Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors. © 2005 Elsevier Inc. All rights reserved.

Numerical investigation of effects of addition of ethanol to gasoline on Laminar Flame Speed (LFS), autoignition, and wall quenching

Since the advent of automobiles, alcohol has been considered a possible engine fuel1,2. With the recent increased concern about the high price of crude oil due to fluctuating supply and demand and environmental issues, interest in alcohol based fuels has increased2,3. However, using pure alcohols or blends with conventional fuels in high percentages requires changes to the engine and fuel system design2. This leads to the need for a simple and accurate conventional fuels-alcohol blends combustion models that can be used in developing parametric burn rate and knock combustion models for designing more efficient Spark Ignited (SI) engines. To contribute to this understanding, numerical simulations were performed to obtain detailed characteristics of Gasoline-Ethanol blends with respect to Laminar Flame Speed (LFS), autoignition and Flame-Wall interactions. The one-dimensional premixed flame code CHEMKIN® was applied to simulate the burning velocity and autoignition characteristics using the freely propagating model and closed homogeneous reactor model respectively. Computational Fluid Dynamics (CFD) was used to obtain detailed flow, temperature, and species fields for Flame-wall interactions. A semi-detailed validated chemical kinetic model for a gasoline surrogate fuel developed by Andrae and Head4 was used for the study of LFS and Autoignition. For the quenching study, a skeletal chemical kinetic mechanism of gasoline surrogate, having 50 species and 174 reactions was used. The surrogate fuel was defined as a mixture of pure n-heptane, isooctane, and toluene. For LFS study, the ethanol volume fraction was varied from 0 to 85%, initial pressure from 4 to 8 bar, initial temperature from 300 to 900K, and dilution from 0 to 32%. Whereas for Autoignition study, the ethanol volume fraction was varied between 0 to 85%, initial pressure was varied between 20 to 60 bar, initial temperature was varied between 800 to 1200K, and the dilution was varied between 0 to 32% at equivalence ratios of 0.5, 1.0 and 1.5 to represent the in-cylinder conditions of a SI engine. For quenching study three Ethanol blends, namely E0, E25 and E85 are described in detail at an initial pressure of 8 atm and 17 atm. Initial wall temperature was taken to be 400 K. Quenching thicknesses and heat fluxes to the wall were computed. The laminar flame speed was found to increase with ethanol concentration and temperature but decrease with pressure and dilution. The autoignition time was found to increase with ethanol concentration at lower temperatures but was found to decrease marginally at higher temperatures. The autoignition time was also found to decrease with pressure and equivalence ratio but increase with dilution. The average quenching thickness was found to decrease with an increase in Ethanol concentration in the blend. Heat flux to the wall increased with increase in ethanol percentage in the blend and at higher initial pressures. Whereas the wall heat flux decreased with an increase in dilution. Unburned Hydrocarbon (UHC) and CO % was also found to decrease with ethanol concentration in the blend.

Critical radius for hot-jet ignition of hydrogen-air mixtures

This study addresses deflagration initiation of lean and stoichiometric hydrogen–air mixtures by the sudden discharge of a hot jet of their adiabatic combustion products. The objective is to compute the minimum jet radius required for ignition, a relevant quantity of interest for safety and technological applications. For sufficiently small discharge velocities, the numerical solution of the problem requires integration of the axisymmetric Navier–Stokes equations for chemically reacting ideal-gas mixtures, supplemented by standard descriptions of the molecular transport terms and a suitably reduced chemical-kinetic mechanism for the chemistry description. The computations provide the variation of the critical radius for hot-jet ignition with both the jet velocity and the equivalence ratio of the mixture, giving values that vary between a few tens microns to a few hundred microns in the range of conditions explored. For a given equivalence ratio, the critical radius is found to increase with increasing injection velocities, although the increase is only moderately large. On the other hand, for a given injection velocity, the smallest critical radius is found at stoichiometric conditions.

Investigação do mecanismo cinético da reação de redução de oxigênio em solventes não aquosos

