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At least 1,117 records · Page 62Linked to original sources
PubMed1998

Estimation of cross-bridge stiffness from maximum thermodynamic efficiency.

In muscle, work is performed by myosin cross-bridges during interactions with actin filaments. The amount of work performed during each interaction can be related to the mechanical properties of the cross-bridge; work is the integral of the force produced with respect to the distance that the cross-bridge moves the actin filament, and force is determined by the stiffness of the attached cross-bridge. In this paper, cross-bridge stiffness in frog sartorius muscle was estimated from thermodynamic efficiency (work/free energy change) using a two-state cross-bridge model, assuming constant stiffness over the working range and tight-coupling between cross-bridge cycles and ATP use. This model accurately predicts mechanical efficiency (work/enthalpy output). A critical review of the literature indicates that a realistic value for maximum thermodynamic efficiency of frog sartorius is 0.45 under conditions commonly used in experiments on isolated muscle. Cross-bridge stiffness was estimated for a range of power stroke amplitudes. For realistic amplitudes (10-15 nm), estimated cross-bridge stiffness was between 1 and 2.2 pN nm-1. These values are similar to those estimated from quick-release experiments, taking into account compliance arising from structures other than cross-bridges, but are substantially higher than those from isolated protein studies. The effects on stiffness estimates of relaxing the tight-coupling requirement and of incorporating more force-producing cross-bridge states are also considered.

Actins↗
PubMed2000

A thermodynamic muscle model and a chemical basis for A.V. Hill's muscle equation.

Direct measurements of a relationship between force and actin-myosin biochemistry in muscle suggest that molecular forces in active muscle rapidly equilibrate among. not within, individual myosin crossbridges [Baker et al. (1999) Biophys J 77: 2657 2664]. This observation suggests a thermodynamic model of muscle contraction in which muscle, not an individual myosin crossbridge, is treated as a near-equilibrium system. The general approach can be applied to any ensemble of molecular motors that undergo a physicochemical step against a constant external potential. In this paper we apply the model to a simple two-state crossbridge scheme like that proposed by A.F. Huxley (1957) [Prog Biophys 7: 255 317], and we immediately obtain A.V. Hill's muscle equation. We show that this equation accurately describes steady-state muscle mechanics, biochemistry and energetics. This thermodynamic model provides a novel description of force-dependent actin-myosin kinetics in muscle and provides precise chemical expressions for myosin cooperativity, myosinduty ratios, the number of working strokes per ATP hydrolyzed, muscle efficiency. and energy transfer.

Energy Metabolism↗
PubMed1991

A new predictive equation for the solubility of drugs based on the thermodynamics of mobile disorder.

The thermodynamics of mobile disorder rejects the static model of the quasi-lattice for liquids. Because cause of the perpetual change of neighbors, during the observation time of thermodynamics of the order of seconds, each molecule of a given kind in a solution has experienced the same environment and had at its disposal the same mobile volume. This domain is not localizable and not orientable. Each molecular group perpetually "visits" successively all parts of this domain. The highest entropy is obtained when the groups visit all the parts of the domain without preference. H-bonds are preferential contacts with given sites of the neighbors that cause deviations with respect to such "random" visiting, thereby decreasing the entropy. The quantitative development of these ideas leads to equations describing the effect of solvent-solvent, solute-solvent, and solute-solute hydrogen bonds on the chemical potential of the solute. A universal equation predicting the solubility of drugs in a given solvent is derived. The effect of H-bonds is governed not by "solubility parameters" but by stability constants from which the order of magnitude can be estimated. From the sole knowledge of the solubility of methylparaben in pentane, the method predicts correctly the order of magnitude of its solubility in 26 other solvents, including alcohols and water.

Chemical Phenomena↗
PubMed1991

Nuclear magnetic resonance (NMR) spectroscopic investigation of interaction energies of ephedrine stereoisomers in noncrystalline solids and its correlation with thermodynamic data.

Equations relating the interaction energies of each of the binary mixtures of ephedrine from linear combinations of the energies of the individual isomers are presented. The interaction energies in the noncrystalline solid mixtures measured from NMR chemical shift data using cross-polarization magic angle spinning nuclear magnetic resonance 13C cross-polarization magic angle spinning nuclear magnetic resonance (13CP/MAS NMR) spectroscopy correlate strongly with interaction energy from thermodynamic data. The summation of changes in relative frequencies for structurally equivalent carbons is used as a measure of differences in electron shielding on mixing. The relative direction of polarization of individual stereoisomers is found to affect association in noncrystalline binary mixtures of solids. NMR chemical shift data of solids may be useful in confirming spectroscopically the interactions of stereoisomers observed thermodynamically.

Carbon Isotopes↗
PubMed1988

Thermodynamics in the prediction of the solubilities of binary mixtures of the diastereoisomers and enantiomers of ephedrine.

