Thermodynamic analysis of ferrous ion binding to Escherichia coli ferritin EcFtnA

Iron oxidation in the bacterial ferritin EcFtnA from Escherichia coli shows marked differences from its homologue human H-chain ferritin (HuHF). While the amino acid residues that constitute the dinuclear center in these proteins are highly conserved, EcFtnA has a third iron-binding site (C site) in close proximity to the dinuclear center that is seemingly responsible for these differences. Here, we describe the first thermodynamic study of Fe2+ binding to EcFtnA and its variants to determine the location of the primary ferrous ion-binding sites on the protein and to better understand the role of the third C site in iron binding. Isothermal titration calorimetric analyses of the wild-type protein reveal the presence of two main classes of binding sites in the pH range of 6.5-7.5, ascribed to Fe2+ binding, first at the A and then the B sites. Site-directed mutagenesis of ligands in the A, B, or C sites affects the apparent Fe2+-binding stoichiometries at the unaltered sites. The data imply some degree of inter- and intrasubunit negative cooperative interaction between sites. Unlike HuHF where only the A site initially binds Fe2+, both A and B sites in EcFtnA bind Fe2+, implying a role for the C site in influencing the binding of Fe2+ at the B site of the di-iron center of EcFtnA. The ITC equations describing a binding model for three classes of independent binding sites are reported here for the first time.

Thermodynamic analysis of snowball Earth hysteresis experiment: Efficiency, entropy production and irreversibility

We present an extensive thermodynamic analysis of a hysteresis experiment performed on a simplified yet Earth-like climate model. We slowly vary the solar constant by 20% around the present value and detect that for a large range of values of the solar constant the realization of snowball or of regular climate conditions depends on the history of the system. Using recent results on the global climate thermodynamics, we show that the two regimes feature radically different properties. The efficiency of the climate machine monotonically increases with decreasing solar constant in present climate conditions, whereas the opposite takes place in snowball conditions. Instead, entropy production is monotonically increasing with the solar constant in both branches of climate conditions, and its value is about four times larger in the warm branch than in the corresponding cold state. Finally, the degree of irreversibility of the system, measured as the fraction of excess entropy production due to irreversible heat transport processes, is much higher in the warm climate conditions, with an explosive growth in the upper range of the considered values of solar constants. Whereas in the cold climate regime a dominating role is played by changes in the meridional albedo contrast, in the warm climate regime changes in the intensity of latent heat fluxes are crucial for determining the observed properties. This substantiates the importance of addressing correctly the variations of the hydrological cycle in a changing climate. An interpretation of the climate transitions at the tipping points based upon macro-scale thermodynamic properties is also proposed. Our results support the adoption of a new generation of diagnostic tools based on the second law of thermodynamics for auditing climate models and outline a set of parametrizations to be used in conceptual and intermediate-complexity models or for the reconstruction of the past climate conditions. Copyright © 2010 Royal Meteorological Society

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Thermodynamic analysis of direct steam reforming of ethanol in molten carbonate fuel cell

