Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

Thermodynamic analysis of a molecular chaperone binding to unfolded protein substrates.

Molecular chaperones are a highly diverse group of proteins that recognize and bind unfolded proteins to facilitate protein folding and prevent nonspecific protein aggregation. The mechanisms by which chaperones bind their protein substrates have been studied for decades. However, there are few reports about the affinity of molecular chaperones for their unfolded protein substrates. Thus, little is known about the relative binding affinities of different chaperones and about the relative binding affinities of chaperones for different unfolded protein substrates. Here we describe the application of SUPREX (stability of unpurified proteins from rates of H-D exchange), an H-D exchange and MALDI-based technique, in studying the binding interaction between the molecular chaperone Hsp33 and four different unfolded protein substrates, including citrate synthase, lactate dehydrogenase, malate dehydrogenase, and aldolase. The results of our studies suggest that the cooperativity of the Hsp33 folding-unfolding reaction increases upon binding with denatured protein substrates. This is consistent with the burial of significant hydrophobic surface area in Hsp33 when it interacts with its substrate proteins. The SUPREX-derived K(d) values for Hsp33 complexes with four different substrates were all found to be within the range of 3-300 nM.

Biomass-derived Oxymethylene Ethers as Diesel Additives: A Thermodynamic Analysis

Conversion of biomass for production of liquid fuels can help in reducing the greenhouse gas (GHG) emissions which are predominantly generated by combustion of fossil fuels. Adding oxymethylene ethers (OMEs) in conventional diesel fuel has the potential to reduce soot formation during the combustion in a diesel engine. OMEs are downstream products of syngas, which can be generated by the gasification of biomass. In this research, a thermodynamic analysis has been conducted through development of data intensive process models of all the unit operations involved in production of OMEs from biomass. Based on the developed model, the key process parameters affecting the OMEs production including equivalence ratio, H2/CO ratio, and extra water flow rate were identified. This was followed by development of an optimal process design for high OMEs production. It was found that for a fluidized bed gasifier with heat capacity of 28 MW, the conditions for highest OMEs production are at an air amount of 317 tonne/day, at H2/CO ratio of 2.1, and without extra water injection. At this level, the total OMEs production is 55 tonne/day (13 tonne/day OME3 and 9 tonne/day OME4). This model would further be used in a techno-economic assessment study of the whole biomass conversion chain to determine the most attractive pathways.

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.