SEARCH · PubMed Health

Results for “Kinetics”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed1994

Kinetics of hydrolysis of dansyl peptide substrates by thermolysin: analysis of fluorescence changes and determination of steady-state kinetic parameters.

The stopped-flow fluorescence technique has been used to study the hydrolysis of 10 dansyl peptides by thermolysin. The origin of the fluorescence changes observed during the reactions has been investigated in detail. Depending on the substrate and the excitation wavelength, the dansyl fluorescence changes observed arise either from energy transfer (maximal at lambda ex = 230 and 280 nm) between Trp residues of thermolysin and the dansyl group of the substrate in enzyme-substrate (ES) complexes or from both sources. These excitation (maximal at lambda ex = 245 and 340 nm) of the free substrate and product, or from both sources. These two types of fluorescence signals reflect the concentrations of ESi and free substrate, respectively. Both types of fluorescence changes have been used to monitor the reaction progress, and different mathematical formalisms have been used to determine the kinetic parameters for the reactions with results that are in good agreement. The efficiency of Trp quenching by a series of five dansyl tripeptides is shown to be related to the fractional saturation of enzyme and follows the KM-1 values for the substrates. The quenching efficiency for a dansyl tetrapeptide is weaker due to the greater distance between the dansyl group and the Trp-115 donor in thermolysin. On the basis of these studies, substrates capable of supporting more detailed kinetic studies of thermolysin have been identified.

Amino Acid Sequence↗

PubMed1982

Comparison of the kinetics of ribooligonucleotide, deoxyribooligonucleotide, and hybrid oligonucleotide double-strand formation by temperature-jump kinetics.

The kinetics of double-strand formation were measured by using temperature-jump kinetic techniques for the DNA oligonucleotides dCA5G + dCT5G, the analogous RNA oligonucleotides rCA5G + rCU5G, and the hybrid rCA5G + dCT5G. The DNA oligonucleotides have a faster rate of recombination and a slower rate of dissociation at 12.0 degrees C than the RNA oligonucleotides; the hybrid has about the same recombination rate and a slightly faster dissociation rate than the RNA oligonucleotides. The activation energies for recombination for the DNA and RNA oligonucleotides are both near 0 kcal/mol. The difference in dissociation and recombination activation energies is consistent with the thermodynamic results obtained earlier. The relaxation process is composed of two exponential components for the RNA and hybrid oligonucleotides at temperatures of 12.0 degrees C and lower. One exponential component is observed for these oligonucleotides above 12.0 degrees C and for the DNA oligonucleotides at all temperatures.

Kinetics↗

PubMed1986

Kinetics and extent of fusion between Sendai virus and erythrocyte ghosts: application of a mass action kinetic model.

The kinetics and extent of fusion between Sendai virus and erythrocyte ghosts were investigated with an assay for lipid mixing based on the relief of self-quenching of fluorescence. The results were analyzed in terms of a mass action kinetic model, which views the overall fusion reaction as a sequence of a second-order process of virus-cell adhesion followed by the first-order fusion reaction itself. The fluorescence development during the course of the fusion process was calculated by numerical integration, employing separate rate constants for the adhesion step and for the subsequent fusion reaction. Dissociation of virus particles from the cells was found to be of minor importance when fusion was initiated by mixing the particles at 37 degrees C. However, besides the initiation of fusion, extensive dissociation does occur after a preincubation of a concentrated suspension of particles at 4 degrees C followed by a transfer of the sample to 37 degrees C. The conclusion drawn from the levels of fluorescence increase obtained after 20 h of incubation is that in principle most virus particles can fuse with the ghosts at 37 degrees C and pH 7.4. However, the number of Sendai virus particles that actually fuse with a single ghost is limited to 100-200, despite the fact more than 1000 particles can bind to one cell. This finding may imply that 100-200 specific fusion sites for Sendai virus exist on the erythrocyte membrane. A simple equation can yield predictions for the final levels of fluorescence for a wide range of ratios of virus particles to ghosts.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

Analysis of the kinetic isotope effects on initial rates in transient kinetics.

