Pseudo-first Order Approximation Research Articles

Tractable RNA\u2013ligand interaction kinetics

BackgroundThe binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene regulation implemented by a wide variety of riboswitches. The associated refolding processes often cannot be explained by thermodynamic effects alone. Instead, they are governed by the kinetics of RNA folding. While the computational analysis of RNA folding can make use of well-established models of the thermodynamics of RNA structures formation, RNA–RNA interaction, and RNA–ligand interaction, kinetic effects pose fundamentally more challenging problems due to the enormous size of the conformation space. The analysis of the combined process of ligand binding and structure formation even for small RNAs is plagued by intractably large state spaces. Moreover, the interaction is concentration-dependent and thus is intrinsically non-linear. This precludes the direct transfer of the strategies previously used for the analysis of RNA folding kinetics.ResultsIn our novel, computationally tractable approach to RNA–ligand kinetics, we overcome the two main difficulties by applying a gradient-based coarse graining to RNA–ligand systems and solving the process in a pseudo-first order approximation. The latter is well-justified for the most common case of ligand excess in RNA–ligand systems. We present the approach rigorously and discuss the parametrization of the model based on empirical data. The method supports the kinetic study of RNA–ligand systems, in particular at different ligand concentrations. As an example, we apply our approach to analyze the concentration dependence of the ligand response of the rationally designed, artificial theophylline riboswitch RS3.ConclusionThis work demonstrates the tractability of the computational analysis of RNA–ligand interaction. Naturally, the model will profit as more accurate measurements of folding and binding parameters become available. Due to this work, computational analysis is available to support tasks like the design of riboswitches; our analysis of RS3 suggests strong co-transcriptional effects for this riboswitch.The method used in this study is available online, cf. Section “Availability of data and materials”.

Enhanced photocatalytic activity of calcined natural sphalerite under visible light irradiation

The photocatalytic activity of natural sphalerite (the main mineral ore of ZnS) is relatively low in the absence of sacrificial donors. Present work focuses on the improvement of the photocatalytic activity of a natural sphalerite obtained from Abuni deposit, Nigeria, via calcination at 600°C, 700°C and 800°C. The raw and calcined natural sphalerite samples were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), and specific surface area analysis. The activity of the raw and calcined samples was evaluated using photocatalytic decolorization of methyl orange (MO) as the model reaction. The kinetics of photocatalytic decolorization of MO on the raw and calcined natural sphalerite samples was fitted to the pseudo-first order approximation of the Langmuir–Hinshelwood model. The photocatalytic activity of the natural sphalerite was doubled upon calcination at 700°C. The natural sphalerite calcined at 700°C is also more active than the ones calcined at 600°C and 800°C due to the combined effects of chemical composition, crystallite size, specific surface area and oxygen vacancies.

Kinetics of Redox Interaction between Cytochrome c and Thiols

Background: Cytochrome c (cyt c) is well known for its role in mitochondrial electron transport. The redox state of cyt c has recently been linked to apoptosis. In the present study, we investigated and compared the kinetics of cyt c reduction by various thiol antioxidants. Methods: All kinetic experiments were performed by measuring spectrophotometrically the changes in absorbance at 550 nm for 2 min at 25℃ in a reaction buffer (50 mM Tris HCl, pH 7.4) containing cyt c (5 μM) and thiols (100 μM). Electrostatic effects on the rate of reduction of cyt c were determined by varying the ionic strength of the reaction buffer. The kinetic data were treated by applying a pseudo first-order approximation. Results: The results show that, among all thiols studied, cysteine reduces cyt c at the highest rate. The second-order rate constant is on the order of 10^2 M^(-1)s^(-1) for cellular thiol reductants, GSH and cysteine. Most thiols of therapeutic importance exhibit extremely low reduction rates. Moreover, the rate of cyt c reduction was found to correlate negatively with the pK(subscript a) of the SH group. This study further demonstrates that a complex electrostatic interaction may occur between cyt c and thiols. Conclusions: Given the high abundance of GSH in cells, our kinetic data suggest that GSH may out-compete other reductants for cyt c; and is therefore an important mediator of the cellular redox state of cyt c.

