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.

CFD analysis of thermodynamic cycles in a pulse tube refrigerator

The objectives of this paper are to study the thermodynamic cycles in an inertance tube pulse tube refrigerator (ITPTR) by means of CFD method The simulation results show that gas parcels working in different parts of ITPTR undergo different thermodynamic cycles The net effects of those thermodynamic cycles are pumping heat from the low temperature part to the high temperature part of the system The simulation results also show that under different frequencies of piston movement the gas parcels working in the same part of the system will undergo the same type of thermodynamic cycles The simulated thermal cycles are compared with those thermodynamic analysis results from a reference Comparisons show that both CFD simulations and theoretical analysis predict the same type of thermal cycles at the same location However only CFD simulation can give the quantitative results while the thermodynamic analysis is still remaining in quality (C) 2010 Elsevier Ltd All rights reserved

Topography of the combining region of a Thomsen-Friedenreich-antigen-specific lectin jacalin (Artocarpus integrifolia agglutinin). A thermodynamic and circular-dichroism spectroscopic study

Thermodynamic analysis of carbohydrate binding by Artocarpus integrifolia (jackfruit) agglutinin (jacalin) shows that, among monosaccharides, Me alpha GalNAc (methyl-alpha-N-acetylgalactosamine) is the strongest binding ligand. Despite its strong affinity for Me alpha GalNAc and Me alpha Gal, the lectin binds very poorly when Gal and GalNAc are in alpha-linkage with other sugars such as in A- and B-blood-group trisaccharides, Gal alpha 1-3Gal and Gal alpha 1-4Gal. These binding properties are explained by considering the thermodynamic parameters in conjunction with the minimum energy conformations of these sugars. It binds to Gal beta 1-3GalNAc alpha Me with 2800-fold stronger affinity over Gal beta 1-3GalNAc beta Me. It does not bind to asialo-GM1 (monosialoganglioside) oligosaccharide. Moreover, it binds to Gal beta 1-3GalNAc alpha Ser, the authentic T (Thomsen-Friedenreich)-antigen, with about 2.5-fold greater affinity as compared with Gal beta 1-3GalNAc. Asialoglycophorin A was found to be about 169,333 times stronger an inhibitor than Gal beta 1-3GalNAc. The present study thus reveals the exquisite specificity of A. integrifolia lectin for the T-antigen. Appreciable binding of disaccharides Glc beta 1-3GalNAc and GlcNAc beta 1-3Gal and the very poor binding of beta-linked disaccharides, which instead of Gal and GalNAc contain other sugars at the reducing end, underscore the important contribution made by Gal and GalNAc at the reducing end for recognition by the lectin. The ligand-structure-dependent alterations of the c.d. spectrum in the tertiary structural region of the protein allows the placement of various sugar units in the combining region of the lectin. These studies suggest that the primary subsite (subsite A) can accommodate only Gal or GalNAc or alpha-linked Gal or GalNAc, whereas the secondary subsite (subsite B) can associate either with GalNAc beta Me or Gal beta Me. Considering these factors a likely arrangement for various disaccharides in the binding site of the lectin is proposed. Its exquisite specificity for the authentic T-antigen, Gal beta 1-3GalNAc alpha Ser, together with its virtual non-binding to A- and B-blood-group antigens, Gal beta 1-3GalNAc beta Me and asialo-GM1 should make A. integrifolia lectin a valuable probe for monitoring the expression of T-antigen on cell surfaces.

Thermodynamic modeling to analyse composition of carbonaceous coatings of MnO and other oxides of manganese grown by MOCVD

Equilibrium thermodynamic analysis has been applied to the low-pressure MOCVD process using manganese acetylacetonate as the precursor. ``CVD phase stability diagrams'' have been constructed separately for the processes carried out in argon and oxygen ambient, depicting the compositions of the resulting films as functions of CVD parameters. For the process conduced in argon ambient, the analysis predicts the simultaneous deposition of MnO and elemental carbon in 1: 3 molar proportion, over a range of temperatures. The analysis predicts also that, if CVD is carried out in oxygen ambient, even a very low flow of oxygen leads to the complete absence of carbon in the film deposited oxygen, with greater oxygen flow resulting in the simultaneous deposition of two different manganese oxides under certain conditions. The results of thermodynamic modeling have been verified quantitatively for low-pressure CVD conducted in argon ambient. Indeed, the large excess of carbon in the deposit is found to constitute a MnO/C nanocomposite, the associated cauliflower-like morphology making it a promising candidate for electrode material in supercapacitors. CVD carried out in oxygen flow, under specific conditions, leads to the deposition of more than one manganese oxide, as expected from thermodynamic analysis ( and forming an oxide-oxide nanocomposite). These results together demonstrate that thermodynamic analysis of the MOCVD process can be employed to synthesize thin films in a predictive manner, thus avoiding the inefficient trial-and-error method usually associated with MOCVD process development. The prospect of developing thin films of novel compositions and characteristics in a predictive manner, through the appropriate choice of CVD precursors and process conditions, emerges from the present work.