Equations derived from the Clausius-Clapeyron and Prigogine-Defay equations were used to determine the free energy of mixing for diastereoisomers and enantiomers from heats of fusion and transition temperature data. These equations are applied to the thermodynamics of mixing of the six binary equimolar combinations of (1R,2S)-ephedrine, (1S,2R)-ephedrine; and (1R,2R)- and (1S,2S)-pseudoephedrine isomers. The relative equilibrium solubility of the binary mixtures in water is consistent with thermodynamic calculations.

Chemical Phenomena↗
PubMed1999

Thermodynamic in vitro studies as a method to investigate the pharmacodynamic behavior of adenosine A1 receptor ligands.

PURPOSE: A thermodynamic analysis of the binding to rat cortex adenosine A1 receptor of N6-substituted (full agonists) and N6-substituted-deoxyribose (partial agonists) adenosine derivatives was performed. The intrinsic activity of the compounds was evaluated by measurements of the inhibition of forskolin stimulated 3', 5'-cyclic adenosine monophosphate (c-AMP) levels in isolated epididymal rat adipocytes. METHODS: The thermodynamic parameters deltaG(o) (standard free energy), deltaH(o) (standard enthalpy), and deltaS(o) (standard entropy) of the binding equilibrium were determined by means of affinity measurements carried out at different temperatures (0, 10, 20, 25, 30 degrees C). Levels of c-AMP were evaluated performing competitive protein binding assays. RESULTS: The binding of the ligands increases with temperature enhancement and, as a consequence, is totally entropy driven. Standard entropy values correlate significantly with intrinsic activity ones. CONCLUSIONS: It is proposed the data obtained by these in vitro experiments can be used to investigate the in vivo pharmacodynamic of A, full and partial agonists.

Adenosine↗
PubMed2003

Thermodynamics of solutions I: benzoic acid and acetylsalicylic acid as models for drug substances and the prediction of solubility.

PURPOSE: To investigate the solution process of drug substances (exemplified by benzoic acid. BA. and acetylsalicylic acid, ASA), particularly the interrelation between enthalpic and entropic terms of Gibbs energy, in different solvents. To develop an approach for the estimation of standard solution enthalpies based on a self-consistent thermochemical scale. METHOD: Two independent methods, solubility experiments (concentrations of saturated solutions) and solution calorimetry (standard solution enthalpies) in aliphatic alcohols and individual organic solvents were used. Correlation between the thermodynamic functions in various solvents were analyzed by standard statistical methods. Multiple regression analysis between delta Ho(sol) values and the parameters of the solvents was run on the Koppel-Palm equation. RESULTS: Based on experimental data, a compensation effect between thermodynamic functions was observed. Correlation was found between delta Ho (sol) (BA) and delta Ho(sol) (ASA) [where the delta Ho(sol) (BA)-values were used as a self-consistent thermochemical scale]. Furthermore, delta Ho(sol) correlated with the Koppel-Palm basicity of the solvents. CONCLUSION: The model based on solubility and solution experiments might be useful for the prediction of solubility or solvation of drug substances in different media. The regression equation based on the self-consistent thermochemical scale makes it possible to approximate the ability to solvate a drug substance in comparison with structure-relative substances.

Alcohols↗
PubMedDate not supplied

Nonlinear thermodynamic models of voltage-dependent currents.

Hodgkin and Huxley provided the first quantitative description of voltage-dependent currents and adjusted their model to experimental data using empirical functions of voltage. A physically plausible formalism was proposed later by assuming that transition rates depend exponentially on a free-energy barrier, by analogy with the theory of reaction rates. It was also assumed that the free energy depends linearly on voltage. This thermodynamic formalism can accurately describe many processes, but the resulting time constants can be arbitrarily fast, which may also lead to aberrant behavior. We considered here a physically plausible solution to this problem by including nonlinear effects of the electrical field on the free energy. We show that including effects such as mechanical constraints, inherent to the structure of the ion channel protein, leads to more accurate thermodynamic models. These models can account for voltage-dependent transitions that are rate-limited in a given voltage range, without invoking additional states. We illustrate their applicability to fit experimental data by considering the case of the T-type calcium current in thalamic neurons.

Animals↗
PubMed2000

Kinetic and thermodynamic control of the relative yield of the deamidation of asparagine and isomerization of aspartic acid residues.

Selective deamidation of Asn67 of RNase A to beta-Asp67 and Asp67 residues at neutral pH initially produces greater amounts of the beta-Asp derivative. As the reaction proceeds the relative concentration of [Asp67]-RNase A increases and, at equilibrium, becomes predominant. Such a discrepancy between the kinetic and thermodynamic control on reaction products is discussed in light of information from X-ray three-dimensional analysis and the lower thermodynamic stability of the beta-Asp derivative relative to the parent enzyme.