Reduction of aldehydes and hydrogen cyanide yields in mainstream cigarette smoke using an amine functionalised ion exchange resin

BackgroundCigarette smoking is a well recognized cause of diseases such as lung cancer, chronic obstructive pulmonary disease and cardiovascular disease. Of the more than 5000 identified species in cigarette smoke, at least 150 have toxicological activity. For example, formaldehyde and acetaldehyde have been assigned as Group 1 and Group 2B carcinogens by IARC, and hydrogen cyanide has been identified as a respiratory and cardiovascular toxicant. Active carbon has been shown to be an effective material for the physical adsorption of many of the smoke volatile species. However, physical adsorption of acetaldehyde, formaldehyde and also hydrogen cyanide from smoke is less effective using carbon. Alternative methods for the removal of these species from cigarette smoke are therefore of interest. A macroporous, polystyrene based ion-exchange resin (Diaion®CR20) with surface amine group functionality has been investigated for its ability to react with aldehydes and HCN in an aerosol stream, and thus selectively reduce the yields of these compounds (in particular formaldehyde) in mainstream cigarette smoke.ResultsResin surface chemistry was characterized using vapour sorption, XPS, TOF-SIMS and 15N NMR. Diaion®CR20 was found to have structural characteristics indicating weak physisorption properties, but sufficient surface functionalities to selectively remove aldehydes and HCN from cigarette smoke. Using 60 mg of Diaion®CR20 in a cigarette cavity filter gave reductions in smoke formaldehyde greater than 50% (estimated to be equivalent to >80% of the formaldehyde present in the smoke vapour phase) independent of a range of flow rates. Substantial removal of HCN (>80%) and acetaldehyde (>60%) was also observed. The performance of Diaion®CR20 was found to be consistent over a test period of 6 months. The overall adsorption for the majority of smoke compounds measured appeared to follow a pseudo-first order approximation to second order kinetics.ConclusionsThis study has shown that Diaion®CR20 is a highly selective and efficient adsorbent for formaldehyde, acetaldehyde and HCN in cigarette smoke. The reductions for these compounds were greater than those achieved using an active carbon. The results also demonstrate that chemisorption can be an effective mechanism for the removal of certain vapour phase toxicants from cigarette smoke.

Progress curve analysis of enzyme reactions by flow microcalorimetry: Use of a pseudo-first order approximation

We describe a method for determining the pseudo-first order rate constant of a chemical reaction by flow microcalorimetry operating in the flow-through mode. The impulse response of the instrument was described by a Gamma distribution and the equation of the thermogram was computed analytically. The resulting equation was fitted to the data by simulated annealing. The method was applied to an enzyme reaction following Michaelis–Menten kinetics by means of a new empirical equation relating the apparent rate constant to the kinetic parameters Vmax and Km. The method was exemplified by a kinetic study of horse serum butyrylcholinesterase.

Introducing total substrates simplifies theoretical analysis at non-negligible enzyme concentrations: pseudo first-order kinetics and the loss of zero-order ultrasensitivity

The Briggs-Haldane standard quasi-steady state approximation and the resulting rate expressions for enzyme driven biochemical reactions provide crucial theoretical insight compared to the full set of equations describing the reactions, mainly because it reduces the number of variables and equations. When the enzyme is in excess of the substrate, a significant amount of substrate can be bound in intermediate complexes, so-called substrate sequestration. The standard quasi-steady state approximation is known to fail under such conditions, a main reason being that it neglects these intermediate complexes. Introducing total substrates, i.e., the sums of substrates and intermediate complexes, provides a similar reduction of the number of variables to consider but without neglecting the contribution from intermediate complexes. The present theoretical study illustrates the usefulness of such simplifications for the understanding of biochemical reaction schemes. We show how introducing the total substrates allows a simple analytical treatment of the relevance of significant enzyme concentrations for pseudo first-order kinetics and reconciles two proposed criteria for the validity of the pseudo first-order approximation. In addition, we show how the loss of zero-order ultrasensitivity in covalent modification cycles can be analyzed, in particular that approaches such as metabolic control analysis are immediately applicable to scenarios described by the total substrates with enzyme concentrations higher than or comparable to the substrate concentrations. A simple criterion which excludes the possibility of zero-order ultrasensitivity is presented.