A method was described recently for circumventing the difficulties in determining intrinsic kinetic isotope effects from eigenvalues obtained in transient kinetic experiments (Maniscalco, Tally, and Fisher (2004) Arch. Biochem. Biophys. 425, 165-172). The method, based on the isotope effects on initial rates of formation of intermediates, was validated by numerical simulation for only a few linear reaction sequences. A general analytical proof of the validity of the method is given in this work. The mathematical approach, using rate laws and L'Hôpital's rule, allows more complex reaction schemes to be analyzed. Several are analyzed in this article, illustrating the broad applicability and possible complications in this approach for determining intrinsic isotope effects. Some possible applications are noted, with particular attention being paid to nonlinear reaction schemes, the effect of measuring signals rather than concentration, and the ability to distinguish stepwise from concerted reactions.

Deuterium↗

PubMed1997

Pre-steady-state kinetic analysis of 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase: kinetic evidence for enol/keto tautomerization.

The reaction catalyzed by 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase (MhpC) was analyzed by stopped-flow UV-visible kinetics at 317 nm (substrate depletion) and 270 nm (product formation) at pH 5.0 and 4.0. Comparison of the rates and amplitudes of product formation versus substrate depletion provided evidence for the formation of a discrete keto-intermediate, as predicted from previous isotope exchange experiments [Lam, W. W. Y., & Bugg, T. D. H. (1997) Biochemistry, 36, 12242-12251]. Accurate modeling of the concentration data could only be achieved using a branched kinetic mechanism in which the intermediate is released at a rate comparable to its catalytic turnover, consistent with the earlier isotope exchange data. The apparent "leakiness" of the active site and relatively weak substrate binding (Kd = 30 microM) are consistent with a mechanism in which the enzyme binds the dienol substrate in a strained, nonplanar conformation which promotes ketonization in the C-5 position to give a keto-intermediate.

Catalysis↗

PubMed2000

Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. stopped-flow kinetic studies using fluorescent, ribose-, and base-modified nucleotide analogues.

The kinetic mechanism of binding nucleotide cofactors to the Escherichia coli primary replicative helicase DnaB protein has been studied, using the fluorescence stopped-flow technique. The experiments have been performed with fluorescent ATP and ADP analogues bearing the modification on the ribose, MANT-AMP-PNP and MANT-ADP, and on the base, epsilonAMP-PNP and epsilonADP. Association of the DnaB helicase with nucleotide cofactors is characterized by four relaxation times that indicate that the binding occurs by a minimum of four-steps. The simplest mechanism which can describe the data is a four-step sequential process where the bimolecular binding step is followed by three isomerization steps. This mechanism is described by the following equation: [equation in text]. The binding mechanism is independent of the location of the nucleotide cofactor modification and is an intrinsic property of the DnaB helicase-nucleotide system. Quantitative amplitude analyses, using the matrix projection operator technique, allowed us to determine specific fluorescence changes accompanying the formation of all intermediates relative to the fluorescence of the free nucleotide. It shows that the major conformational change of the DnaB helicase-nucleotide complex occurs in the formation of the (H-N)(1). Moreover, the value of the bimolecular rate constant, k(1), is 3-4 orders of magnitude lower than the value expected for the diffusion-controlled reaction. These results indicate that the determined first step includes formation of the collision and an additional transition of the enzyme-nucleotide complex. The obtained results provide evidence of profoundly different conformational states of the ribose and base regions of the nucleotide-binding site in different intermediates. The sequential nature of the mechanism of the nucleotide binding to the DnaB helicase indicates the lack of the existence of a kinetically significant conformational equilibrium of the helicase protomer and the DnaB hexamer prior to the binding. The significance of these results for the functioning of the DnaB helicase is discussed.

Adenosine Diphosphate↗

PubMed2006

Dissolution kinetics of titanium dioxide nanoparticles: the observation of an unusual kinetic size effect.

Different types of industrially produced titanium dioxide nanoparticles and a precipitated titanium dioxide have been dissolved in aqueous NaCl solutions at temperatures of 25 and 37 degrees C. The titanium concentration in solution with regard to dependence on time has been determined up to 3000 h after starting the dissolution experiment. The effect of particle size, pH value, temperature, background electrolyte concentration, and mass concentration of titanium dioxide exposed to the liquid phase has been studied. The nanoparticles have been characterized by N2 physisorption measurements and XRD. The total dissolved titanium in solution has been determined by adsorptive stripping voltammetry (AdSV) and inductively coupled plasma mass spectrometry (ICP-MS). A new kinetic size effect has been observed. It turns out that this effect can be explained by applying an already existing phenomenological thermodynamic and kinetic model. The model describes all possible phenomena in a colloidal dispersion, nucleation, growth of particles, Ostwald ripening, and dissolution of particles using a uniform concept.

