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Results for “Kinetic modeling”

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At least 667 records · Page 37Linked to original sources
PubMed2005

A kinetic model of quantitative real-time polymerase chain reaction.

Real-time polymerase chain reaction (PCR) is one of the most sensitive and accurate methods for quantifying transcript levels especially for those expressed at low abundance. The selective amplification of target DNA over multiple cycles allows its initial concentration to be determined. The amplification rate is a complex interplay of the operating conditions, initial reactant concentrations, and reaction rate constants. Experimentally, the compounded effect of all factors is quantified in terms of an effective efficiency, which is estimated by curve fitting to the amplification data. We present a comprehensive model of PCR to study the effect of various reactant concentrations on the amplification efficiency. The model is used to calculate the kinetic progression of the target DNA concentration with cycle number under conditions when different species are stoichiometrically or kinetically limiting. The reaction efficiency remains constant for the initial cycles. As the primer concentration becomes limiting, the efficiency is marked by a gradual decrease. This is in contrast to a steep decline under nucleotide limiting conditions. Under some conditions, commonly used experimentally, increasing primer concentration has the adverse effect of reducing the final amplified template concentration. This phenomenon seen at times experimentally is explained by the simulation results under rate limiting enzyme concentrations. Primer dimer formation is shown to significantly affect the reaction rates, effective efficiency, and the estimated initial concentrations. This model, by describing the interplay of the many operating variables, will be a useful tool in designing PCR conditions and evaluating its results.

Computer Simulation↗
PubMedDate not supplied

[A kinetic model of the cleavage of permutational variants of the antigenomic HDV-ribozyme].

The kinetic characteristics have been studied for noncircularly permuted variants of the human hepatitis delta virus (HDV) antigenomic ribozyme to find out the cause of the two-phase kinetics of the self-cleavage reaction. Different ways of reaction initiation, suboptimal conditions, and jumpwise changes of reaction conditions have been used, and the temperature dependences have been studied. A correlation has been shown between the apparent kinetic constant of the first reaction phase and the portion of the ribozyme molecules that self-cleaved during the first phase. Partial restoration of the initial reaction characteristics has been shown by the reinitiation of reaction being stopped after completing the first phase. On the basis of all the data obtained, a scheme of the self-cleavage reaction has been proposed including: (i) activation of the ribozyme with energy of 40-50 kcal/mol and a characteristic time of several deciminutes under optimal reaction conditions; (ii) fast and reversible reaction of the phosphodiester bond cleavage; (iii) reaction leading to isomerization of the 3',5'-phosphodiester bond to the 2',5' bond in the self-cleavage site with a characteristic activation time of tens of minutes; and (iv) practically irreversible conformational change leading to fixation of the cleavage by immobilization of the 5'-terminal nucleotide of the product in the center of the formed structure and displacement of the 3'-terminal nucleotide to the periphery. The latter process has a characteristic time of tens of minutes and a low activation energy.

Base Sequence↗
PubMed1997

Kinetics of low-density lipoprotein receptor activity in Hep-G2 cells: derivation and validation of a Briggs-Haldane-based kinetic model for evaluating receptor-mediated endocytotic processes in which receptors recycle.

The process of receptor-mediated endocytosis for receptors that recycle to the cell surface in an active form can be considered as being kinetically analogous to that of a uni-substrate, uni-product enzyme-catalysed reaction. In this study we have derived steady-state initial-velocity rate equations for this process, based on classical Briggs-Haldane and King-Altman kinetic approaches to multi-step reactions, and have evaluated this kinetic paradigm, using as a model system the low-density lipoprotein (LDL)-receptor-mediated endocytosis of the trapped label [14C]sucrose-LDL in uninduced, steady-state Hep-G2 cells. Using the derived rate equations, together with experimentally determined values for Bmax (123 fmol/mg of cell protein), Kd (14.3 nM), the endocytotic rate constant ke (analogous to kcat; 0.163 min-1), Km (80 nM) and maximal internalization velocity (26.4 fmol/min per mg), we have calculated the ratio ke/Km (0.00204 nM-1.min-1), the bimolecular rate constant for LDL and LDL-receptor association (0. 00248 nM-1.min-1), the first-order rate constant for LDL-LDL-receptor complex dissociation (0.0354 min-1), the total cellular content of LDL receptors (154 fmol/mg of cell protein), the intracellular LDL receptor concentration (30.7 fmol/mg of cell protein) and the pseudo-first-order rate constant for LDL receptor recycling (0.0653 min-1). Based on this mathematical model, the kinetic mechanism for the receptor-mediated endocytosis of [14C]sucrose-LDL by steady-state Hep-G2 cells is one of constitutive endocytosis via independent internalization sites that follows steady-state Briggs-Haldane kinetics, such that LDL-LDL-receptor interactions are characterized by a rapid-high-affinity ligand-receptor association, followed by ligand-receptor complex internalization that is rapid relative to complex dissociation, and by receptor recycling that is more rapid than complex internalization and that serves to maintain 80% of cellular LDL receptors on the cell surface in the steady-state. The consistency with which these quantitative observations parallel previous qualitative observations regarding LDL-receptor-mediated endocytosis, together with the high correlation between theoretical internalization velocities (calculated from determined rate constants) and experimental internalization velocities, underscore the validity of considering receptor-mediated endocytotic processes for recycling receptors in catalytic terms.