A Serpin from the Gut Bacterium Bifidobacterium longum Inhibits Eukaryotic Elastase-like Serine Proteases

Serpins form a large class of protease inhibitors involved in regulation of a wide spectrum of physiological processes. Recently identified prokaryotic members of this protein family may provide a key to the evolutionary origins of the unique serpin fold and the associated inhibitory mechanism. We performed a biochemical characterization of a serpin from Bifidobacterium longum, an anaerobic Gram-positive bacterium that naturally colonizes human gastrointestinal tract. The B. longum serpin was shown to efficiently inhibit eukaryotic elastase-like proteases with a stoichiometry of inhibition close to 1. Porcine pancreatic elastase and human neutrophil elastase were inhibited with the second order association constants of 4.7 x 10(4) m(-1) s(-1) and 2.1 x 10(4) m(-1) s(-1), respectively. The B. longum serpin is expected to be active in the gastrointestinal tract, because incubation of the purified recombinant serpin with mouse feces produces a stable covalent serpin-protease adduct readily detectable by SDS-PAGE. Bifidobacteria may encounter both pancreatic elastase and neutrophil elastase in their natural habitat and protection against exogenous proteolysis may play an important role in the interaction between these commensal bacteria and their host.

Viscometric determination of dialdehyde content in periodate oxycellulose Part II. Topochemistry of oxidation

The kinetics of periodate oxidation of cellulose was followed through the alkaline degradation of the dialdehyde groups by measuring the viscometric degree of polymerisation and the alkali consumption. The obtained results show that a fast but limited attack of periodate occurs in the amorphous region of cellulose, causing the decrease of degree of polymerisation to its levelling-off value. The alkali consumption indicates at least two further slower reactions, that lead to the asymptotic complete oxidation of cellulose units. With the pseudo first-order approximation, the oxidation half-time of these three reactions can be calculated, corresponding to 1.2, 20 and 854 h respectively. In spite of the high oxidation of the analysed samples (up to about 46%), the residue after alkaline degradation shows a relatively high value of degree of polymerisation rather than the narrow molecular weight distribution of oligomers expected from a random oxidation, thus indicating that periodate oxidises cellulose in isolated domains. The sequence of analyses over the same sample utilised in this work (titrimetry, weight loss and viscometry), performed at room temperature in mild conditions, makes it possible to investigate the topochemistry of oxidation of paper and textiles of historic and artistic value with microdistructive techniques on a single, very small fragment of material.

The catalytic hydrodechlorination of mono-, di- and trichlorobenzenes over supported nickel

The gas phase hydrodechlorination (HDC) of chlorobenzene (CB), chlorotoluene(s) (CT), 3-chlorophenol (3-CP), dichlorobenzene(s) (DCB) and trichlorobenzene(s) (TCB) over the temperature range 473K≤T≤573K has been studied using 1.5% and 6.1% (w/w) Ni/SiO2 catalysts; the catalytic data have been obtained in the absence of any appreciable short-term deactivation. HDC of DCB and TCB generated the partially or the fully dechlorinated aromatic product + HCl and there was no significant cyclohexene or cyclohexane in the effluent stream. The conversion of mono-chloroarenes yielded the following reactivity sequence CB < 2-CT < 3-CT < 4-CT < 3-CP, i.e. the presence of an electron donating ring substituent enhances HDC and steric hindrance lowers reactivity. HDC kinetics have been adequately represented by a pseudo-first order approximation. Chlorine removal from DCB and TCB isomers proceeded through sequential and concerted routes, the relative importance of each dependent on the nature of the isomer and reaction conditions; apparent HDC activation energy increases in the order CB < DCB < TCB. The relationship between dechlorination selectivity and residence time/fractional conversion is addressed. The higher Ni loaded catalyst delivered consistently higher (specific) dechlorination rates and higher benzene yields from a polychlorinated feedstock. Catalytic HDC over Ni/SiO2 is presented as a viable means of treating/detoxifying concentrated chlorinated gas streams and the best strategy for generating the parent benzene or a target partially dechlorinated product is discussed.