Fuel cell as molten carbonate fuel cell (MCFC) operates at high temperatures. Thus, cogeneration processes may be performed, generating heat for its own process or for other purposes of steam generation in the industry. The use of ethanol is one of the best options because this is a renewable and less environmentally offensive fuel, and is cheaper than oil-derived hydrocarbons, as in the case of Brazil. In that country, because of technical, environmental, and economic advantages, the use of ethanol by steam reforming process has been the most investigated process. The objective of this study is to show a thermodynamic analysis of steam reforming of ethanol, to determine the best thermodynamic conditions where the highest volumes of products are produced, making possible a higher production of energy, that is, a more efficient use of resources. To attain this objective, mass and energy balances were performed. Equilibrium constants and advance degrees were calculated to get the best thermodynamic conditions to attain higher reforming efficiency and, hence, higher electric efficiency, using the Nernst equation. The advance degree (according to Castellan 1986, Fundamentos da Fisica/Quimica, Editora LTC, Rio de Janeiro, p. 529, in Portuguese) is a coefficient that indicates the evolution of a reaction, achieving a maximum value when all the reactants' content is used of reforming increases when the operation temperature also increases and when the operation pressure decreases. However, at atmospheric pressure (1 atm), the advance degree tends to stabilize in temperatures above 700 degrees C; that is, the volume of supplemental production of reforming products is very small with respect to high use of energy resources necessary. The use of unused ethanol is also suggested for heating of reactants before reforming. The results show the behavior of MCFC. The current density, at the same tension, is higher at 700 degrees C than other studied temperatures such as 600 and 650 degrees C. This fact occurs due to smaller use of hydrogen at lower temperatures that varies between 46.8% and 58.9% in temperatures between 600 and 700 degrees C. The higher calculated current density is 280 mA/cm(2). The power density increases when the volume of ethanol to be used also increases due to higher production of hydrogen. The highest produced powers at 190 mA/cm(2) are 99.8, 109.8, and 113.7 mW/cm(2) for 873, 923, and 973 K, respectively. The thermodynamic efficiency has the objective to show the connection among operational conditions and energetic factors, which are some parameters that describe a process of internal steam reforming of ethanol.

Thermodynamic analysis of a non linear lattice

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thermodynamic analysis of the cogeneration system expansion in a sugar-alcohol factory

In this work it was performed energetic and exergetic analyses of three thermal plants to assessment a cogeneration system in expansion of a sugar-alcohol factory. The initial configuration considered is constituted by a low pressure steam generator, single stage steam turbines for electricity generation and crusher, shredder and mills with mechanical driving. In the intermediary configuration, the low pressure steam generator was substituted by another which generates steam at higher pressure and higher temperature, the steam turbines for electricity generation were substituted by a multiple stages extraction-condensation turbine and the other steam turbines were maintained. The final configuration consists in the substitution of these last turbines by electrical motors. Thermodynamic analyses were performed to evaluate the equipment and the overall plants efficiencies to permit a comparison among the plants. Besides of this, some important parameters of the sugar-alcohol factories were calculated.

Thermodynamic analysis of direct steam reforming of ethanol in molten carbonate fuel cell

Fuel cell as MCFC (molten carbonate fuel cell) operate at high temperatures, and due to this issue, cogeneration processes may be performed, sending heat for own process or other purposes as steam generation in an industry. The use of ethanol for this purpose is one of the best options because this is a renewable and less environmentally offensive fuel, and cheaper than oil-derived hydrocarbons (in the case of Brazil). In the same country, because of technical, environmental and economic advantages, the use of ethanol by steam reforming process have been the most investigated process. The objective of this study is to show a thermodynamic analysis of steam reforming of ethanol, to determine the best thermodynamic conditions where are produced the highest volumes of products, making possible a higher production of energy, that is, a most-efficient use of resources. To attain this objective, mass and energy balances are performed. Equilibrium constants and advance degrees are calculated to get the best thermodynamic conditions to attain higher reforming efficiency and, hence, higher electric efficiency, using the Nernst equation. The advance degree of reforming increases when the operation temperature also increases and when the operation pressure decreases. But at atmospheric pressure (1 atm), the advance degree tends to the stability in temperatures above 700°C, that is, the volume of supplemental production of reforming products is very small for the high use of energy resources necessary. Reactants and products of the steam-reforming of ethanol that weren't used may be used for the reforming. The use of non-used ethanol is also suggested for heating of reactants before reforming. The results show the behavior of MCFC. The current density, at same tension, is higher at 700°C than other studied temperatures as 600 and 650°C. This fact occurs due to smaller use of hydrogen at lower temperatures that varies between 46.8 and 58.9% in temperatures between 600 and 700°C. The higher calculated current density is 280 mA/cm 2. The power density increases when the volume of ethanol to be used also increases due to higher production of hydrogen. The highest produced power at 190 mW/cm 2 is 99.8, 109.8 and 113.7 mW/cm2 for 873, 923 and 973K, respectively. The thermodynamic efficiency has the objective to show the connection among operational conditions and energetic factors, which are some parameters that describes a process of internal steam reforming of ethanol.

