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At least 775 records · Page 43Linked to original sources

PubMed2005

Determination of kinetic parameters of Cu(II) interaction with chemically modified thin chitosan membranes.

In this work, vanillin-modified thin chitosan membranes were utilized as adsorbents for the removal of Cu(II) from aqueous solutions. A rise of temperature accelerates mass transfer of Cu(II) to the membranes surfaces. The kinetic data did present a rough fit to the traditional Lagergren adsorption kinetic equations. An alternative Avrami kinetic equation was successfully fitted to the kinetic adsorption quantities. From this new equation, from one to three regions presenting distinct kinetic parameters were found, and the use of the parameter n was also related to the determination of the kinetic orders. Variations of the adsorption rate in relation to the contact time and the temperature were also calculated and are discussed.

Carbohydrate Conformation↗

PubMed2005

Multistep adsorption of anionic dyes on silica/chitosan hybrid. 1. Comparative kinetic data from liquid- and solid-phase models.

In this work, a hybrid silica/chitosan was synthesized and characterized by nitrogen elemental analysis and thermal analysis (TG, DTG, DTA, and DSC) and BET surface area. The hybrid was used in adsorption studies of two anionic dyes from aqueous solutions. A rise of temperature accelerates mass transfer of dyes into the hybrid. However, the maximum adsorption capacities reach similar values from 25 to 55 degrees C. The kinetic data were first evaluated in relation to the decrease of the time-related residual concentration of the dyes in solution, where the second-order model has presented the best fitting. The solid-phase interaction of dye data presents a rough fitting to the traditional first-order Lagergren kinetic model. However, a modified Avrami kinetic equation was successfully fitted to the kinetic quantities, where from five to seven kinetic regions were found. A pore-diffusion model has also demonstrated that the diffusion is the rate-controlling interaction mechanism. However, the experimental-calculated comparative values are the best way to evaluate a specific aqueous- or solid-phase kinetic model.

Adsorption↗

PubMed2006

Selection of optimum sorption kinetics: comparison of linear and non-linear method.

Comparison of linear least-squares method and a trial and error non-linear method of estimating the kinetic parameters was examined to the experimental data of methylene blue onto activated carbon. Two most commonly used kinetic equations first order kinetics and pseudo second order kinetics was used to analyze the experimental data. The four different form of Ho's pseudo second order kinetic was also discussed. Present investigation showed that the non-linear analysis method as more appropriate method to determine the rate kinetic parameters.

Adsorption↗

PubMed2006

Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments.

It appears plausible that natural selection constrains, to some extent at least, the stability in many natural proteins. If, during protein evolution, stability fluctuates within a comparatively narrow range, then mutations are expected to be fixed with frequencies that reflect mutational effects on stability. Indeed, we recently reported a robust correlation between the effect of 27 conservative mutations on the thermodynamic stability (unfolding free energy) of Escherichia coli thioredoxin and the frequencies of residues occurrences in sequence alignments. We show here that this correlation likely implies a lower limit to thermodynamic stability of only a few kJ/mol below the unfolding free energy of the wild-type (WT) protein. We suggest, therefore, that the correlation does not reflect natural selection of thermodynamic stability by itself, but of some other factor which is linked to thermodynamic stability for the mutations under study. We propose that this other factor is the kinetic stability of thioredoxin in vivo, since( i) kinetic stability relates to irreversible denaturation, (ii) the rate of irreversible denaturation in a crowded cellular environment (or in a harsh extracellular environment) is probably determined by the rate of unfolding, and (iii) the half-life for unfolding changes in an exponential manner with activation free energy and, consequently, comparatively small free energy effects can have deleterious consequences for kinetic stability. This proposal is supported by the results of a kinetic study of the WT form and the 27 single-mutant variants of E. coli thioredoxin based on the global analyses of chevron plots and equilibrium unfolding profiles determined from double-jump unfolding assays. This kinetic study suggests, furthermore, one of the factors that may contribute to the high activation free energy for unfolding in thioredoxin (required for kinetic stability), namely the energetic optimization of native-state residue environments in regions, which become disrupted in the transition state for unfolding.