Animals↗
PubMedDate not supplied

Thermodynamics of the B-Z transition in superhelical DNA.

One of the most exciting events in recent years in molecular biology was the discovery of the left-handed Z form of the DNA double helix. Originally found in linear self-complementary d(GC)x . d(GC)x polymers and oligomers in non-physiological conditions (a rather high salt concentration), it was recently shown to be easily enough adopted in physiological conditions when purine-pyrimidine sequences are inserted into superhelical DNA. From such a system, superhelical DNA carrying an artificial purine-pyrimidine insert, we can obtain data allowing the determination of the energy of the junction between the B and Z stretches, Fj, and the free energy change delta FBZ per base pair (bp). We present here a simple thermodynamic consideration of the B-Z transition in such a system. By applying the results to experimental data we have shown that the thermodynamic parameters for both sequences studied so far (d(GC)x . d(GC)x and d(GT)x . d(AC)x) are similar and equal to Fj = 4-5 kcal per mol per junction and delta FBZ = 0.5 divided by 0.7 kcal per mol per bp.

Base Sequence↗
PubMed2000

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.

A lattice model with side chains was used to investigate protein folding with computer simulations. In this model, we rigorously demonstrate the existence of a specific folding nucleus. This nucleus contains specific interactions not present in the native state that, when weakened, slow folding but do not change protein stability. Such a decoupling of folding kinetics from thermodynamics has been observed experimentally for real proteins. From our results, we conclude that specific non-native interactions in the transition state would give rise to straight phi-values that are negative or larger than unity. Furthermore, we demonstrate that residue Ile 34 in src SH3, which has been shown to be kinetically, but not thermodynamically, important, is universally conserved in proteins with the SH3 fold. This is a clear example of evolution optimizing the folding rate of a protein independent of its stability and function.

Amino Acid Sequence↗
PubMed2006

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data.

As one of the most recent members of the omics family, large-scale quantitative metabolomics data are currently complementing our systems biology data pool and offer the chance to integrate the metabolite level into the functional analysis of cellular networks. Network-embedded thermodynamic analysis (NET analysis) is presented as a framework for mechanistic and model-based analysis of these data. By coupling the data to an operating metabolic network via the second law of thermodynamics and the metabolites' Gibbs energies of formation, NET analysis allows inferring functional principles from quantitative metabolite data; for example it identifies reactions that are subject to active allosteric or genetic regulation as exemplified with quantitative metabolite data from Escherichia coli and Saccharomyces cerevisiae. Moreover, the optimization framework of NET analysis was demonstrated to be a valuable tool to systematically investigate data sets for consistency, for the extension of sub-omic metabolome data sets and for resolving intracompartmental concentrations from cell-averaged metabolome data. Without requiring any kind of kinetic modeling, NET analysis represents a perfectly scalable and unbiased approach to uncover insights from quantitative metabolome data.

Computational Biology↗
PubMed2006

Childhood obesity: behavioral aberration or biochemical drive? Reinterpreting the First Law of Thermodynamics.

Childhood obesity has become epidemic over the past 30 years. The First Law of Thermodynamics is routinely interpreted to imply that weight gain is secondary to increased caloric intake and/or decreased energy expenditure, two behaviors that have been documented during this interval; nonetheless, lifestyle interventions are notoriously ineffective at promoting weight loss. Obesity is characterized by hyperinsulinemia. Although hyperinsulinemia is usually thought to be secondary to obesity, it can instead be primary, due to autonomic dysfunction. Obesity is also a state of leptin resistance, in which defective leptin signal transduction promotes excess energy intake, to maintain normal energy expenditure. Insulin and leptin share a common central signaling pathway, and it seems that insulin functions as an endogenous leptin antagonist. Suppressing insulin ameliorates leptin resistance, with ensuing reduction of caloric intake, increased spontaneous activity, and improved quality of life. Hyperinsulinemia also interferes with dopamine clearance in the ventral tegmental area and nucleus accumbens, promoting increased food reward. Accordingly, the First Law of Thermodynamics can be reinterpreted, such that the behaviors of increased caloric intake and decreased energy expenditure are secondary to obligate weight gain. This weight gain is driven by the hyperinsulinemic state, through three mechanisms: energy partitioning into adipose tissue; interference with leptin signal transduction; and interference with extinction of the hedonic response to food.

Child↗
PubMed2002

The effect of thermodynamic data on computer model predictions of uranium speciation in natural water systems.