Experimental results and thermodynamic analysis of a natural gas small scale cogeneration plant for power and refrigeration purposes

In this work, experimental results are reported for a small scale cogeneration plant for power and refrigeration purposes. The plant includes a natural gas microturbine and an ammonia/water absorption chiller fired by steam. The system was tested under different turbine loads, steam pressures and chiller outlet temperatures. An evaluation based on the 1st and 2nd Laws of Thermodynamics was also performed. For the ambient temperature around 24°C and microturbine at full load, the plant is able to provide 19 kW of saturated steam at 5.3 bar (161 °C), corresponding to 9.2 kW of refrigeration at -5 °C (COP = 0.44). From a 2nd law point-of-view, it was found that there is an optimal chiller outlet temperature that maximizes the chiller exergetic efficiency. As expected, the microturbine presented the highest irreversibilities, followed by the absorption chiller and the HRSG. In order to reduce the plant exergy destruction, it is recommended a new design for the HRSG and a new insulation for the exhaust pipe. © 2013 Elsevier Ltd. All rights reserved.

Thermodynamic analysis and comparison of downdraft gasifiers integrated with gas turbine, spark and compression ignition engines for distributed power generation

The objective of the present article is to assess and compare the performance of electricity generation systems integrated with downdraft biomass gasifiers for distributed power generation. A model for estimating the electric power generation of internal combustion engines and gas turbines powered by syngas was developed. First, the model determines the syngas composition and the lower heating value; and second, these data are used to evaluate power generation in Otto, Diesel, and Brayton cycles. Four synthesis gas compositions were tested for gasification with: air; pure oxygen; 60% oxygen with 40% steam; and 60% air with 40% steam. The results show a maximum power ratio of 0.567 kWh/Nm(3) for the gas turbine system, 0.647 kWh/Nm(3) for the compression ignition engine, and 0.775 kWh/Nm(3) for the spark-ignition engine while running on synthesis gas which was produced using pure oxygen as gasification agent. When these three systems run on synthesis gas produced using atmospheric air as gasification agent, the maximum power ratios were 0.274 kWh/Nm(3) for the gas turbine system, 0.302 kWh/Nm(3) for CIE, and 0.282 kWh/Nm(3) for SIE. The relationship between power output and synthesis gas flow variations is presented as is the dependence of efficiency on compression ratios. Since the maximum attainable power ratio of CIE is higher than that of SIE for gasification with air, more research should be performed on utilization of synthesis gas in CIE. (C) 2014 Elsevier Ltd. All rights reserved.

Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis

Transthyretin (TTR) is a carrier protein involved in human amyloidosis. The development of small molecules that may act as TTR amyloid inhibitors is a promising strategy to treat these pathologies. Here we selected and characterized the interaction of flavonoids with the wild type and the V30M amyloidogenic mutant TTR. TTR acid aggregation was evaluated in vitro in the presence of the different flavonoids. The best TTR aggregation inhibitors were studied by Isothermal Titration Calorimetry (ITC) in order to reveal their thermodynamic signature of binding to TTRwt. Crystal structures of TTRwt in complex with the top binders were also obtained, enabling us to in depth inspect TTR interactions with these flavonoids. The results indicate that changing the number and position of hydroxyl groups attached to the flavonoid core strongly influence flavonoid recognition by TTR, either by changing ligand affinity or its mechanism of interaction with the two sites of TTR. We also compared the results obtained for ITRwt with the V30M mutant structure in the apo form, allowing us to pinpoint structural features that may facilitate or hamper ligand binding to the V30M mutant. Our data show that the TTRwt binding site is labile and, in particular, the central region of the cavity is sensible for the small differences in the ligands tested and can be influenced by the Met30 amyloidogenic mutation, therefore playing important roles in flavonoid binding affinity, mechanism and mutant protein ligand binding specificities. (C) 2012 Elsevier Inc. All rights reserved.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Thermodynamic Analysis of Rare Earth Chlorination and Bromination Processes