Hydrogen-Ion Concentration↗

PubMed1989

Kinetic and chemometric studies of the determination of creatinine using the Jaffé reaction. Part 2. Application to human serum samples: kinetic behaviour and chemometric evaluation of the determination.

The kinetic behaviour of the reaction of alkaline picrate with creatinine in human serum samples was found to be similar to that for standard creatinine solutions containing albumin. A chemometric evaluation of the kinetic determination of creatinine using the Jaffé reaction was carried out. The analysis of variance (ANOVA) method applied to the delta A45,180 values, obtained from two replicates of three different serum samples over a period of 10 d, showed that the between-day and between-replicate variations added a component to the total variability, the residual error (delta R2) being 5 X 10(-5). A study of the accuracy of the determination was carried out by means of percentage recovery experiments, Youden's method and the standard additions method. Percentage recovery experiments showed that albumin has a marked effect on the results obtained. The application of Youden's method to four serum samples indicated that the method does not have a constant bias error, but, by applying the standard additions method it was concluded that the method has a proportional bias error. The recovery factor, defined as the ratio of the slope of the standard additions graph to that of the standard response graph, was also calculated for the four serum samples. The best values were obtained with different standard response graphs (7.7, 15.4 and 25.6 g l-1 of albumin) for each sample. A modification of the routine procedure used in clinical laboratories is proposed. This modification is based on the principles of the standard additions method and gives better results for creatinine content than those obtained with the routine procedure.

Creatinine↗

PubMed1973

D-3-hydroxybutyrate dehydrogenase from Rhodopseudomonas spheroides. Kinetic mechanism from steady-state kinetics of the reaction catalysed by the enzyme in solution and covalently attached to diethylaminoethylcellulose.

1. The reversible NAD(+)-linked oxidation of d-3-hydroxybutyrate to acetoacetate in 0.1m-sodium pyrophosphate buffer, pH8.5, at 25.0 degrees C, catalysed by d-3-hydroxybutyrate dehydrogenase (d-3-hydroxybutyrate-NAD(+) oxidoreductase, EC 1.1.1.30), was studied by initial-velocity, dead-end inhibition and product-inhibition analysis. 2. The reactions were carried out on (a) the soluble enzyme from Rhodopseudomonas spheroides and (b) an insoluble derivative of this enzyme prepared by its covalent attachment to DEAE-cellulose by using 2-amino-4,6-dichloro-s-triazine as coupling agent. 3. The insolubilized enzyme preparation contained 5mg of protein/g wet wt. of total material, and when freshly prepared its specific activity was 1.2mumol/min per mg of protein, which is 67% of that of the soluble dialysed enzyme. 4. The reactions catalysed by both the enzyme in solution and the insolubilized enzyme were shown to follow sequential pathways in which the nicotinamide nucleotides bind obligatorily first to the enzyme. Evidence is presented for kinetically significant ternary complexes and that the rate-limiting step(s) of both catalyses probably involves isomerization of the enzyme-nicotinamide nucleotide complexes and/or dissociation of the nicotinamide nucleotides from the enzyme. Both catalyses therefore are probably best described as ordered Bi Bi mechanisms, possibly with multiple enzyme-nicotinamide nucleotide complexes. 5. The kinetic parameters and the calculable rate constants for the catalysis by the soluble enzyme are similar to the corresponding parameters and rate constants for the catalysis by the insolubilized enzyme.

Acetoacetates↗

PubMed1984

Regulatory kinetics of wheat-germ aspartate transcarbamoylase. Adaptation of the concerted model to account for complex kinetic effects of uridine 5'-monophosphate.