Carcinoma, Hepatocellular↗
PubMed2006

Adsorption of 18-crown-6 from aqueous solution on granular activated carbon: a kinetic modeling study.

Granular activated carbon was used for the removal of 18-crown-6 from aqueous solution by adsorption. The influence of two experimental parameters, initial 18-crown-6 concentration and temperature, on the adsorption kinetics was evaluated. The kinetics data obtained were modeled by pseudo-first-order and pseudo-second-order models, respectively. The process of adsorption follows a pseudo-second-order rate model. The most important result of the present study is that the correlation coefficient is not a sufficient criterion for selection of a kinetic model, and therefore several criteria are suggested for its selection.

Journal Article↗
PubMed1999

Kinetic modeling of 52Fe/52mMn-citrate at the blood-brain barrier by positron emission tomography.

The kinetics of iron at the blood-brain barrier of the monkey were studied in vivo using positron emission tomography (PET) and the tracer 52Fe/52mMn-citrate. 52mMn is the beta(+)-emitting daughter nuclide of 52Fe and therefore contributes to the observed signal and background in the PET images and may influence the quantification of physiological relevant iron parameters. The kinetics of pure (52m)Mn-citrate at the blood-brain barrier of the monkey were studied experimentally, and the analysis of the data with a reasonable compartment model led to equal efflux and influx parameters for Mn (1.35 +/- 0.3 x 10(-2) min(-1)). By using complexes between Mn and diethylenetriaminepentaacetic acid, the validity of the proposed model could be confirmed. To describe the observed kinetics of 52Fe/(52m)Mn-citrate, the manganese model was coupled to an iron model, which finally allowed the quantification of two iron-specific parameters: an input rate into global brain tissue of 7.15 +/- 2.6 x 10(-4) min(-1) and a time delay of roughly 24 min to account for the observed activities. The simpler linearization procedure has been proposed and could be applied to all our data sets and is able to replace the complicated nonlinear iron/manganese tracer kinetic model neglecting any influence of manganese on the analysis.

Animals↗
PubMed2005

Modeling kinetics of Cu and Zn release from soils.

Kinetics of Cu and Zn release from soil particles was studied using two surface soils with a stirred-flow method. Different solution pH, dissolved organic matter (DOM) concentrations, and flow rates were tested in this study. A model for kinetics controlled sorption/desorption reactions between soils and solutions was globally fit to all experimental data simultaneously. Results were compared to a model that assumes local instantaneous equilibrium. We obtained one unique set of model parameters applicable to different pH, dissolved organic carbon (DOC), and flow conditions. We included DOM complexation of copper ions, which decreased their sorption. The effect of pH was included by assuming proton competition with metal ions for binding sites on soil particles. These results provide the basis for developing predictive models for metal release from soil particles to surface waters and soil solution.

Carbon↗
PubMed2002

The incorporation of quantum effects in enzyme kinetics modeling.

We present an overview of new procedures for including quantum mechanical effects in enzyme kinetics. Quantum effects are included in three ways: (1) The electronic structure of the atoms in the catalytic center is treated quantum mechanically in order to calculate a realistic potential energy surface for the bond rearrangement process. (2) The discrete nature of quantum mechanical vibrational energies is incorporated in the treatment of nuclear motion for computing the potential of mean force. (3) Multidimensional tunneling contributions are included. These procedures are illustrated by applications to proton abstractions catalyzed by enolase and methylamine dehydrogenase and hydride-transfer reactions by alcohol dehydrogenase and xylose isomerase.

Catalysis↗
PubMed1979

A kinetic model of prostaglandin metabolism in the lung.

