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At least 1,261 records · Page 70Linked to original sources
PubMed1989

Tissue heating during radiofrequency catheter ablation: a thermodynamic model and observations in isolated perfused and superfused canine right ventricular free wall.

The characteristics of radiofrequency catheter ablation induced injury in the heart are not well characterized. Since the mechanism of injury by radiofrequency energy is thermal, this study was performed to determine the temperature gradient in myocardial tissue during radiofrequency (RF) catheter ablation, and to validate a thermodynamic model derived to describe these observations. Lesions were created by RF heating in an experimental model of isolated perfused and superfused canine right ventricular (RV) free wall. RF power output was adjusted to maintain electrode tip temperature at 80 degrees C for 120 seconds in 151 serial lesions and radial temperature gradients were measured. With increasing distance from the electrode, the temperature of the myocardium decreased in a hyperbolic form that was closely predicted by a derived thermodynamic model (P = 0.0001, r = 0.98). This gradient and resultant lesion sizes were unaffected by the rate of coronary perfusion. The utility of tip temperature monitoring as a predictor of lesion size was tested in 104 serial lesions with tip temperatures that were varied between 50 and 85 degrees C. The tip temperature correlated closely with lesion depth (P = 0.0001, r = 0.92) and width (P = 0.0001, r = 0.88), and was a better predictor of lesion size than measurements of power, current or energy. The temperature at the margin between viable and nonviable tissue was estimated to be 47.9 degrees C. These data demonstrate that during radiofrequency catheter ablation, the radial temperature gradient is predictably hyperbolic and appears to be independent of intramyocardial perfusion if constant electrode temperature is maintained. The use of tip temperature monitoring can accurately predict the ultimate size of radiofrequency-induced lesions.

Animals↗
PubMed1998

Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3.

Using site-directed mutagenesis, x-ray crystallography, microcalorimetric, equilibrium sedimentation and surface plasmon resonance detection techniques, we have examined the structure of an antibody-antigen complex and the structural and thermodynamic consequences of removing specific hydrogen bonds and van der Waals interactions in the antibody-antigen interface. These observations show that the complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody and antigen side chains that form contacts. Alterations in interface solvent structure for two of the mutant complexes appear to compensate for the unfavorable enthalpy changes when antibody-antigen interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. In concert, data from structural studies, reaction rates, calorimetric measurements and site directed mutations are beginning to detail the nature of antibody-protein antigen interactions.

Alanine↗
PubMed2006

Mycobacterium tuberculosis H37Rv ESAT-6-CFP-10 complex formation confers thermodynamic and biochemical stability.

The 6-kDa early secretory antigenic target (ESAT-6) and culture filtrate protein-10 (CFP-10), expressed from the region of deletion-1 (RD1) of Mycobacterium tuberculosis H37Rv, are known to play a key role in virulence. In this study, we explored the thermodynamic and biochemical changes associated with the formation of the 1 : 1 heterodimeric complex between ESAT-6 and CFP-10. Using isothermal titration calorimetry (ITC), we precisely determined the association constant and free energy change for formation of the complex to be 2 x 10(7) M(-1) and -9.95 kcal.mol(-1), respectively. Strikingly, the thermal unfolding of the ESAT-6-CFP-10 heterodimeric complex was completely reversible, with a T(m) of 53.4 degrees C and DeltaH of 69 kcal.mol(-1). Mixing of ESAT-6 and CFP-10 at any temperature below the T(m) of the complex led to induction of helical conformation, suggesting molecular recognition between specific segments of unfolded ESAT-6 and CFP-10. Enhanced biochemical stability of the complex was indicated by protection of ESAT-6 and an N-terminal fragment of CFP-10 from proteolysis with trypsin. However, the flexible C-terminal of CFP-10 in the complex, which has been shown to be responsible for binding to macrophages and monocytes, was cleaved by trypsin. In the presence of phospholipid membranes, ESAT-6, but not CFP-10 and the complex, showed an increase in alpha-helical content and enhanced thermal stability. Overall, complex formation resulted in structural changes, enhanced thermodynamic and biochemical stability, and loss of binding to phospholipid membranes. These features of complex formation probably determine the physiological role of ESAT-6, CFP-10 and/or the complex in vivo. The ITC and thermal unfolding approach described in this study can readily be applied to characterization of the 11 other pairs of ESAT-6 family proteins and for screening ESAT-6 and CFP-10 mutants.

Antigens, Bacterial↗
PubMed1982

Thermodynamic parameters of molecular complexes in aqueous solution: enthalpy-entropy compensation in a series of complexes of caffeine with beta- naphthoxyacetic acid and drug-related aromatic compounds.