Amino Acid Sequence↗

PubMed2005

Pulmonary O2 uptake on-kinetics in rowing and cycle ergometer exercise.

The purpose of this study was to characterise, for the first time, the pulmonary O2 uptake (V(O2)) on-kinetic responses to step transitions to moderate and heavy intensity rowing ergometer exercise, and to compare the responses to those observed during upright cycle ergometer exercise. We hypothesised that the recruitment of a greater muscle mass in rowing ergometer exercise (Row) might limit muscle perfusion and result in slower Phase II V(O2) kinetics compared to cycle exercise (Cyc). Eight healthy males (aged 28+/-5 years) performed a series of step transitions to moderate (90% of the mode-specific gas exchange threshold, GET) and heavy (50% of the difference between the mode-specific GET and V(O2) max) work rates, for both Row and Cyc exercise. Pulmonary V(O2) was measured breath-by-breath and the V(O2) on-kinetics were described using standard non-linear regression techniques. With the exception of delta V(O2)delta WR which was approximately 12% greater for Row, the V(O2) kinetic responses were similar between the exercise modes. There was no significant difference in the time constant describing the Phase II V(O2) kinetics between the exercise modes for either moderate (rowing: 25.9+/-6.8 s versus cycling: 25.7+/-8.6 s) or heavy (rowing: 26.5+/-3.0 s versus cycling: 27.8+/-5.1s) exercise. Furthermore, there was no significant difference in the amplitude of the V(O2) slow component between the exercise modes (rowing: 0.34+/-0.13 L min(-1) versus cycling: 0.35+/-0.12 L min(-1)). These data suggest that muscle V(O2) increases towards the anticipated steady-state requirement at essentially the same rate following a step increase in ATP turnover in the myocytes, irrespective of the mode of exercise, at least in subjects with no particular sport specialism. The recruitment of a greater muscle mass in rowing compared to cycling apparently did not compromise muscle perfusion sufficiently to result either in slower Phase II V(O2) kinetics or a greater V(O2) slow component amplitude during heavy exercise.

Adult↗

PubMed2005

Kinetics of tumor growth of prostate carcinoma estimated using prostate-specific antigen.

OBJECTIVES: To investigate whether the second-order kinetics model of prostate-specific antigen (PSA) increase would be more appropriate in some cases than the traditionally assumed first-order model. PSA levels are used to detect tumor recurrence after radical prostatectomy, and the rate of PSA increase is used to predict patients' prognosis. METHODS: Sequential PSA values from 147 patients showing detectable PSA after radical prostatectomy were analyzed by nonlinear regression analysis. The best-fitting model was chosen using the lowest sum of squares residual error. RESULTS: Of the 147 cases, 90 (61.2%) followed the first-order kinetics, and 57 (38.8%) were better described by second-order kinetics. The order of PSA increase correlated with the Gleason score of the tumor in the radical prostatectomy specimens. The first-order kinetics were associated with tumors with Gleason scores of 5 to 6, 7, and 9, and the second-order kinetics were associated with tumors with a Gleason score of 8 (P < 0.01). Our data did not show a correlation between the order of PSA increase and the clinical prognosis. CONCLUSIONS: The presence of a group of tumors in which the increase in PSA follows second-order kinetics is significant. Such an increase may be associated with an autocatalytic mechanism assisting tumor growth. The existence of such a mechanism requires additional investigation.

Humans↗

PubMed2006

Chlorination kinetics of glyphosate and its by-products: modeling approach.

Chlorination reactions of glyphosate, glycine, and sodium cyanate were conducted in well-agitated reactors to generate experimental kinetic measurements for the simulation of chlorination kinetics under the conditions of industrial water purification plants. The contribution of different by-products to the overall degradation of glyphosate during chlorination has been identified. The kinetic rate constants for the chlorination of glyphosate and its main degradation products were either obtained by calculation according to experimental data or taken from published literature. The fit of the kinetic constants with experimental data allowed us to predict consistently the concentration of the majority of the transitory and terminal chlorination products identified in the course of the glyphosate chlorination process. The simulation results conducted at varying aqueous chlorine/glyphosate molar ratios have shown that glyphosate is expected to degrade in fraction of a second under industrial aqueous chlorination conditions. Glyphosate chlorination products are not stable under the conditions of drinking water chlorination and are degraded to small molecules common to the degradation of amino acids and other naturally occurring substances in raw water. The kinetic studies of the chlorination reaction of glyphosate, together with calculations based on kinetic modeling in conditions close to those at real water treatment plants, confirm the reaction mechanism that we have previously suggested for glyphosate chlorination.