O aumento no consumo energético e a crescente preocupação ambiental frente à emissão de gases poluentes criam um apelo mundial favorável para pesquisas de novas tecnologias não poluentes de fontes de energia. Baterias recarregáveis de lítio-ar em solventes não aquosos possuem uma alta densidade de energia teórica (5200 Wh kg-1), o que as tornam promissoras para aplicação em dispositivos estacionários e em veículos elétricos. Entretanto, muitos problemas relacionados ao cátodo necessitam ser contornados para permitir a aplicação desta tecnologia, por exemplo, a baixa reversibilidade das reações, baixa potência e instabilidades dos materiais empregados nos eletrodos e dos solventes eletrolíticos. Assim, neste trabalho um modelo cinético foi empregado para os dados experimentais de espectroscopia de impedância eletroquímica, para a obtenção das constantes cinéticas das etapas elementares do mecanismo da reação de redução de oxigênio (RRO), o que permitiu investigar a influência de parâmetros como o tipo e tamanho de partícula do eletrocatalisador, o papel do solvente utilizado na RRO e compreender melhor as reações ocorridas no cátodo dessa bateria. A investigação inicial se deu com a utilização de sistemas menos complexos como uma folha de platina ou eletrodo de carbono vítreo como eletrodos de trabalho em 1,2-dimetoxietano (DME)/perclorato de lítio (LiClO4). A seguir, sistemas complexos com a presença de nanopartículas de carbono favoreceu o processo de adsorção das moléculas de oxigênio e aumentou ligeiramente (uma ordem de magnitude) a etapa de formação de superóxido de lítio (etapa determinante de reação) quando comparada com os eletrodos de platina e carbono vítreo, atribuída à presença dos grupos laterais mediando à transferência eletrônica para as moléculas de oxigênio. No entanto, foi observada uma rápida passivação da superfície eletrocatalítica através da formação de filmes finos de Li2O2 e Li2CO3 aumentando o sobrepotencial da bateria durante a carga (diferença de potencial entre a carga e descarga > 1 V). Adicionalmente, a incorporação das nanopartículas de platina (Ptnp), ao invés da folha de platina, resultou no aumento da constante cinética da etapa determinante da reação em duas ordens de magnitude, o qual pode ser atribuído a uma mudança das propriedades eletrônicas na banda d metálica em função do tamanho nanométrico das partículas, e estas modificações contribuíram para uma melhor eficiência energética quando comparado ao sistema sem a presença de eletrocatalisador. Entretanto, as Ptnp se mostraram não específicas para a RRO, catalisando as reações de degradação do solvente eletrolítico e diminuindo rapidamente a eficiência energética do dispositivo prático, devido ao acúmulo de material no eletrodo. O emprego de líquido iônico como solvente eletrolítico, ao invés de DME, promoveu uma maior estabilização do intermediário superóxido formado na primeira etapa de transferência eletrônica, devido à interação com os cátions do líquido iônico em solução, o qual resultou em um valor de constante cinética da formação do superóxido de três ordens de magnitude maior que o obtido com o mesmo eletrodo de carbono vítreo em DME, além de diminuir as reações de degradação do solvente. Estes fatores podem contribuir para uma maior potência e ciclabilidade da bateria de lítio-ar operando com líquidos iônicos.

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.

Lead compounds for antimalarial chemotherapy: Purine base analogs discriminate between human and P-falciparum 6-oxopurine phosphoribosyltransferases

The malarial parasite Plasmodium falciparum depends on the purine salvage enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) to convert purine bases from the host to nucleotides needed for DNA and RNA synthesis. An approach to developing antimalarial drugs is to use HGXPRT to convert introduced purine base analogs to nucleotides that are toxic to the parasite. This strategy requires that these compounds be good substrates for the parasite enzyme but poor substrates for the human counterpart, HGPRT. Bases with a chlorine atom in the 6-position or a nitrogen in the 8-position exhibited strong discrimination between P. falciparum HGXPRT and human HGPRT. The k(cat)/K-m values for the Plasmodium enzyme using 6-chloroguanine and 8-azaguanine as substrates were 50-80-fold and 336-fold higher than for the human enzyme, respectively. These and other bases were effective in inhibiting the growth of the parasite in vitro, giving IC50 values as low as 1 mu M.

Multiscale modelling of heterogeneously catalysed transesterification reaction process:an overview

Biodiesel is fast becoming one of the key transport fuels as the world endeavours to reduce its carbon footprint and find viable alternatives to oil derived fuels. Research in the field is currently focusing on more efficient ways to produce biodiesel, with the most promising avenue of research looking into the use of heterogeneous catalysis. This article presents a framework for kinetic reaction and diffusive transport modelling of the heterogeneously catalysed transesterification of triglycerides into fatty acid methyl esters (FAMEs), unveiled by a model system of tributyrin transesterification in the presence of MgO catalysts. In particular, the paper makes recommendations on multicomponent diffusion calculations such as the diffusion coefficients and molar fluxes from infinite dilution diffusion coefficients using the Wilke and Chang correlation, intrinsic reaction kinetic studies using the Eley-Rideal kinetic mechanism with methanol adsorption as the rate determining steps and multiscale reaction-diffusion process simulation between catalytic porous and bulk reactor scales. © 2013 The Royal Society of Chemistry.

