Least activation path for protein folding: investigation of staphylococcal nuclease folding by stopped-flow circular dichroism.

Is the pathway of protein folding determined by the relative stability of folding intermediates, or by the relative height of the activation barriers leading to these intermediates? This is a fundamental question for resolving the Levinthal paradox, which stated that protein folding by a random search mechanism would require a time too long to be plausible. To answer this question, we have studied the guanidinium chloride (GdmCl)-induced folding/unfolding of staphylococcal nuclease [(SNase, formerly EC 3.1.4.7; now called microbial nuclease or endonuclease, EC 3.1.31.1] by stopped-flow circular dichroism (CD) and differential scanning microcalorimetry (DSC). The data show that while the equilibrium transition is a quasi-two-state process, kinetics in the 2-ms to 500-s time range are triphasic. Data support the sequential mechanism for SNase folding: U3 <--> U2 <--> U1 <--> N0, where U1, U2, and U3 are substates of the unfolded protein and N0 is the native state. Analysis of the relative population of the U1, U2, and U3 species in 2.0 M GdmCl gives delta-G values for the U3 --> U2 reaction of +0.1 kcal/mol and for the U2 --> U1 reaction of -0.49 kcal/mol. The delta-G value for the U1 --> N0 reaction is calculated to be -4.5 kcal/mol from DSC data. The activation energy, enthalpy, and entropy for each kinetic step are also determined. These results allow us to make the following four conclusions. (i) Although the U1, U2, and U3 states are nearly isoenergetic, no random walk occurs among them during the folding. The pathway of folding is unique and sequential. In other words, the relative stability of the folding intermediates does not dictate the folding pathway. Instead, the folding is a descent toward the global free-energy minimum of the native state via the least activation path in the vast energy landscape. Barrier avoidance leads the way, and barrier height limits the rate. Thus, the Levinthal paradox is not applicable to the protein-folding problem. (ii) The main folding reaction (U1 --> N0), in which the peptide chain acquires most of its free energy (via van der Waals' contacts, hydrogen bonding, and electrostatic interactions), is a highly concerted process. These energy-acquiring events take place in a single kinetic phase. (iii) U1 appears to be a compact unfolded species; the rate of conversion of U2 to U1 depends on the viscosity of solution. (iv) All four relaxation times reported here depend on GdmCl concentrations: it is likely that none involve the cis/trans isomerization of prolines. Finally, a mechanism is presented in which formation of sheet-like chain conformations and a hydrophobic condensation event precede the main-chain folding reaction.

Negative activation enthalpies in the kinetics of protein folding.

Although the rates of chemical reactions become faster with increasing temperature, the converse may be observed with protein-folding reactions. The rate constant for folding initially increases with temperature, goes through a maximum, and then decreases. The activation enthalpy is thus highly temperature dependent because of a large change in specific heat (delta Cp). Such a delta Cp term is usually presumed to be a consequence of a large decrease in exposure of hydrophobic surfaces to water as the reaction proceeds from the denatured state to the transition state for folding: the hydrophobic side chains are surrounded by "icebergs" of water that melt with increasing temperature, thus making a large contribution to the Cp of the denatured state and a smaller one to the more compact transition state. The rate could also be affected by temperature-induced changes in the conformational population of the ground state: the heat required for the progressive melting of residual structure in the denatured state will contribute to delta Cp. By examining two proteins with different refolding mechanisms, we are able to find both of these two processes; barley chymotrypsin inhibitor 2, which refolds from a highly unfolded state, fits well to a hydrophobic interaction model with a constant delta Cp of activation, whereas barnase, which refolds from a more structured denatured state, deviates from this ideal behavior.

Significant discrepancies between van't Hoff and calorimetric enthalpies.