Chlorine↗

PubMed2005

Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics.

This paper presents a practical approach to estimate the kinetic parameters of a metabolic network from in vivo kinetics experiments. This method is based on the linlog kinetics format (Visser and Heijnen, 2003, Metab. Eng. 5(3), 164-176; Wu et al., 2004, Eur. J. Biochem. 271, 3348-3359), of which the kinetic parameters, called elasticities, are estimated by an iterative linear optimization followed by non-linear optimization, from transient metabolite concentration data which are directly obtainable from rapid pulse experiments. In this way, not only the parameters are estimated but also a full kinetic model, based on linlog kinetics, is developed. The obtained elasticities also allow immediate calculation of all control coefficients. As an in silico case study, the estimation of elasticities of a linear pathway is presented. The method is shown to be able to estimate the elasticities quite accurately and to be robust toward errors in the metabolite data originating from sampling and measurement inaccuracy. The method allows experimental redesign to get more accurate estimated parameters and accommodates various types of experimentally applied disturbances in the pathway: changes in independent metabolites, dependent metabolites or enzyme levels/activities.

Computer Simulation↗

PubMed2003

Effects of Ca2+ and EGTA on P680*+ reduction kinetics and O2 evolution of Photosystem II.

We report for the first time significant changes in the P680*+ reduction kinetics of Photosystem II (PS II) in which the 17 and 23 kDa extrinsic polypeptides are intact, in the presence of Ca(2+) or ethylene glycol bis (beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) which were added to vary the Ca(2+) concentration from 5 microM to 30 mM. The decrease in the extent of normal P680*+ reduction decay with lifetimes of 40-370 ns and a corresponding increase in the extent of kinetics with lifetimes of 20-220 micros was interpreted as being due to electron transfer from Y(Z) to P680*+ being replaced by slow forward conduction and by processes including P680*+/Q(A)(-) recombination. The question of whether changes in P680*+ reduction kinetics were caused by loss of Ca(2+) from PS II or by direct interaction of EGTA with PS II was addressed by lowering the free-Ca(2+) concentration of suspensions of PS II core complexes by serial dilution in the absence of EGTA. Despite a significant decrease in the rate of O(2) evolution after this treatment, only small changes in the P680*+ reduction kinetics were observed. Loss of Ca(2+) did not affect P680*+ reduction associated with electron transfer from Y(Z). Since much larger changes in the P680*+ reduction kinetics of intact PS II occurred at comparable free-Ca(2+) concentrations in the presence of EGTA, we conclude that EGTA influenced the P680*+ reduction kinetics by directly interacting with PS II rather than by lowering the free Ca(2+) concentration of the surrounding media. Notwithstanding these effects, we show that useful information about Ca(2+) binding to PS II can be obtained when direct interaction of EGTA is taken into account.

Calcium↗

PubMed2000

Kinetics and mechanism of the reaction of aminoguanidine with the alpha-oxoaldehydes glyoxal, methylglyoxal, and 3-deoxyglucosone under physiological conditions.