Research funded by the Army Research Laboratory (ARL), the Metallurgical and Materials Engineering Department at Montana Tech investigated various methods of extracting and refining rare earth elements (REEs) from mineral ores and concentrates. Extensive thermodynamic, thermogravimetric and differential thermal analyses were performed to evaluate the relative stabilities of various REE compounds in order to assess potential methods for selective separation and recovery of specific REEs. Conversion of rare earth oxides (REO) to rare earth chlorides or bromides is a possible initial step in pyrometallurgical and hydrometallurgical processing of REEs. REO can be converted to chlorides or bromides by roasting in the presence of a chloridizing or bromidizing reactant. (e.g. NH4Cl and NH4Br).

Scaling laws and thermodynamic analysis for vascular branching of microvessels

When blood flows through small vessels, the two-phase nature of blood as a suspension of red cells (erythrocytes) in plasma cannot be neglected, and with decreasing vessel size, a homogeneous continuum model become less adequate in describing blood flow. Following the Haynes’ marginal zone theory, and viewing the flow as the result of concentric laminae of fluid moving axially, the present work provides models for fluid flow in dichotomous branching composed by larger and smaller vessels, respectively. Expressions for the branching sizes of parent and daughter vessels, that provides easier flow access, are obtained by means of a constrained optimization approach using the Lagrange multipliers. This study shows that when blood behaves as a Newtonian fluid, Hess – Murray law that states that the daughters-to-parent diameter ratio must equal to 2^(-1/3) is valid. However, when the nature of blood as a suspension becomes important, the expression for optimum branching diameters of vessels is dependent on the separation phase lengths. It is also shown that the same effect occurs for the relative lengths of daughters and parent vessels. For smaller vessels (e. g., arterioles and capillaries), it is found that the daughters-to-parent diameter ratio may varies from 0,741 to 0,849, and the daughters-to-parent length ratio varies from 0,260 to 2,42. For larger vessels (e. g., arteries), the daughters-to-parent diameter ratio and the daughters-to-parent length ratio range from 0,458 to 0,819, and from 0,100 to 6,27, respectively. In this paper, it is also demonstrated that the entropy generated when blood behaves as a single phase fluid (i. e., continuum viscous fluid) is greater than the entropy generated when the nature of blood as a suspension becomes important. Another important finding is that the manifestation of the particulate nature of blood in small vessels reduces entropy generation due to fluid friction, thereby maintaining the flow through dichotomous branching vessels at a relatively lower cost.

An air-standard cycle and a thermodynamic perspective on operational limits of Ranque-Hilsh or vortex tubes

A Thermodynamic air-standard cycle was envisaged for Ranque-Hilsh (R-H) or Vortex Tubes to provide relevant Thermodynamic analysis and tools for setting operating limits according to the conservation laws of mass and energy, as well as the constraint of the Second Law of Thermodynamics. The study used an integral or control volume approach and resulted in establishing working equations for evaluating the performance of an R-H tube. The work proved that the coefficient of performance does not depend on the R-H tube operating mode, i.e., the same value is obtained independently if the R-H tube operates either as a heat pump or as a refrigeration device. It was also shown that the isentropic coefficient of performance displays optima values of cold and hot mass fractions for a given operating pressure ratio. Finally, the study was concluded by comparing the present analysis with some experimental data available in the literature for operating pressures ranging 2-11 atm. (C) 2010 Elsevier Ltd and IIR. All rights reserved.