In this paper we show that the usual assumption in studies of the temperature variation of equilibrium constants for equilibria of the form A+B <-->AB that a plot of ln K vs. 1/T (K = equilibrium constant, T = temperature in degrees kelvin) is a straight line with slope equal to -delta HvH/R (delta HvH = van't Hoff or apparent enthalpy, R = gas constant) is not valid in many cases. In all the cases considered here, delta HvH is temperature dependent and is significantly different from the true or calorimetrically measured enthalpy, and the respective values for delta Cp are also significantly different.

Painéis de partículas de saco de cimento e embalagem longa vida aplicados como forro em protótipos de aviários

No presente trabalho, considerou o estudo do potencial de utilização de sacos de cimento e embalagens de longa vida com o intuito de agregar valor a esses resíduos, mediante a fabricação de painéis de partículas para uso como forro em protótipos de galpões avícolas. Para fabricação desse material foi utilizado sacos de cimento descartados nas obras civis, embalagens longa vida residuais e resina poliuretana bicomponente à base de óleo de mamona. O estudo foi dividido em quatro etapas: 1) Caracterização da matéria-prima (sacos de cimento); 2) Efeito da densidade e teor de resina nas propriedades físicas, mecânicas e térmicas de painéis de partículas de saco de cimento; 3) Avaliação do desempenho de embalagens longa vida e verniz como revestimentos dos painéis selecionados na etapa anterior; 4) Determinação do desempenho térmico de protótipos de aviários executados em escala reduzida e distorcida com forro de painel de saco de cimento e embalagem longa vida. Os resultados obtidos indicaram: Em razão do painel com 0,6 g.cm-3 e 12% de resina ter apresentado melhor desempenho nas propriedades investigadas, essa combinação foi selecionada para avaliar o desempenho do material (físicas, mecânicas e térmicas) quando revestido com embalagens longa vida, adotando a testemunha e o verniz como um revestimento comparativo. Dentre os revestimentos avaliados, os painéis com embalagens de longa vida, foram superiores aos revestidos com verniz, quando comparados as suas propriedades físicas, mecânicas e térmicas. Dessa maneira, painéis com 0,6 g.cm-3 e 12% de resina revestidos embalagens longa vida, foram testados como forro quanto ao desempenho térmico (primavera, verão, outono e inverno) em protótipos em escala reduzida e distorcida, mediante a determinação de índices de conforto térmico (Entalpia e IAPfc) para aves de corte. A associação do forro sob o protótipo permitiu reduzir a temperatura interna do ar e dos índices de conforto térmico na primavera, verão e outono, enquanto que no inverno não foi constatado eficácia do material. Dentre as estações estudadas, o verão e a primavera, demonstraram serem as épocas mais críticas para criação de aves corte em instalações avícolas que apresentem características semelhantes aos protótipos experimentais.

Kinetic study of thermal 1,3-dipolar cycloaddition of azomethine ylides using differential scanning calorimetry as monitoring window

Kinetics of 1,3-dipolar cycloaddition involving azomethine ylides, generated from thermal [1,2]-prototropy of the corresponding imino ester, employing differential scanning calorimetry (DSC), is surveyed. Glycine and phenylalanine derived imino esters have different behavior. The first one prefers reacting with itself at 75 ºC, rather than with the dipolarophile. However, the α-substituted imino ester gives the cycloadduct at higher temperatures. The thermal dynamic analysis by 1H NMR of the neat reaction mixture of the glycine derivative reveals the presence of signals corresponding to the dipole in very small proportion. The non-isothermal and isothermal DSC curves of the cycloaddition of phenylalaninate and diisobutyl fumarate are obtained from freshly prepared samples. The application of known kinetic models and mathematical multiple non-linear regressions (NLR) allow to determine and to compare Ea, lnA, reaction orders, and reaction enthalpy. Finally a rate equation for each different temperature can be established for this particular thermal cycloaddition.