Aminoguanidine (AG), a prototype agent for the preventive therapy of diabetic complications, reacts with the physiological alpha-oxoaldehydes glyoxal, methylglyoxal, and 3-deoxyglucosone (3-DG) to form 3-amino-1,2,4-triazine derivatives (T) and prevent glycation by these agents in vitro and in vivo. The reaction kinetics of these alpha-oxoaldehydes with AG under physiological conditions pH 7.4 and 37 degrees was investigated. The rate of reaction of AG with glyoxal was first order with respect to both reactants; the rate constant k(AG,G) was 0.892 +/- 0.037 M(-1) sec(-1). The kinetics of the reaction of AG with 3-DG were more complex: the rate equation was d[T](o)/dt (initial rate of T formation) = [3-DG](k(AG,3-DG)[AG] + k(3-DG)), where k(AG,3-DG) = (3. 23 +/- 0.25) x 10(-3) M(-1) sec(-1) and k(3-DG) = (1.73 +/- 0.08) x 10(-5) sec(-1). The kinetics of the reaction of AG with methylglyoxal were consistent with the reaction of both unhydrated (MG) and monohydrate (MG-H(2)O) forms. The rate equation was d[T](o)/dt = ¿k(1)k(AG,MG)/(k(-1) + k(AG,MG)[AG]) + k(AG, MG-H(2)O)¿[MG-H(2)O][AG], where the rate constant for the reaction of AG with MG, k(AG,MG), was 178 +/- 15 M(-1) sec(-1) and for the reaction of AG with MG-H(2)O, k(AG,MG-H(2)O), was 0.102 +/- 0.001 M(-1) sec(-1); k(1) and k(-1) are the forward and reverse rate constants for methylglyoxal dehydration MG-H(2)O right harpoon over left harpoon MG. The kinetics of these reactions were not influenced by ionic strength, but the reaction of AG with glyoxal and with methylglyoxal under MG-H(2)O dehydration rate-limited conditions increased with increasing phosphate buffer concentration. Kinetic modelling indicated that the rapid reaction of AG with the MG perturbed the MG/MG-H(2)O equilibrium, and the ratio of the isomeric triazine products varied with initial reactant concentration. AG is kinetically competent to scavenge the alpha-oxoaldehydes studied and decrease related advanced glycated endproduct (AGE) formation in vivo. This effect is limited, however, by the rapid renal elimination of AG. Decreased AGE formation is implicated in the prevention of microvascular complications of diabetes by AG.

Deoxyglucose↗

PubMed2003

Kinetics of the micelle-to-vesicle transition: aqueous lecithin-bile salt mixtures.

Important routes to lipid vesicles (liposomes) are detergent removal techniques, such as dialysis or dilution. Although they are widely applied, there has been only limited understanding about the structural evolution during the formation of vesicles and the parameters that determine their properties. We use time-resolved static and dynamic light scattering to study vesicle formation in aqueous lecithin-bile salt mixtures. The kinetic rates and vesicle sizes are found to strongly depend on total amphiphile concentration and, even more pronounced, on ionic strength. The observed trends contradict equilibrium calculations, but are in agreement with a kinetic model that we present. This model identifies the key kinetic steps during vesicle formation: rapid formation of disk-like intermediate micelles, growth of these metastable micelles, and their closure to form vesicles once line tension dominates bending energy. A comparison of the rates of growth and closure provides a kinetic criterion for the critical size at which disks close and thus for the vesicle size. The model suggests that liposomes are nonequilibrium, kinetically trapped structures of very long lifetime. Their properties are hence controlled by kinetics rather than thermodynamics.

Animals↗

PubMed1992

Long tail kinetics in biophysics?

Long tail kinetics describe a variety of data from complex, disordered materials that cannot be described by conventional kinetics. It is suggested that the kinetics of diffusive motion in complex biological media, such as cytoplasm or biomembranes, might also have long tails. The effects of long tail kinetics are investigated for two standard biophysical measurements, fluorescence recovery after photobleaching (FRAP), and dynamic light scattering (DLS). It is shown that long tail kinetic data would yield significantly distorted and misleading results when analyzed assuming conventional kinetics.

Kinetics↗

PubMed1993

Structural relaxation and nonexponential kinetics of CO-binding to horse myoglobin. Multiple flash photolysis experiments.

The geminate recombination kinetics of CO-myoglobin strongly deviates from single exponential behavior in contrast to what is expected for unimolecular reactions (1). At low temperatures, this result was attributed to slowly exchanging conformational states which differ substantially in barrier height for ligand binding. Above 160 K the kinetics apparently slow down with temperature increase. Agmon and Hopfield (2) explain this result in terms of structural relaxation perpendicular to the reaction coordinate, which enhances the activation energy. In their model, structural relaxation homogenizes the kinetic response. Recently, Steinbach et al. (3) proposed a relaxation model which conserves the kinetic inhomogeneity. Below we test these conjectures by single and multiple excitation experiments. This method allows for discrimination between parallel (inhomogeneous) and sequential (homogeneous) kinetic schemes. The kinetic anomaly above 160 K is shown to result from a homogeneous, structurally relaxed intermediate. However a second anomaly is found above 210 K concerning the inhomogeneous phase which may indicate either a shift in activation energy or entropy.