Stability constants and thermodynamic parameters have been evaluated for the complexation reaction in aqueous solution of caffeine with beta-naphthoxy acetic acid. The values were higher than those previously reported for the complexation of other ligands with methyl xanthines. In nearly all aromatic ligands complexing with caffeine and theophylline for which data are available, both entropy and free energy of complexation were linearly related to the enthalpy, giving an isoequilibrium relationship. Salicylamide, sodium benzoate and cis-methyl cinnamate exhibited slight deviations on the delta G-delta H plot; the non-aromatic dehydroacetic acid showed the largest deviation. The isoequilibrium relationship was shown to be valid statistically (349-365 K, caffeine systems; 353-372 K, caffeine and theophylline systems) indicating underlying chemical causation. Thermodynamic equations are presented for analysis of the factor involved, which are attributed to a combination of substrate-ligand interactions and solvent effects. The substrate-ligand overlap area is considered as a common parameter through which the solvent and interaction forces might cooperate to give rise to linearity in the isoequilibrium relationship. The increasingly negative experimental values of the enthalpy and entropy with increase in ligand planar overlap area are discussed in relation to the underlying forces involved in the complexation.

Caffeine↗
PubMed1985

Optimization of bioavailability of topical steroids: non-occluded penetration enhancers under thermodynamic control.

The non-occluded vasoconstrictor test under thermodynamic control assessed the effect of penetration enhancers on the topical bioavailability of a model steroid betamethasone 17-benzoate, using aqueous dimethylisosorbide (DMI) as a standard solvent. The aqueous potential penetration enhancers used were at 10% steroid saturation i.e. ideally at identical steroid thermodynamic activity. In the vasoconstrictor test, 2-pyrrolidone, N-methyl-2-pyrrolidone, propylene glycol with oleic acid, propylene glycol with azone and dimethylformamide (DMF) increased the steroid bioavailability compared with that from DMI, while propylene glycol alone produced borderline improvement. Azone and oleic acid in combination with DMI or Betnovate cream did not increase the steroid bioavailability indicating the importance of the correct cosolvent. The pyrrolidones established superior stratum corneum reservoirs compared with DMI, the other vehicles being similar to DMI. It was concluded that excepting DMI, the solvents tested were penetration enhancers for the model steroid betamethasone 17-benzoate and are worthy of further study. However, irritant effects may make some of them unacceptable for clinical use.

Administration, Topical↗
PubMed2004

Thermodynamic nonequilibrium phase change behavior and thermal properties of biological solutions for cryobiology applications.

Understanding the phase change behavior of biomaterials during freezing/thawing including their thermal properties at low temperatures is essential to design and improve cryobiology applications such as cryopreservation and cryosurgery. However, knowledge of phase change behavior and thermal properties of various biomaterials is still incomplete, especially at cryogenic temperatures (< or = -40 degrees C). Moreover, in these applications, chemicals are often added to improve their outcome, which can result in significant variation in the phase change behavior and thermal properties from those of the original biomaterials. These chemical additives include cryoprotective agents (CPAs), antifreeze protein (AFP), or cryosurgical adjuvants like sodium chloride (NaCl). In the present study, phase change behavior and thermal properties of saline solutions--either water-NaCl or phosphate buffered saline (PBS)--with various chemical additives were investigated. The chemical additives studied are glycerol and raffinose as CPAs, an AFP (Type III, molecular weight = 6500), and NaCl as a cryosurgical adjuvant. The phase change behavior was investigated using a differential scanning calorimeter (DSC) and a cryomicroscope. The specific and latent heat of these solutions were also measured with the DSC. The saline solutions have two distinct phase changes--water/ice and eutectic phase changes. During freezing, eutectic solidification of both water-NaCl and PBS are significantly supercooled below their thermodynamic equilibrium eutectic temperatures. However, their melting temperatures are close to thermodynamic equilibrium during thawing. These eutectic phase changes disappear when even a small amount (0.1 M glycerol) of CPA was added, but they are still observed after the addition of an AFP. The specific heats of these solutions are close to that of ice at very low temperatures (< or = -100 degrees C) regardless of the additives, but they increase between -100 degrees C and -30 degrees C with the addition of CPAs. The amount of latent heat, which is evaluated with sample weight, generally decreases with the addition of the additives, but can be normalized to approximately 300 J/g based on the weight of water which participates in the phase change. This illustrates that thermal properties, especially latent heat, of a biomaterial should be evaluated based on the understanding of its phase change behavior. The results of the present study are discussed in the context of the implications for cryobiology applications.

Biomimetic Materials↗
PubMedDate not supplied

Thermodynamics of movable inductively heated seeds for the treatment of brain tumors.