Mapping Binary Liquid-Vapor or Liquid-Liquid-Vapor Equilibria Regions, including the Different Azeotropic Behaviours, as a Function of the NRTL Binary Parameters

13th Mediterranean Congress of Chemical Engineering (Sociedad Española de Química Industrial e Ingeniería Química, Fira Barcelona, Expoquimia), Barcelona, September 30-October 3, 2014

Improving some thermodynamic consistency tests for VLE data evaluation

Thermodynamics Conference 2013 (Statistical Mechanics and Thermodynamics Group of the Royal Society of Chemistry), The University of Manchester, 3-6 September 2013.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

The plasticisation effect of glycerol and water on the gelatinisation of wheat starch

In the extrusion manufacture of starch-based thermoplastics, such as biodegradable packaging materials, glycerol is an effective additive as a plasticiser, that is, to diminish the brittle nature of the product and provide the desired extent of flexibility. However, the addition of glycerol may also affect the gelatinisation behaviour of the starch-water mixture, and hence the required processing conditions for producing a homogeneously gelatinised starch-based material. The effect of glycerol on the gelatinisation of wheat starch was studied using differential scanning calorimetry (DSC). Mixtures of starch, water and glycerol were investigated with a water content ranging from 12 - 40% and a glycerol concentration up to 75%. Dependent on composition, the enthalpy of gelatinisation ranged from 1.7 - 12.6 J/g (on a dry starch basis), while the onset and peak temperatures varied from 54 to 86 degreesC and 60 to 90 degreesC, respectively. As expected, water acted as a plasticiser in that the onset temperature for gelatinisation (TO) decreased with increasing moisture content. Glycerol, however, increased To. It is shown that the T-0 of starch-glycerol-water mixtures may be predicted on the basis of the effective moisture content of the starch fraction of these mixtures resulting from the relative speed of moisture absorption by glycerol and starch, respectively. Moisture sorption kinetics of wheat starch and glycerol in 100% relative humidity were determined and used to predict the preferential water absorption by glycerol in starch-glycerol-water mixtures and hence the resulting T-0 of the system.

Glass transition behaviour of fructose

The glass transition temperature and the second transition (the endothermic change between the glass transition and melting temperatures) of fructose were studied. The thermal history strongly affected both transitions of fructose. Storage for 10 days at 22degreesC increased the dynamic glass transition temperature from 16 to 25degreesC and decreased the second transition of fructose from 110 to 98degreesC in the first differential scanning calorimetric (DSC) scan. The amplitude of the second transition increased slightly with storage time and reached 260% of the first transition for vacuum oven dried samples. The effect of thermal history on the glass transition temperature of fructose can be removed by scanning the sample in a DSC to 130degreesC. The effects of water content, glucose and sucrose on the two transitions were also investigated.

Gelatinisation of starch in mixtures of sugars. II. Application of differential scanning calorimetry

Differential scanning calorimetry was used to investigate the effect of mixtures of glucose and fructose, and five types of honeys on starch gelatinisation. At a 1:1 starch:water ratio, glucose generally increased the enthalpy (DeltaH(gel)) and temperatures (T-onset, T-peak and T-end) of gelatinisation more than fructose. Upon mixing, DeltaH(gel) of the low-temperature endotherm decreased in comparison to the sole sugars, but was fairly constant (7.7 +/- 0.33 J/g dry starch). DeltaH(gel) of the high-temperature endotherm increased with the fructose content. For both endotherms, the gelatinisation temperatures were unchanged (CV less than or equal to 3%) for the mixtures. With the honeys (moisture, 14.9-18.0%; fructose, 37.2-44.0%; glucose, 28.3-31.9%) added at 1.1-4.4 g per g dry starch, the enthalpy and temperatures of gelatinisation did not vary significantly (CV less than or equal to 6%). Typical thermograms are presented, and the results are interpreted in the light of the various proposed mechanisms for starch gelatinisation in sugar-water systems, total sugar content and possible sugar-sugar interactions. The thermograms were broader in the presence of the sugars and honeys, and a biphasic character was consistently exhibited. The application of an exponential equation to the gelatinisation temperatures of the starch-honey mixtures revealed an opposing influence of fructose and glucose during gelatinisation. The mechanism of starch gelatinisation may be better understood if techniques could be perfected to quantify breakage and formation of hydrogen bonds in the starch granules, and suggested techniques are discussed. (C) 2004 Elsevier Ltd. All rights reserved.