The kinetic effects of the end-product inhibitor UMP on aspartate transcarbamoylase (EC 2.1.3.2) purified to homogeneity from wheat germ were studied. In agreement with an earlier study of the relatively crude enzyme [Yon (1972) Biochem. J. 128, 311-320], the half-saturating concentrations of UMP and of the first substrate, carbamoyl phosphate (but not of the second, L-aspartate), were found to be strongly interdependent. However, the kinetic behaviour of the pure enzyme differed from that of the crude enzyme in several important respects, namely: (a) the apparent affinity for UMP was lower with the pure enzyme; (b) sigmoidicity was absent from plots of initial rate versus carbamoyl phosphate concentration, each at a fixed UMP concentration; (c) sigmoidicity was greatly exaggerated in plots of initial rate versus UMP concentration, each at a fixed carbamoyl phosphate concentration, owing to the occurrence of a slight but definite maximum in each plot at low UMP concentration; (d) there was a relative increase in this maximum in the presence of N-phosphonacetyl-L-aspartate, an inhibitor competitive with carbamoyl phosphate. It is shown that a modified two-conformation concerted-transition model can be used to account for most of these features of the pure enzyme. The model treats carbamoyl phosphate and UMP as antagonistic allosteric ligands binding to alternative conformational states [Monod, Wyman & Changeux (1965) J. Mol. Biol. 12, 88-118], carbamoyl phosphate binding non-exclusively (dissociation constants 20 microM and 85 microM respectively) and UMP binding exclusively (dissociation constant 2.5 microM). The model postulates further that the conformation with lower affinity for carbamoyl phosphate has the higher value of kcat., and that it binds UMP in competition with carbamoyl phosphate. Parameters giving the best fit of experimental data to this model were found by a non-linear least-squares search procedure.

Aspartate Carbamoyltransferase↗

PubMed1987

Kinetics of hexokinase D ('glucokinase') with inosine triphosphate as phosphate donor. Loss of kinetic co-operativity with respect to glucose.

When ATP, the normal phosphate donor for hexokinase D ('glucokinase'), is replaced by ITP, the positive co-operativity with respect to glucose disappears. This may be rationalized in relation to kinetic models for hexokinase D co-operativity, which assume that with the normal substrates the chemical reaction and subsequent release of products occur so rapidly that binding of substrates cannot approach equilibrium and is therefore not constrained by the thermodynamic requirement that the Hill coefficient for substrate binding cannot exceed the number of binding sites. ITP is a much poorer substrate than ATP, however: its Km value at high glucose concentrations is 24 times the value for ATP, whereas the value of the limiting rate V is decreased about 8-fold. Consequently it is no longer possible for the ternary complex to be converted into products rapidly enough to generate kinetic co-operativity. The negative co-operativity with respect to glucose observed in 2H2O with ATP as phosphate donor also disappears when ITP is used instead of ATP.

Animals↗

PubMed1975

[The pharmaco-kinetics of angiographic contrast media with special reference to the extra-vascular spaces. Fundamental studies on dog for the characterisation of angiographic media. I The pharmaco-kinetics of various contrast media under conditions of constant infusion (balanced flow)].

The pharmaco-kinetics of angiographic contrast media in the extra-vascular space, which are largely unknown, were investigated experimentally in dogs. As part of a basic study, using radio-active contrast media, it was possible to determine the concentration and rate of elimination in practically all organs and tissues. Measurements were carried out first after prolonged infusion of the contrast under conditions of balanced flow, and secondly six hours after the end of the infusion. It was therefore possible to determine the inflow and loss of contrast medium in various organs, or organs systems. The most commonly used angiographic contrast media in Germany were investigated. Their kinetic behaviour is largely identical, their pattern of distribution and elimination depended principally on the organ or tissue. A comprehensive discussion of the results of all the experiments will be given in the third article.

Animals↗

PubMed1997

Oxidation kinetics of ethanol by human cytochrome P450 2E1. Rate-limiting product release accounts for effects of isotopic hydrogen substitution and cytochrome b5 on steady-state kinetics.

A number of cytochrome P450 (P450) 2E1 substrates are known to show kinetic deuterium isotope effects of approximately 5 on Km (DK = DKm/HKm), but not on kcat, in rat liver microsomes (e.g. N-nitrosodimethylamine, ethanol, and CH2Cl2). We observed DKm values of 3-5 for recombinant human P450 2E1-catalyzed ethanol oxidation. Replacing NADPH and O2 with the oxygen surrogate cumene hydroperoxide yielded similar results. Ferric P450 2E1 reduction was fast (k >1000 min-1) even in the absence of substrate. These results indicate that the basis for the increase in Km is in the latter portion of the catalytic cycle. The intrinsic isotope effect (Dk) for ethanol oxidation was determined (competitively) to be 3.8, indicating that C-H bond cleavage is isotopically sensitive. Pre-steady-state studies showed a burst of product formation (k = 410 min-1), with the burst amplitude corresponding to the P450 concentration. Deuteration of ethanol resulted in an isotope effect of 3.2 on the rate of the burst. We conclude that product release is rate-limiting in the oxidation of ethanol to acetaldehyde by P450 2E1. The steady-state kinetics can be described by a paradigm in which the kcat approximates the rate of product release, and Km is an expression in which the denominator is dominated by the rate of C-H bond breaking.