Computer models have found widespread application in order to help elucidate and predict changes in environmental systems. One such application is the prediction of trace metal speciation in aqueous systems. This is achieved by solving a set of non-linear equations involving equilibrium constants for all the components in the system, within mass and charge balance constraints. In this study a comparison of the predicted uranium speciation from two computer programs, WHAM and PHREEQCI, is used to illustrate the effect variations in thermodynamic data can have on the models produced. Using the original thermodynamic data provided with the models, WHAM predicted the UO2(2+) ion as the major species (84%) while PHREEQCI predicted UO2(HPO4)2(2-) as the major species (86%). Substituting uranium data from the Nuclear Energy Agency Thermochemical Database project (NEA-TDB) into both programs produced similar results from each program, with UO2F+ predicted to dominate (68%) in a groundwater sample. Natural water samples often contain humic substances. The possible interaction of such substances with uranium was also modelled. The WHAM program includes a discreet site electrostatic humic substance model, however in order to use the PHREEQCI program to model humic substance interactions, a 'model fulvic acid' dataset was added to the program. These models predicted 85 to 98% uranium-humic substance species at neutral pH. This indicates that humic substances do need to be taken into account when modelling uranium speciation in natural water samples.

Computer Simulation↗
PubMed2005

Coordination properties of 3-functionalized beta-cyclodextrins. Thermodynamic stereoselectivity of copper(II) complexes of the A,B-diamino derivative and its exploitation in LECE.

The bis-amino AB derivative of beta-cyclodextrin on the secondary rim was synthesised and spectroscopically characterised by different techniques. Its binary systems both with protons and copper(II) were thermodynamically characterised by pH-metric potentiometry. In addition the ternary systems with each of the enantiomers of tryptophan and alanine were investigated. A thermodynamic stereoselectivity was observed for the tryptophan enantiomers and this was exploited to separate them by capillary electrophoresis through a ligand exchange mechanism (LECE). LECE separation of racemates of phenylalanine and tyrosine was also obtained.

Binding Sites↗
PubMed2005

Molecular thermodynamics for swelling of a mesoscopic ionomer gel in 1 : 1 salt solutions.

For a microphase-separated diblock copolymer ionic gel swollen in salt solution, a molecular-thermodynamic model is based on the self-consistent field theory in the limit of strongly segregated copolymer subchains. The geometry of microdomains is described using the Milner generic wedge construction neglecting the packing frustration. A geometry-dependent generalized analytical solution for the linearized Poisson-Boltzmann equation is obtained. This generalized solution not only reduces to those known previously for planar, cylindrical and spherical geometries, but is also applicable to saddle-like structures. Thermodynamic functions are expressed analytically for gels of lamellar, bicontinuous, cylindrical and spherical morphologies. Molecules are characterized by chain composition, length, rigidity, degree of ionization, and by effective polymer-polymer and polymer-solvent interaction parameters. The model predicts equilibrium solvent uptakes and the equilibrium microdomain spacing for gels swollen in salt solutions. Results are given for details of the gel structure: distribution of mobile ions and polymer segments, and the electric potential across microdomains. Apart from effects obtained by coupling the classical Flory-Rehner theory with Donnan equilibria, viz. increased swelling with polyelectrolyte charge and shrinking of gel upon addition of salt, the model predicts the effects of microphase morphology on swelling.

Algorithms↗
PubMed2006

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics.

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.

Computer Simulation↗
PubMed1974

The hybridization of glyceraldehyde 3-phosphate dehydrogenases from rabbit muscle and yeast. Kinetics and thermodynamics of the reaction and isolation of the hybrid.

A kinetic and thermodynamic study was made of the formation of the hybrid (R(2)Y(2)) glyceraldehyde 3-phosphate dehydrogenase from the yeast (Y(4)) and rabbit (R(4)) enzymes. The values of the thermodynamic parameters for the equilibrium between R(4), Y(4) and R(2)Y(2) suggest that the R(2)-R(2) and Y(2)-Y(2) interactions are similar. However, the failure to observe the RY(3) and R(3)Y hybrids is interpreted in terms of differences at the interfaces of the R-R and Y-Y interactions (the glyceraldehyde 3-phosphate dehydrogenase molecule being regarded as a dimer of dimers). The kinetics of formation of the R(2)Y(2) hybrid were studied and a model was proposed to account for the results. Best-fit values for the rate constants of the individual steps were evaluated by computer simulation, and the rate-limiting steps were identified as the dissociation of tetramers to dimers. It is proposed that the cleavage plane for dissociation of the tetramers corresponds to the region of low electron density through the centre of the molecule in the X-ray-crystallographic structure for human glyceraldehyde 3-phosphate dehydrogenase (Watson et al., 1972), which is probably the plane containing the Q and R axes in the lobster enzyme (Buehner et al., 1974). The R(2)Y(2) hybrid was isolated in milligram amounts by ion-exchange chromatography and its rate of reversion to the native enzyme was shown to be consistent with the kinetic model proposed from the hybrid-formation experiments.

Animals↗