Investigation of the starch gelatinisation phenomena in water-glycerol systems: application of modulated temperature differential scanning calorimetry

The use of modulated temperature differential scanning calorimetry (MTDSC) has provided further insight into the gelatinisation process since it allows the detection of glass transition during gelatinisation process. It was found in this work that the glass transition overlapped with the gelatinisation peak temperature for all maize starch formulations studied. Systematic investigation on maize starch gelatinisation over a range of water-glycerol concentrations with MTDSC revealed that the addition of glycerol increased the gelatinisation onset temperature with an extent that depended on the water content in the system. Furthermore, the addition of glycerol promoted starch gelatinisation at low water content (0.4 g water/g dry starch) and the enthalpy of gelatinisation varied with glycerol concentration (0.73-19.61 J/g dry starch) depending on the water content and starch type. The validities of published gelatinisation models were explored. These models failed to explain the glass transition phenomena observed during the course of gelatinisation and failed to describe the gelatinisation behaviour observed over the water-glycerol concentrations range investigated. A hypothesis for the mechanisms involved during gelatinisation was proposed based on the side chain liquid crystalline polymer model for starch structure and the concept that the order-disorder transition in starch requires that the hydrogen bonds (the major structural element in the granule packing) to be broken before the collapse of order (helix-coil transition) can take place. (C) 2004 Elsevier Ltd. All rights reserved.

Experimental expansion tube study of the flow over a toroidal ballute

An experimental investigation of high-enthalpy flow over a toroidal ballute (balloon/parachute) was conducted in an expansion tube facility. The ballute, proposed for use in a number of future aerocapture missions, involves the deployment of a large toroidal-shaped inflatable parachute behind a space vehicle to generate drag on passing through a planetary atmosphere, thus, placing the spacecraft in orbit. A configuration consisting of a spherical spacecraft, followed by a toroid, was tested in a superorbital facility. Measurements at moderate-enthalpy conditions (15-20 MJ/kg) in nitrogen and carbon dioxide showed peak heat transfer rates of around 20 MW/m(2) on the toroid. At higher enthalpies (>50 MJ/kg) in nitrogen, carbon dioxide, and a hydrogen-neon mixture, heat transfer rates above 100 MW/m(2) were observed. Imaging using near-resonant holographic interferometry showed that the flows were steady except when the opening of the toroid was blocked.

Grand canonical Monte Carlo simulation study of methane adsorption at an open graphite surface and in slitlike carbon pores at 273 K

Grand canonical Monte Carlo (GCMC) simulation was used for the systematic investigation of the supercritical methane adsorption at 273 K on an open graphite surface and in slitlike micropores of different sizes. For both considered adsorption systems the calculated excess adsorption isotherms exhibit a maximum. The effect of the pore size on the maximum surface excess and isosteric enthalpy of adsorption for methane storage at 273 K is discussed. The microscopic detailed picture of methane densification near the homogeneous graphite wall and in slitlike pores at 273 K is presented with selected local density profiles and snapshots. Finally, the reliable pore size distributions, obtained in the range of the microporosity, for two pitch-based microporous activated carbon fibers are calculated from the local excess adsorption isotherms obtained via the GCMC simulation. The current systematic study of supercritical methane adsorption both on an open graphite surface and in slitlike micropores performed by the GCMC summarizes recent investigations performed at slightly different temperatures and usually a lower pressure range by advanced methods based on the statistical thermodynamics.

Interpretation of the temperature dependence of rate constants in biosensor studies

A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory. (C) 2004 Elsevier Inc. All rights reserved.