A thermodynamic study is presented of temperature distributions created by an inductively heated 6-mm-diam Ni sphere imbedded in vivo and in vitro into porcine brain tissue. This study was performed in support of the development of a system that creates localized heat-induced lesions in deep-seated brain tumors. In this system, a magnetic "seed" will be remotely repositioned within the brain by an externally produced magnetic field. Convective effects of a hot moving seed will produce a different thermodynamic situation than that arising from an array of static implants. In this work, a study is presented of part of the expected change, in which a static sphere is heated to high temperature. Measurements were made of the temporal and spatial dependence of the temperature rise in the vicinity of the heated sphere, in vivo in four animals and in one that was euthanized immediately prior to experimentation. These results are used for parameter estimation with a theoretical model based on a point source solution to a form of the thermal diffusion equation, i.e., the "bioheat transfer equation." With this model thermal distributions from a power source of arbitrary geometry can be found using appropriate integration methods, and the method has widespread applicability. Estimates of blood flow rates, tissue thermal conductivity, and seed power absorption were found using the parameter estimation algorithm. The estimated blood perfusion exhibits a step increase following the first heating in multiple heating experiments. Thermal conductivity estimated using data from the nonperfused (in vitro) animal is 0.6 W/m degrees C. Seed power absorption is estimated correspondingly to be 0.9 W, a result confirmed independently with calorimetry. Statistical uncertainty is established for the radial decrease of the tissue temperature rise created by this method. This result allows estimation of a cell death boundary uncertainty of 0.6 mm, caused by fluctuations in power delivered to the seed, uncertainty in the temperature probe placements, and thermal properties such as blood perfusion and tissue thermal conductivity.

Animals↗
PubMed1984

Measurement of the acoustic nonlinearity parameter B/A in human tissues by a thermodynamic method.

A thermodynamic method for measuring the acoustic nonlinearity parameter B/A in tissues is presented. It is based on the measurement of change in phase velocity as a function of time as the hydrostatic pressure of the sample is quickly reduced from a known value. This technique circumvents the effect of the attenuation in the medium and does not require a prior knowledge of the thermodynamic parameters of the tissues. The method is used to estimate nonlinearity parameters for normal and malignant tissues in the temperature range 20 degrees to 37 degrees C. The values and the temperature dependence of these parameters are found to vary with the nature of the tissues.

Adipose Tissue↗
PubMed2006

Organic glasses with exceptional thermodynamic and kinetic stability.

Vapor deposition has been used to create glassy materials with extraordinary thermodynamic and kinetic stability and high density. For glasses prepared from indomethacin or 1,3-bis-(1-naphthyl)-5-(2-naphthyl)benzene, stability is optimized when deposition occurs on substrates at a temperature of 50 K below the conventional glass transition temperature. We attribute the substantial improvement in thermodynamic and kinetic properties to enhanced mobility within a few nanometers of the glass surface during deposition. This technique provides an efficient means of producing glassy materials that are low on the energy landscape and could affect technologies such as amorphous pharmaceuticals.

Calorimetry, Differential Scanning↗
PubMed1989

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.

Alanine↗
PubMed2004

Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil.

Propionate is an important intermediate of the degradation of organic matter in many anoxic environments. In methanogenic environments, due to thermodynamic constraints, the oxidation of propionate requires syntrophic cooperation of propionate-fermenting proton-reducing bacteria and H(2)-consuming methanogens. We have identified here microorganisms that were active in syntrophic propionate oxidation in anoxic paddy soil by rRNA-based stable-isotope probing (SIP). After 7 weeks of incubation with [(13)C]propionate (<10 mM) and the oxidation of approximately 30 micromol of (13)C-labeled substrate per g dry weight of soil, we found that archaeal nucleic acids were (13)C labeled to a larger extent than those of the bacterial partners. Nevertheless, both terminal restriction fragment length polymorphism and cloning analyses revealed Syntrophobacter spp., Smithella spp., and the novel Pelotomaculum spp. to predominate in "heavy" (13)C-labeled bacterial rRNA, clearly showing that these were active in situ in syntrophic propionate oxidation. Among the Archaea, mostly Methanobacterium and Methanosarcina spp. and also members of the yet-uncultured "rice cluster I" lineage had incorporated substantial amounts of (13)C label, suggesting that these methanogens were directly involved in syntrophic associations and/or thriving on the [(13)C]acetate released by the syntrophs. With this first application of SIP in an anoxic soil environment, we were able to clearly demonstrate that even guilds of microorganisms growing under thermodynamic constraints, as well as phylogenetically diverse syntrophic associations, can be identified by using SIP. This approach holds great promise for determining the structure and function relationships of further syntrophic or other nutritional associations in natural environments and for defining metabolic functions of yet-uncultivated microorganisms.

Archaea↗
PubMed1985

Thermodynamic characterization of the partially denatured states of ribonuclease A in calcium chloride and lithium chloride.

