi. Substrates were divided into two groups on this thermodynamic basis and the division was shown to accord with previous experimental reports; those substrates which released an average of at least 8-4 kcal per electron pair (35-2 kJ per electron pair) were able to support growth whilst those releasing less than 8-4 kcal were unable to do so. It is proposed that the thermodynamic assessment could be applied to a wide range of possible substrates to predict the likelihood of their serving as sole substrates for growth of these organisms. The literature concerning the use of hydrocarbons by sulphate reducers is confused and indefinite, but inclines toward the idea that use of long-chain hydrocarbons by these organisms is possible. In contrast, however, thermodynamic analysis showed that the highest energy release is from the short-chain alkynes.

Acetylene↗
PubMed1997

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Journal Article↗
PubMed1997

Thermodynamic Studies of the Adsorbed Films and Micelles of Sodium Taurodeoxycholate.

Surface tension of aqueous solutions was measured for sodium taurodeoxycholate, as a typical example of the bile salt compounds, in the temperature range 20 to 35 degreesC at 2.5 degreesC intervals and concentration range 0 to 7 mmol kg-1. We examined thermodynamic quantities obtainable from the surface tension measurements according to the thermodynamic relations given by K. Motomura [J. Colloid Interface Sci. 64, 348 (1978)]. Sodium taurodeoxycholate was strongly adsorbed and formed the saturated adsorbed film at low concentrations. However, the gaseous/expanded phase transition does not take place in the film. The thermodynamic quantities associated with adsorption did not change as markedly at the critical micelle concentration as those observed for typical surfactants. It was suggested that molecular interactions between sodium taurodeoxycholate molecules in aqueous solutions and adsorbed films are too weak to induce critical changes in the thermodynamic quantities. Copyright 1997 Academic Press.

Journal Article↗
PubMed1999

Modeling of Random Formation of Microporous Material Following Thermodynamic Limitations.

The problem of pore formation in limited (small) volume has been considered. General equations describing the system in the continuous (many particles) and discrete (few particles) cases have been obtained. It has been shown that pore formation is not limited by nucleus genesis because of entropic reasons. Kinetic limitation leads to the auto-acceleration-like form of the dependence of the number of empty cells and the internal area functions. The percolation problem has been solved for 2- and 3-dimensional cases with comparison of systems obtained by traditional Monte Carlo and thermodynamic factors. The 3-dimensional situation leads to reduction of the percolation threshold. However, the difference in the values of percolation thresholds estimated by the ordinary Monte Carlo simulation and with thermodynamic limitation is not significant (less than the eventual error). The change of tortuosity was estimated. At the percolation threshold, the tortuosity decreases rapidly, then very slowly with an increase in microporosity, and only at very high microporosity (close to 1) the decrease in tortuosity is again sharp. The influence of the thermodynamic limitation on the regularity of the micropore cluster has been analyzed based on the consideration of behavior of free energy and surface area of the cluster. It has been found that both of these structural parameters significantly decrease if the thermodynamic limitation is imposed. Copyright 1999 Academic Press.

Journal Article↗
PubMed1999

The Electrochemical Thermodynamics for Chemical Reactions in Dispersed Cells.

There is a large specific surface area in a dispersed cell, so much so that there are some notable differences in thermodynamic quantities for a chemical reaction in the cell because of the strong surface effect. The thermodynamic relations between the electromotive force (emf) and the dispersity of a cell and between each of thermodynamic properties and the dispersivity of the cell are derived, and the effects of degree of dispersion of substances in the cell on the emf and the thermodynamic properties are discussed. The results show that the emf, the equilibrium constant, the entropy for reaction, the heat of reaction, and the enthalpy of reaction vary with the dispersivities of the reactants or/and the products in the cell. And two new concepts, surface emf and dispersion cell, are put forward in this paper. Copyright 1999 Academic Press.

Journal Article↗
PubMed1999

The Excess Thermodynamic Quantities of Adsorption of a Binary Nonionic Surfactant Mixture.

The thermodynamic relations were developed for examining the miscibility of surfactants in the adsorbed film from the viewpoints of the thermodynamic quantities of adsorption such as Gibbs free energy, entropy, volume, enthalpy, and energy. The deviation from the additivity relation, the straight line connecting the thermodynamic quantities of the respective pure surfactants as a function of the composition of the adsorbed film, was proved to yield the corresponding excess quantities of adsorption. The criterion of the ideal mixing was offered and summarized with respect to the composition of adsorbed film, the mean area occupied by surfactants, and the thermodynamic quantities of adsorption. The resulting equations were applied to the simple nonionic surfactants mixture of decyl methyl sulfoxide (DeMS) and octyl methyl sulfoxide (OMS). The surface tension of the aqueous solution was measured as a function of not only the total molality and mole fraction of surfactants but also temperature under atmospheric pressure. Copyright 1999 Academic Press.