We have measured the instantaneous extraction of prostaglandin E1 (PGE1) after a single bolus injection of PGE1 and indocyanine green dye into the pulmonary artery of isolated cat lungs. The extraction ratio versus time curves exhibited a characteristic shape; at early times they were concave upward and later in time concave downward. To evaluate this date we utilized a model in which themechanism of PGE1 uptake is saturable and follows Michaelis-Menten kinetics. The model assumes heterogeneous perfusion of the exchanging region of the lung and can be solved by regression analysis to obtain Km and Vmax from the data collected from a single bolus injection. The results indicate that the shape of the extraction ratio curve manifests the influence of nonlinear uptake and heterogeneous perfusion and that the kinetic parameters may be calculated from the data obtained after a single bolus injection ofPGE1.

Animals↗
PubMed2001

Kinetic modeling and simulation of in vitro transcription by phage T7 RNA polymerase.

This study provides a mathematical model of T7 RNA polymerase (T7 RNAP) kinetics under in vitro conditions targeted at application of this model to simulation of dynamic transcription performance. A functional dependence of transcript synthesis rate is derived based on: (a) essential reactant concentrations, including T7 RNAP and its promoter, substrate nucleotides, and the inhibitory byproduct inorganic pyrophosphate; (b) a distinction among vector characteristics such as recognition sequences regulating transcription initiation and termination, respectively; and (c) specific properties of the nucleotide sequence including both transcript length and nucleotide composition. Inactivation kinetics showed a half-life of T7 RNAP activity of 50 min under the conditions applied in vitro using the isolated enzyme. Model parameters and their precision are estimated using dynamic simulation and nonlinear regression analysis. The particular novelty of this model is its capability to incorporate linear genomic sequence information for simulation of nonlinear in vitro transcription kinetics.

Computer Simulation↗
PubMed2004

Analysis of tensiograms of cerebrospinal fluid with a kinetic model.

We develop a model for estimation of the parameters of dynamic tensiometry of biological fluids based on equations of formal chemical kinetics. The model considers diffusion of low- and high-molecular compounds and conformational restructuring of these compounds in the surface layer. This model was tested on cerebrospinal fluid from patients with meningitis. Some correlations between the parameters of tensiometric curves and protein, chloride, neutrophil, and lymphocyte content in the liquor are detected.

Cerebrospinal Fluid↗
PubMed1988

Effects of adsorbed water vapor on the adsorption rate constant and the kinetic adsorption capacity of the Wheeler kinetic model.

A recent trend in occupational safety and health has focused on the use of respiratory protective equipment to supplant engineering controls as the primary means of protecting workers from toxic substances. Respirator adsorbent cartridges have been demonstrated to have a finite capacity to adsorb toxic vapors. The knowledge of when this limit is approached or has been exceeded is crucial to the user. The Wheeler kinetic breakthrough model has been shown to describe accurately organic vapor penetration through beds of activated carbon. The model, however, does not account for competitive adsorption of water vapor or other organic vapors. The investigations reported here demonstrate the effect of adsorbed water vapor on the kinetic adsorption parameters (kinetic rate constant and kinetic saturation capacity) of the Wheeler equation. Adsorbent beds were equilibrated at varying concentrations of water vapor and then challenged with carbon tetrachloride vapor-laden air. Dry carbon had an initial rate constant of 62.5 s-1 and a kinetic adsorption capacity of 0.36 g of adsorbed CCl4/gram (g/g) of adsorbent. These parameters decreased in proportion to the amount of water vapor adsorbed, with the minimum predicted values occurring at 100% relative humidity. The minimum experimental value for the kinetic rate constant was 17.6 s-1, a decrease of 73% from the dry carbon values. The minimum predicted value for the kinetic adsorption capacity was 0.16 g/g, a decrease of 45%.

Adsorption↗
PubMed2000

An elementary kinetic model of energy coupling in biological membranes.

The purpose of this work is to contribute to the understanding of the fundamental kinetic properties of the processes of energy coupling in biological membranes. For this, we consider a model of a microorganism that, in its plasma membrane, expresses two electrogenic enzymes (E(1) and E(2)) transporting the same monovalent cation C and electrodiffusive paths for C and for a monovalent anion A. E(1) (E(2)) couples transport C to the reaction S(1)<-->P(1) (S(2)<-->P(2)). We developed a mathematical model that describes the rate of change of the electrical potential difference across the membrane, of the internal concentrations of C and A, and of the concentrations of S(2) and P(2). The enzymes are incorporated via two-state kinetic models; the passive ionic fluxes are represented by classical formulations of electrodiffusion. The microorganism volume is maintained constant by accessory regulatory devices. The model is utilized for stationary and dynamic studies for the case of bacteria employing the electrochemical gradient of Na(+) as energetic intermediate. Among other conclusions, the results show that the membrane potential represents the relevant kinetic intermediate for the overall coupling between the energy donor reaction S(1)<-->P(1) and the synthesis of S(2).

Bacteria↗