The denaturations of ribonuclease A by calcium chloride and lithium chloride were studied by circular dichroism measurements in the far-ultraviolet region. The temperature dependence of the equilibrium constant for the unfolding of the protein by calcium chloride and lithium chloride gave values of 46 and 52 kcal mol-1 (1 cal = 4.1868 J) for the enthalpy of denaturation at 25 degrees C and pH 7.0, respectively. Thermodynamic parameters for the denaturation by calcium chloride and lithium chloride are compared with those for the heat and guanidine hydrochloride denaturation. It has been observed that the thermodynamic quantity, be it free energy, entropy, or enthalpy, cannot be related quantitatively to the extent of unfolding measured by various conformational properties of the protein.

Animals↗
PubMed2005

A thermodynamic multiphase scheme treating polymer crystallization and melting.

A comparison of transition and melting temperatures of n-alkanes with experimentally determined ticknesses and melting points of polyethylene lamellae shows that the variation of the thickness with the crystallization temperature virtually agrees with the chain length dependence of the crystalline-mesomorphic phase transition in n-alkanes. Mesomorphic polyethylene layers are stable objects up to the thickness set by this phase transition. The findings lend further support to the view that polymer crystallization generally uses a route which includes a passage via a mesomorphic phase. We construct a thermodynamic scheme dealing with the transitions between melt, mesomorphic layers and lamellar crystallites, assuming for the latter ones that they exist both in an initial "native" and a final "stabilized" form. Application of the scheme in a reconsideration and quantitative evaluation of SAXS and DSC results previously obtained for PE, sPP, iPS and P(epsilonCL) yields the equilibrium transition temperatures between the various phases, latent heats of transition and surface free energies. According to the results the mesomorphic phases are not liquid-like, but have thermodynamic properties which place them truly intermediate between melt and crystals.

Computer Simulation↗
PubMed2005

Stationary cell size distributions and mean protein chain length distributions of Archaea, Bacteria and Eukaryotes described with an increment model in terms of irreversible thermodynamics.

In terms of an increment model irreversible thermodynamics allows to formulate general relations of stationary cell size distributions observed in growing colonies. The treatment is based on the following key postulates: i) The growth dynamics covers a broad spectrum of fast and slow processes. ii) Slow processes are considered to install structural patterns that operate in short periods as temporary stationary states of reference in the sense of irreversible thermodynamics. iii) Distortion during growth is balanced out via the many fast processes until an optimized stationary state is achieved. The relation deduced identifies the numerous different stationary patterns as equivalents, predicting that they should fall on one master curve. Stationary cell size distributions of different cell types, like Hyperphilic archaea, E. coli (Prokaryotes) and S. cerevisiae (Eukaryotes), altogether taken from the literature, are in fact consistently described. As demanded by the model they agree together with the same master curve. Considering the "protein factories" as subsystems of cells the mean protein chain length distributions deduced from completely sequenced genomes should be optimized. In fact, the mean course can be described with analogous relations as used above. Moreover, the master curve fits well to the patterns of different species of Archaea, Bacteria and Eukaryotes. General consequences are discussed.

Archaea↗
PubMed1999

Thermodynamics and kinetics of ligand-protein binding studied with the weighted histogram analysis method and simulated annealing.

The thermodynamics of ligand-protein molecular recognition is investigated by the energy landscape approach for two systems: methotrexate(MTX)--dihydrofolate reductase(DHFR) and biotin-streptavidin. The temperature-dependent binding free energy profile is determined using the weighted histogram analysis method. Two different force fields are employed in this study: a simplified model of ligand-protein interactions and the AMBER force field with a soft core smoothing component, used to soften the repulsive part of the potential. The results of multiple docking simulations are rationalized from the shape of the binding free energy profile that characterizes the thermodynamics of the binding process.

Biotin↗
PubMed1989

Proton production in relativistic heavy ion collisions; comparison with a thermodynamical model.

Experimental results concerning proton production in nuclear collisions, obtained at Saturne with the Diogene 4 pi facility, are compared with the predictions of a thermodynamical model, using collective velocity distributions combined with a statistical thermodynamics in local rest frames. Experimental differential cross sections for alpha + nucleus and Neon + nucleus central collisions at incident energies between 200 and 800 MeV per nucleon are well reproduced by the model, for an angular range 30-110 degrees in the laboratory system. Extracted values of the temperatures are compared with those given by other authors.

Models, Theoretical↗
PubMed1995

Thermodynamics of partly folded intermediates in proteins.

Until recently, the energetics of protein-folding intermediates eluded direct measurement by high-sensitivity microcalorimetric techniques. But during the past year, the direct measurement of thermodynamic parameters for folding intermediates of alpha-lactalbumin, apomyoglobin, cytochrome c, and staphylococcal nuclease has provided new insights on the nature of the forces involved in the stabilization of nascent protein structures. In this review, I summarize those results and discuss the structural implications of the observed thermodynamic behavior.

Algorithms↗
PubMed2004

The thermodynamics of DNA structural motifs.

DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.

Algorithms↗