Journal Article↗
PubMed2000

Thermodynamics of the Laminar Donnan System.

Thermodynamic quantities of a polyelectroyte immersed in salt solution are derived modeling the polyelectrolyte by a sequence of charged parallel flat plates. The starting point for the analysis is the derivation of the Gibbs free enthalpy in its canonic variables pressure (p) and temperature (T), i.e., as a thermodynamic potential. From this, further thermodynamic quantities such as Helmoltz free energy, entropy, internal energy, compressibility, isobar and isochor heat capacities, and expansive force are derived in analytical expressions by differentiation. All these formulas contain the parameter plate surface charge density (sigma) that provides a measure of the discontinuity of the polymer charge distribution that can be used to fit the theory to experimental data. Thermodynamic quantities are also known from the classical Donnan equilibrium that treats the polyelectroyte charge network as a charge continuum. A limiting process is used to perform the transition from the laminar Poisson- Boltzmann model to the continuous Donnan equilibrium. In general, the expressions of the Donnan system are recovered for plate charge density sigma-->0, number of plates Z-->infinity, and sigma Z=constant. Copyright 2000 Academic Press.

Journal Article↗
PubMed2001

Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding.

Site-specific DNA binding of architectural protein integration host factor (IHF) is involved in formation of functional multiprotein-DNA assemblies in Escherichia coli, while non-specific binding of IHF and other histone-like proteins serves to structure the nucleoid. Here, we report an isothermal titration calorimetry study of the thermodynamics of binding IHF to a 34 bp fragment composed entirely of the specific H' site from lambda-phage DNA. At low to moderate [K(+)] (60-100 mM), strong competition is observed between specific and non-specific binding as a result of a low specificity ratio (approximately 10(2)) and a very small non-specific site size. In this [K(+)] range, both specific and non-specific binding are enthalpy-driven, with large negative enthalpy, entropy and heat capacity changes and binding constants that are insensitive to [K(+)]. Above 100 mM K(+), only specific binding is observed, and both the binding constant and the magnitudes of enthalpy, entropy and heat capacity changes all decrease strongly with increasing [K(+)]. When interpreted in the context of the structure of the specific complex, the thermodynamics provide compelling evidence for a previously unrecognized design principle by which proteins that form extensive binding interfaces with nucleic acids control binding constants, binding site sizes and effects of temperature and ion concentrations on stability and specificity. We propose that up to 22 of the 23 IHF cationic side-chains that are located within 6 A of DNA phosphate oxygen atoms in the complex, are masked in the absence of DNA by pairing with anionic carboxylate groups in intramolecular salt-bridges (dehydrated ion-pairs). These salt-bridges increase in stability with increasing temperature and decreasing [K(+)]. To explain the unusual thermodynamics of IHF-DNA interactions, we propose that both specific and non-specific binding at low [K(+)] require disruption of salt-bridges (as many as 18 for specific binding) whereupon many of the unmasked charged groups hydrate and the cationic groups interact with DNA. From structural or thermodynamic parallels with IHF, we propose that large-scale coupling of disruption of protein salt-bridges to DNA binding is significant for other large-interface DNA wrapping proteins including the nucleosome, lac repressor core tetramer, RNA polymerase core protein, HU and SSB.

Bacterial Proteins↗
PubMed2005

Thermodynamically stable vesicle formation from glycolipid biosurfactant sponge phase.

Thermodynamically stable vesicle (L(alpha1)) formation from glycolipid biosurfactant sponge phase (L(3)) and its mechanism were investigated using a "natural" biocompatible mannosyl-erythritol lipid-A (MEL-A)/L-alpha-dilauroylphosphatidylcholine (DLPC) mixture by varying the composition. The trapping efficiency for calcein and turbidity measurements clearly indicated the existence of three regions: while the trapping efficiencies of the mixed MEL-A/DLPC assemblies at the compositions with X(DLPC)< or =0.1 or X(DLPC)> or =0.8 were almost zero, the mixed assemblies at the compositions with 0.1 or =0.8 were multilamellar vesicles (L(alpha)) with diameter from 2 to 10 microm. Meanwhile, dynamic light scattering (DLS) measurement revealed that the average size of the vesicles at the composition of X(DLPC)=0.3 was 633.2 nm, which is remarkably small compared to other compositions. Moreover, the mixed vesicle solution at the composition of X(DLPC)=0.3 was slightly bluish and turbid and kept its dispersion stability at 25 degrees C for more than 3 months, indicating the formation of a thermodynamically stable vesicle (L(alpha1)). These results exhibited the formation of a thermodynamically stable vesicle (L(alpha1)) with a high dispersibility from the MEL-A/DLPC mixture. The asymmetric distribution of MEL-A and DLPC in the two vesicle monolayers caused by the difference in geometrical structures is very likely to have changed their self-assembled structure from a sponge phase (L(3)) to a thermodynamically stable vesicle (L(alpha1)).

Freeze Fracturing↗