Thermodynamic investigation of the MOCVD of copper films from bis(2,2,6,6-tetramethyl-3,5-heptadionato)copper(II)

Equilibrium concentrations of various condensed and gaseous phases have been thermodynamically calculated, using the free energy minimization criterion, for the metalorganic chemical vapour deposition (MOCVD) of copper films using bis(2,2,6,6-tetramethyl-3,5-heptadionato)copper(II) as the precursor material. From among the many chemical species that may possibly result from the CVD process, only those expected on the basis of mass spectrometric analysis and chemical reasoning to be present at equilibrium, under different CVD conditions, are used in the thermodynamic calculations. The study predicts the deposition of pure, carbon-free copper in the inert atmosphere of argon as well as in the reactive hydrogen atmosphere, over a wide range of substrate temperatures and total reactor pressures. Thin films of copper, grown on SiO2/Si(100) substrates from this metalorganic precursor by low pressure CVD have been characterized by XRD and AES. The experimentally determined composition of CVD-grown copper films is in reasonable agreement with that predicted by thermodynamic analysis.

Exergetic analysis of carbon dioxide vapour compression refrigeration cycle using the new fundamental equation of state

The purpose of this paper is to present exergy charts for carbon dioxide (CO2) based on the new fundamental equation of state and the results of a thermodynamic analysis of conventional and trans-critical vapour compression refrigeration cycles using the data thereof. The calculation scheme is anchored on the Mathematica platform. There exist upper and lower bounds for the high cycle pressure for a given set of evaporating and pre-throttling temperatures. The maximum possible exergetic efficiency for each case was determined. Empirical correlations for exergetic efficiency and COP, valid in the range of temperatures studied here, are obtained. The exergy losses have been quantified. (C) 2003 Elsevier Ltd. All rights reserved.

Thermochemistry of Ionic Liquid-Catalyzed Reactions: Theoretical and Experimental Study of the Beckmann Rearrangement-Kinetic or Thermodynamic Control?

A thermodynamic analysis of the experimental conditions of the Beckmann rearrangement reaction of oximes into amides has been undertaken to examine whether the reaction is under thermodynamic or kinetic control. To answer this question, the thermodynamic properties of the typical Beckmann rearrangement reactions in the ideal gaseous state-cyclohexanone oxime to caprolactam and 2-butanone oxime to N-methylpropanarnide-were studied by using the quantum mechanical method. Gibbs energy and equilibrium constants of the Beckmann rearrangement have been assessed in the gaseous and the liquid phases. Results of the thermodynamic analysis have shown that Beckmann rearrange ments are kinetically controlled. Thus, a search for possible active ionic liquid based catalysts for the mild reaction conditions has been performed.

Physical-chemical and thermodynamic analyses of ethanol steam reforming for hydrogen production

Steam reforming is the most usual method of hydrogen production due to its high production efficiency and technological maturity the use of ethanol for this purpose is an interesting option because it is a renewable and environmentally friendly fuel. The objective of this article is to present the physical-chemical, thermodynamic, and exergetic analysis of a steam reformer of ethanol, in order to produce 0.7 Nm(3)/h of hydrogen as feedstock of a 1 kW PEMFC the global reaction of ethanol is considered. Superheated ethanol reacts with steam at high temperatures producing hydrogen and carbon dioxide, depending strongly on the thermodynamic conditions of reforming, as well as on the technical features of the reformer system and catalysts. The thermodynamic analysis shows the feasibility of this reaction in temperatures about 206 degrees C. Below this temperature, the reaction trends to the reactants. The advance degree increases with temperature and decreases with pressure. Optimal temperatures range between 600 and 700 degrees C. However, when the temperature attains 700 degrees C, the reaction stability occurs, that is, the hydrogen production attains the limit. For temperatures above 700 degrees C, the heat use is very high, involving high costs of production due to the higher volume of fuel or electricity used. The optimal pressure is 1 atm., e.g., at atmospheric pressure. The exergetic analysis shows that the lower irreversibility is attained for lower pressures. However the temperature changes do not affect significantly the irreversibilities. This analysis shows that the best thermodynamic conditions for steam reforming of ethanol are the same conditions suggested in the physical-chemical analysis.