Nickel particle size effects in catalytic hydrogenation and hydrodechlorination: phenolic transformations over nickel/silica

The gas phase hydrodechlorination of 2,4-dichlorophenol (2,4-DCP) and 2-chlorophenol (2-CP) has been studied over three series of Ni/SiO2 catalysts prepared by three different methods, i.e. (i) impregnation with nickel nitrate, (ii) impregnation with nickel ethanediamine and (iii) deposition-precipitation. This has led to catalysts with a wide range of Ni loadings (0.7–20.9% w/w Ni) and an average Ni particle size from 1.4 to 16.8 nm. The chloroarene was continuously fed to the reactor as a methanolic or aqueous solution (with subsequent vaporisation) where consistently higher hydrodechlorination activities were associated with the aqueous feed due to methanol/support interactions that served to inhibit the surface hydrogenolytic reaction. Hydrodechlorination of 2-CP yielded the fully dechlorinated aromatic product (phenol) and HCl while 2,4-DCP also yielded the partially dechlorinated (2-CP) aromatic product. There was no detectable aromatic ring reduction and the hydrodechlorination kinetics can be represented by a pseudo-first order approximation. Structure sensitivity has been conclusively established where the specific Cl removal was consistently greater with an increase in the average Ni particle diameter. The specific hydrodechlorination rate for 2,4-DCP was lower than that for 2-CP, diagnostic of a deactivating electronic effect associated with the Cl substituent(s) and this was manifested by higher apparent activation energies (ΔEa) for the 2,4-DCP reaction; the ΔEa values were unaffected by catalyst preparation/activation/Ni loading. The direct hydrogenation of phenol (as feed) was largely insensitive to Ni particle size albeit there was a discernible decrease in specific phenol consumption over average Ni diameters less than ca. 3 nm. Hydrogenation selectivity remained unchanged and cyclohexanol was the predominant product irrespective of Ni loading or synthesis route.

Modeling the kinetics of UV/hydrogen peroxide oxidation of some mono-, di-, and trichlorophenols

The decomposition of a number of chlorophenols (CPs), namely 2-CP, 2,4-dichlorophenol and 2,4,6-trichlorophenol, has been studied in aqueous solution by UV-catalyzed oxidation with H 2O 2 under UV radiation emitted by a 125-W medium pressure Hg lamp in an immersion well-type quartz photoreactor, and the organic-bound chlorine has been converted into the environmentally harmless inorganic chloride. For oxidant/CP mole ratios between 1:1 and 16:1, the reaction kinetics were modeled and the corresponding rate constants found by periodically measuring the remaining CP, hydrogen peroxide and converted chloride in solution. A theoretical model for the degradation pathway is proposed expressing the rate as a linear function of the concentrations of CP and oxidant. The rate constants for the pseudo-first order approximation of the CP degradation were compared. H 2O 2, when combined with UV, is an effective photoactivated oxidant. The photodegradation order in terms of the initial rate of CPs destruction was: Cl 3·Ph≥Cl 2·Ph>Cl·Ph.

The effect of a limiting non-key reactant on pseudo first-order reactions in porous catalysts

Effectiveness factor correlations are derived for the kinetic model describing a pseudo first- order mechanism up to the point of penetration in the catalyst pellet at which the non-key reactant is completely consumed. The pseudo first-order approximation is shown to be satisfactory for the rate equation describing the hydrogenation of ethylene on a copper—magnesia catalyst, and the model predictions are found to be in good agreement with previously published experimental results for this system.