Animals↗

PubMed1994

Comparison of kinetics of formation of helices and hydrophobic core during the folding of staphylococcal nuclease from acid.

Our previous kinetic study of the acid and base-induced folding/unfolding transitions of staphylococcal nuclease (SNase) has monitored Trp-140 fluorescence. Trp-140 is located near the flexible COOH terminus and whether or not its fluorescence reflects the overall conformation of the protein has yet to be established. Here we show that the fluorescence intensity of Try-140 correlated closely with the thermal stability (i.e., the calorimetric enthalpy, delta Hcal, of unfolding) of the protein in the pH range 7 to 2.5, confirming that it is a good measure of the overall protein structure. Circular dichroism (CD) at 222 nm, which reflects the helical content of the protein molecule, was used to follow the same folding/unfolding transition in order to compare kinetics of the helix formation and of the appearance of the hydrophobic core. In addition to the three kinetic phases reported earlier with the fluorescence detection, there were a rapid reaction (completed within the 25 ms mixing time of the instrument), which comprised 15% of the signal, and a very slow reaction (time constant > 300 s), which comprised 19% of the signal. With the fluorescence detection for the folding from acid, only 5% of the signal occurred in the rapid phase and there was no reaction slower than 300 s. By comparing kinetics of folding at pH 7 by the CD and fluorescence detection methods, we concluded that: (a) Roughly 15% of the helix content of SNase accumulated before significant changes in the hydrophobic environment (< 5%) of Trp-140 could be detected. The rapid appearance of CD signal reminiscent of helix formation within 25ms would be consistent with the framework model of protein folding. Note, however, that, 15% of the 22% helix content of the protein amounts to an equivalent of fewer than 5 amino acid residues. (b) For the time-resolved signal between 2 ms and 300s, kinetics measured by both properties are consistent with the sequential model, D4 = D3 = D2 = D1 = No (the four Ds are the four substates of the denatured protein and No is the native state). The major folding step by both signals is the D1 to No transition, which gave approximately a 50% change in fluorescence and CD and had a time constant of 160 ms at 25 degree C, pH7.0. (c) The slow phase with the CD signal (>300 s), which is insensitive to Trp-140 fluorescence, has been assigned to be the cis/trans isomerization of Pro-1 17 by other studies. (d) Kinetics in the unfolding direction are consistent with the above interpretation.

Amino Acid Sequence↗

PubMed1999

Kinetic analysis of high affinity forms of interleukin (IL)-13 receptors: suppression of IL-13 binding by IL-2 receptor gamma chain.

Interleukin-13 (IL-13) is a pleiotropic cytokine that controls growth, differentiation, and apoptosis of immune and tumor cells. To understand the mechanisms of interaction between IL-13 and IL-13 receptors (IL-13R), and the role of the IL-2 receptor common gamma chain (gammac) in IL-13 binding and processing, we have examined IL-13 binding kinetics, dissociation/shedding, and internalization in renal cell carcinoma (RCC) cell lines. We observed a new phenomena in that the apparent rate of association, but not the dissociation, was strongly related to IL-13 concentration. We also observed cooperativity phenomena in IL-13 and IL-13R interaction in control RCC (MLneo) cells, but not in cells transfected with gammac chain (MLgammac). The number of IL-13 binding sites, the effective rate of ligand association, and the dissociation rate constants were reduced in gammac-transfected cells compared to control RCC cells. Two forms of IL-13R were detected in these cell lines, which differed in the kinetics of endocytosis and dissociation/exocytosis. Only a small fraction of bound receptors (14-24%) was rapidly internalized and the same fraction of the ligand-receptor complexes was shed and/or dissociated. The expression of gammac chain did not change any of these processes. A two independent high-affinity and moderate-affinity receptor model fit the kinetic observations in gammac-transfected cells. However, in control cells, the binding kinetics were more complicated. A mathematical model that fit a set of kinetic and steady state data in control cells was selected from a set of possible models. This best-fit model predicts that 1) two different IL-13R are expressed on the cell membrane, 2) a minor fraction of IL-13R exist as microclusters (homodimers and/or heterodimers) without exogenous IL-13, 3) high morphological complexity of the gammac-negative control cell membrane affects the cooperativity phenomena of IL-13 binding, and 4) a large number of co-receptor molecules is present, which helps keep the ligand on the cell surface for a long period of time after fast IL-13 binding and provides a negative control for ligand binding via production of the high affinity inhibitor bound to IL-13. Our data demonstrate that gammac exerts dramatic changes in the kinetic mechanisms of IL-13 binding.