Ultra-Low Temperature Partial Oxidation: Detailed Kinetics, Safety, and Environmental Issues

The innovation in several industrial sectors has been recently characterized by the need for reducing the operative temperature either for economic or environmental related aspects. Promising technological solutions require the acquisition of fundamental-based knowledge to produce safe and robust systems. In this sense, reactive systems often represent the bottleneck. For these reasons, this work was focused on the integration of chemical (i.e., detailed kinetic mechanism) and physical (i.e., computational fluid dynamics) models. A theoretical-based kinetic mechanism mimicking the behaviour of oxygenated fuels and their intermediates under oxidative conditions in a wide range of temperature and pressure was developed. Its validity was tested against experimental data collected in this work by using the heat flux burner, as well as measurements retrieved from the current literature. Besides, estimations deriving from existing models considered as the benchmark in the combustion field were compared with the newly generated mechanism. The latter was found to be the most accurate for the investigated conditions and fuels. Most influential species and reactions on the combustion of butyl acetate were identified. The corresponding thermodynamic parameter and rate coefficients were quantified through ab initio calculations. A reduced detailed kinetic mechanism was produced and implemented in an open-source computational fluid dynamics model to characterize pool fires caused by the accidental release of aviation fuel and liquefied natural gas, at first. Eventually, partial oxidation processes involving light alkenes were optimized following the quick, fair, and smoot (QFS) paradigm. The proposed procedure represents a comprehensive and multidisciplinary approach for the construction and validation of accurate models, allowing for the characterization of developing industrial sectors and techniques.

DNA hybridization mechanism in an interfacial environment: What hides beneath first order k (s(-1)) kinetic constant?

The scientific question addressed in this work is: what hides beneath first order kinetic constant k (s(-1)) measured for hybridization of a DNA target on a biosensor surface. Kinetics hybridization curves were established with a 27 MHz quartz microbalance (9 MHz, third harmonic) biosensor, constituted of a 20-base probe monolayer deposited on a gold covered quartz surface. Kinetics analysis, by a known two-step adsorption-hybridization mechanism, is well appropriate to fit properly hybridization kinetics curves, for complementary 20-base to 40-base targets over two concentration decades. It was found that the K-1 (M-1) adsorption constant, relevant to the first step, concerns an equilibrium between non hybridized targets and hybridized pre-complex and increases with DNA target length. It was established that k(2) (s(-1)), relevant to irreversible formation of a stable duplex, varies in an opposite way to K-1 with DNA target length. (C) 2012 Published by Elsevier B.V.

Shvo's catalyst in chemoenzymatic dynamic kinetic resolution of amines-inner or outer sphere mechanism?

Evidence is provided for the inner-sphere mechanism with actual metal coordination of the racemic amine in the crucial hydrogen transfer step promoted by Shvo's catalyst of the chemoenzymatic dynamic kinetic resolution (DKR) of amines. Key intermediates involved in this H-transfer step were intercepted and continuously monitored by electrospray ionization mass spectrometry (ESI-MS) and characterized by their dissociation chemistries via ESI-MS/MS. © 2013 The Royal Society of Chemistry.

Kinetic stability as a mechanism for protease longevity

The folding of the extracellular serine protease, α-lytic protease (αLP; EC 3.4.21.12) reveals a novel mechanism for stability that appears to lead to a longer functional lifetime for the protease. For αLP, stability is based not on thermodynamics, but on kinetics. Whereas this has required the coevolution of a pro region to facilitate folding, the result has been the optimization of native-state properties independent of their consequences on thermodynamic stability. Structural and mutational data lead to a model for catalysis of folding in which the pro region binds to a conserved β-hairpin in the αLP C-terminal domain, stabilizing the folding transition state and the native state. The pro region is then proteolytically degraded, leaving the active αLP trapped in a metastable conformation. This metastability appears to be a consequence of pressure to evolve properties of the native state, including a large, highly cooperative barrier to unfolding, and extreme rigidity, that reduce susceptibility to proteolytic degradation. In a test of survival under highly proteolytic conditions, homologous mammalian proteases that have not evolved kinetic stability are much more rapidly degraded than αLP. Kinetic stability as a means to longevity is likely to be a mechanism conserved among the majority of extracellular bacterial pro-proteases and may emerge as a general strategy for intracellular eukaryotic proteases subject to harsh conditions as well.