Analysis of the performance of an extraction-condensation steam turbine on a cogeneration system of a Brazilian sugar-alcohol factory

In this work a detailed thermodynamic analysis for an extraction-condensation steam turbine capable to drive a 40 MVA electricity generator in a sugar-alcohol factory was carried out. The use of this turbine in the cogeneration system showed that its efficiency contributed to increase the power generation, although the condensation reduces the overall efficiency of the plant. Sensibility analyses were performed to evaluate the behavior of the overall energy efficiency of a plant with the extraction-condensation turbine in function of the boiler efficiency, the specific consumption of steam in the processes and the condensation rate in the turbine. It was observed that the plant efficiency is very sensible to the condensation rate variation and it increases when there is an increase in the demand of steam for processes.

Study of a hybrid solid oxide fuel cell: Energetic analysis and sankey diagram

In this paper a hybrid solid oxide fuel cell (SOFC) system is analyzed. This system applies a combined cycle utilizing gas turbine associated to a SOFC for rational decentralized energy production. Initially the relative concepts about the fuel cell are presented, followed by some chemical and technical informations such as the change of Gibbs free energy in isothermal fuel oxidation (or combustion) directly into electricity. This represents a very high fraction of the lower heating value (LHV) of a hydrocarbon fuel. In the next step a methodology for the study of SOFC associated with a gas turbine system is developed, considering the electricity and steam production for a hospital, as regard to the Brazilian conditions. This methodology is applied to energetic analysis. Natural gas is considered as a fuel. In conclusion, it is shown by a Sankey Diagram that the hybrid SOFC system may be an excellent opportunity to strengthen the decentralized energy production in Brazil. It is necessary to consider that the cogeneration in this version also is a sensible alternative from the technical point of view, demanding special methods of design, equipment selection and mainly of the contractual deals associated to electricity and fuel supply.

Synthesis and Thermodynamic and Biophysical Properties of Tricyclo-DNA

The DNA analogue tricyclo-DNA, built from conformationally rigid nucleoside analogues that were linked via tertiary phosphodiester functions, can efficiently be synthesized from the corresponding phosphoramidites by conventional solid-phase cyanoethyl phosphoramidite chemistry. 5'-End phosphorylated tricyclo-DNA sequences are chemically stable in aqueous, pH-neutral media at temperatures from 0 to 90 C. Tricyclo-DNA sequences resist enzymatic hydrolysis by the 3'-exonuclease snake venom phosphodiesterase. Homobasic adenine- and thymine-containing tricyclo-DNA octa- and nonamers are extraordinarily stable A-T base-pairing systems, not only in their own series but also with complementary DNA and RNA. Base mismatch formation is strongly destabilized. As in bicyclo-DNA, the tricyclo-DNA purine sequences preferentially accept a complementary strand on the Hoogsteen face of the base. A thermodynamic analysis reveals entropic benefits in the case of hetero-backbone duplex formation (tricyclo-DNA/DNA duplexes) and both an enthalpic and entropic benefit for duplex formation in the pure tricyclo-DNA series compared to natural DNA. Stability of tricyclo-DNA duplex formation depends more strongly on monovalent salt concentration compared to natural DNA. Homopyrimidine DNA sequences containing tricyclothymidine residues form triplexes with complementary double-stranded DNA. Triple-helix stability depends on the sequence composition and can be higher when compared to that of natural DNA. The use of one tricyclothymidine residue in the center of the self-complementary dodecamer duplex (d(CGCGAAT t CGCG), t = tricyclothymidine) strongly stabilizes its monomolecular hairpin loop structure relative to that of the corresponding pure DNA dodecamer ( T m = +20 C), indicating (tetra)loop-stabilizing properties of this rigid nucleoside analogue.

Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding

The T-cell antigen coreceptor CD4 also serves as the receptor for the envelope glycoprotein gp120 of HIV. Extensive mutational analysis of CD4 has implicated residues from a portion of the extracellular amino-terminal domain (D1) in gp120 binding. However, none of these proteins has been fully characterized biophysically, and thus the precise effects on molecular structure and binding interactions are unknown. In the present study, we produced soluble versions of three mutant CD4 molecules (F43V, G47S, and A55F) and characterized their structural properties, thermostability, and ability to bind gp120. Crystallographic and thermodynamic analysis showed minimal structural alterations in the F43V and G47S mutant proteins, which have solvent-exposed mutant side chains. In contrast, some degree of disorder appears to exist in the folded state of A55F, as a result of mutating a buried side chain. Real time kinetic measurements of the interaction of the mutant proteins with gp120 showed affinity decreases of 5-fold for G47S, 50-fold for A55F, and 200-fold for F43V. Although both rate constants for the binding reaction were affected by these mutations, the loss in affinity was mainly due to a decrease in on rates, with less drastic changes occurring in the off rates. These observations suggest the involvement of conformational adaptation in the CD4–gp120 interaction. Together, the structural and kinetic data confirm that F43V is a critical residue in gp120 recognition site, which may also include main chain interactions at residue Gly-47.