Binding, Competitive↗

PubMed2000

Kinetics and mechanics of cell adhesion.

Cell adhesion is mediated by specific interaction between receptors and ligands. Such interaction provides not only physical linkage but also communication between the cell and its environment. The kinetics and mechanics of cell adhesion are coupled, because force can influence the formation and dissociation of receptor-ligand bonds. The kinetic rates and their force dependence determine how likely, how rapidly and how strongly cells bind as well as how long they remain bound. Since adhesion molecules are linked to apposing cellular membranes, their interaction is governed by two-dimensional (2D) kinetics. This is in contrast to the three-dimensional (3D) binding of soluble ligands to cell surface receptors. Unlike the 3D case in which many methods are available for measuring kinetic rates, not until recently have the 2D kinetic rates become experimentally measurable. In this review, I will discuss the recent progress in the experimental methods that enable quantification of the relevant kinetic and mechanical parameters, the fundamental concepts that underlie the physics of the biological phenomena, and the mathematical models that relate functions to the intrinsic properties of the adhesion molecules.

Animals↗

PubMed2003

An alternative Avrami equation to evaluate kinetic parameters of the interaction of Hg(II) with thin chitosan membranes.

In this work, thin chitosan membranes were utilized as an adsorbent for the removal of Hg(II) from aqueous solutions. A rise of temperature accelerates the mass transfer of Hg(II) to the membranes, surfaces. The kinetic data did not present a good fitting to the traditional Lagergren adsorption kinetic equations. An alternative Avrami kinetic equation was employed and successfully fitted to the kinetic adsorption quantities. From this new equation, two regions presenting distinct kinectic parameters were found, and the use of the parameter n was also relationed to the determination of the kinetic order. Variations of the adsorption kinetic rate in relation to the time, the initial Hg(II) concentration, and the temperature were also calculated and are discussed.

Adsorption↗

PubMed2003

Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2. We find that residue-based additive Gō-like contact energies, although native-centric, are by themselves insufficient for protein-like calorimetric two-state cooperativity. Further native biases by local conformational preferences are necessary for protein-like thermodynamics. Kinetically, however, even models with both contact and local native-centric energies do not produce simple two-state chevron plots. Thus a model protein's thermodynamic cooperativity is not sufficient for simple two-state kinetics. The models tested appear to have increasing internal friction with increasing native stability, leading to chevron rollovers that typify kinetics that are commonly referred to as non-two-state. The free energy profiles of these models are found to be sensitive to the choice of native contacts and the presumed spatial ranges of the contact interactions. Motivated by explicit-water considerations, we explore recent treatments of solvent granularity that incorporate desolvation free energy barriers into effective implicit-solvent intraprotein interactions. This additional feature reduces both folding and unfolding rates vis-à-vis that of the corresponding models without desolvation barriers, but the kinetics remain non-two-state. Taken together, our observations suggest that interaction mechanisms more intricate than simple Gō-like constructs and pairwise additive solvation-like contributions are needed to rationalize some of the most basic generic protein properties. Therefore, as experimental constraints on protein chain models, requiring a consistent account of protein-like thermodynamic and kinetic cooperativity can be more stringent and productive for some applications than simply requiring a model heteropolymer to fold to a target structure.

Calorimetry↗