Mechanism of Heparin Acceleration of Tissue Inhibitor of Metalloproteases-1 (TIMP-1) Degradation by the Human Neutrophil Elastase

Heparin has been shown to regulate human neutrophil elastase (HNE) activity. We have assessed the regulatory effect of heparin on Tissue Inhibitor of Metalloproteases-1 [TIMP-1] hydrolysis by HNE employing the recombinant form of TIMP-1 and correlated FRET-peptides comprising the TIMP-1 cleavage site. Heparin accelerates 2.5-fold TIMP-1 hydrolysis by HNE. The kinetic parameters of this reaction were monitored with the aid of a FRET-peptide substrate that mimics the TIMP-1 cleavage site in pre-steady-state conditionsby using a stopped-flow fluorescence system. The hydrolysis of the FRET-peptide substrate by HNE exhibits a pre-steady-state burst phase followed by a linear, steady-state pseudo-first-order reaction. The HNE acylation step (k(2)=21 +/- 1 s(-1)) was much higher than the HNE deacylation step (k(3)=0.57 +/- 0.05 s(-1)). The presence of heparin induces a dramatic effect in the pre-steady-state behavior of HNE. Heparin induces transient lag phase kinetics in HNE cleavage of the FRET-peptide substrate. The pre-steady-state analysis revealed that heparin affects all steps of the reaction through enhancing the ES complex concentration, increasing k(1) 2.4-fold and reducing k(-1) 3.1-fold. Heparin also promotes a 7.8-fold decrease in the k(2) value, whereas the k(3) value in the presence of heparin was increased 58-fold. These results clearly show that heparin binding accelerates deacylation and slows down acylation. Heparin shifts the HNE pH activity profile to the right, allowing HNE to be active at alkaline pH. Molecular docking and kinetic analysis suggest that heparin induces conformational changes in HNE structure. Here, we are showing for the first time that heparin is able to accelerate the hydrolysis of TIMP-1 by HNE. The degradation of TIMP-1is associated to important physiopathological states involving excessive activation of MMPs.

Mechanism and model of the oscillatory electro-oxidation of methanol

A mechanism for the kinetic instabilities observed in the galvanostatic electro-oxidation of methanol is suggested and a model developed. The model is investigated using stoichiometric network analysis as well as concepts from algebraic geometry (polynomial rings and ideal theory) revealing the occurrence of a Hopf and a saddle-node bifurcation. These analytical solutions are confirmed by numerical integration of the system of differential equations. (C) 2010 American Institute of Physics

Oxidation mechanism of Si3N4-bonded SiC ceramics by CO, CO2 and steam

This paper presents a theoretical and experimental investigation into the oxidation reactions of Si3N4-bonded SiC ceramics. Such ceramics which contain a small amount of silicon offer increased oxidation and wear resistance and are widely used as lining refractories in blast furnaces. The thermodynamics of oxidation reactions were studied using the JANAF tables. The weight gain was measured using a thermogravimetric analysis technique to study the kinetics. The temperature range of oxidation measurements is from 1073 to 1573 K and the oxidation atmosphere is water vapour, pure CO and CO-CO2 gas mixtures with various CO-to-CO2 ratios. Thermodynamic simulations showed that the oxidation mechanism of Si3N4-bonded SiC ceramics is passive oxidation and all components contribute to the formation of a silica film. The activated energies of the reactions follow the sequence Si3N4>SiC>Si. The kinetic study revealed that the oxidation of Si3N4-bonded SiC ceramics occurred in a mixed regime controlled by both interface reaction and diffusion through the silica film. Under the atmosphere conditions prevailing in the blast furnace, this ceramic is predicted to be passively oxidized with the chemical reaction rate becoming more dominant as the CO concentration increases. (C) 1998 Chapman & Hall.

Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A

We describe the mechanism of ribonuclease inhibition by ribonuclease inhibitor, a protein built of leucine-rich repeats, based on the crystal structure of the complex between the inhibitor and ribonuclease A. The structure was determined by molecular replacement and refined to an R(cryst) of 19.4% at 2.5 Angstrom resolution. Ribonuclease A binds to the concave region of the inhibitor protein comprising its parallel beta-sheet and loops. The inhibitor covers the ribonuclease active site and directly contacts several active-site residues. The inhibitor only partially mimics the RNase-nucleotide interaction and does not utilize the pi phosphate-binding pocket of ribonuclease A, where a sulfate ion remains bound. The 2550 Angstrom(2) of accessible surface area buried upon complex formation may be one of the major contributors to the extremely tight association (K-i = 5.9 x 10(-14) M). The interaction is predominantly electrostatic; there is a high chemical complementarity with 18 putative hydrogen bonds and salt links, but the shape complementarity is lower than in most other protein-protein complexes. Ribonuclease inhibitor changes its conformation upon complex formation; the conformational change is unusual in that it is a plastic reorganization of the entire structure without any obvious hinge and reflects the conformational flexibility of the structure of the inhibitor. There is a good agreement between the crystal structure and other biochemical studies of the interaction. The structure suggests that the conformational flexibility of RI and an unusually large contact area that compensates for a lower degree of complementarity may be the principal reasons for the ability of RI to potently inhibit diverse ribonucleases. However, the inhibition is lost with amphibian ribonucleases that have substituted most residues corresponding to inhibitor-binding residues in RNase A, and with bovine seminal ribonuclease that prevents inhibitor binding by forming a dimer. (C) 1996 Academic Press Limited