Anaerobiosis↗

PubMed2005

A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. A mutagenic, kinetic, and crystallographic study.

Binding of an agonist to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA) receptor family of the glutamate receptors (GluRs) results in rapid activation of an ion channel. Continuous application results in a non-desensitizing response for agonists like kainate, whereas most other agonists, such as the endogenous agonist (S)-glutamate, induce desensitization. We demonstrate that a highly conserved tyrosine, forming a wedge between the agonist and the N-terminal part of the bi-lobed ligand-binding site, plays a key role in the receptor kinetics as well as agonist potency and selectivity. The AMPA receptor GluR2, with mutations in Tyr-450, were expressed in Xenopus laevis oocytes and characterized in a two-electrode voltage clamp setup. The mutation GluR2(Y450A) renders the receptor highly kainate selective, and rapid application of kainate to outside-out patches induced strongly desensitizing currents. When Tyr-450 was substituted with the larger tryptophan, the (S)-glutamate desensitization is attenuated with a 10-fold increase in steady-state/peak currents (19% compared with 1.9% at the wild type). Furthermore, the tryptophan mutant was introduced into the GluR2-S1S2J ligand binding core construct and co-crystallized with kainate, and the 2.1-A x-ray structure revealed a slightly more closed ligand binding core as compared with the wild-type complex. Through genetic manipulations combined with structural and electrophysiological analysis, we report that mutations in position 450 invert the potency of two central agonists while concurrently strongly shaping the agonist efficacy and the desensitization kinetics of the AMPA receptor GluR2.

Alanine↗

PubMed2004

Supplementation with aromatic amino acids improves leucine kinetics but not aromatic amino acid kinetics in infants with infection, severe malnutrition, and edema.

We investigated whether supplementation with an aromatic amino acid (AAA) cocktail consisting of 0.5 mmol each of phenylalanine, tryptophan, and tyrosine compared with isonitrogenous amounts of alanine (Ala) would improve measures of protein kinetics in 14 (8 with AAA, 6 Ala) children with edematous malnutrition (aged 6-24 mo) during the infected acute malnourished state. Supplementation started immediately after the baseline experiment, 2 d postadmission and continued to the end of the acute phase of treatment. The second (postsupplementation) experiment was done approximately 12 d postadmission. We measured leucine kinetics, phenylalanine and tyrosine fluxes, using an i.g. 8-h prime continuous infusion of (2)H(3)-leucine, and an i.v. 6-h prime continuous infusion of (13)C-leucine, (2)H(2)-tyrosine, and (2)H(5)-phenylalanine in the fed state. Leucine flux tended to be faster (P = 0.06) in the AAA group compared with Ala group after supplementation (mean difference +/- SEM): 22.6 +/- 10.9 micromol/(kg . h). The rate of leucine appearance from protein breakdown [28.1 +/- 9.4 micromol/(kg . h)] and the nonoxidative disposal of leucine [i.e., leucine to protein synthesis; 35.4 +/- 12.9 micromol/(kg . h)] were faster (P < 0.02) in the AAA group than in the Ala group. There was no significant effect of supplementation on leucine splanchnic metabolism, phenylalanine, and tyrosine fluxes. These findings are consistent with the hypothesis that the blunting of the protein catabolic response to infection in children with edematous malnutrition syndrome is due to limited availability of aromatic amino acids.

Alanine↗

PubMed1985

Kinetic study of carboxypeptidase P-catalyzed reaction. Pressure and temperature dependence of kinetic parameters.

Detailed kinetic analyses of carboxypeptidase P-catalyzed reactions were carried out spectrophotometrically using 3-(2-furyl)acryloyl-acylated peptide substrates. The maximum kcat/Km was observed at around pH 3.5 for the synthetic peptide substrates. The kcat/Km value decreased with increasing pH, with an apparent pKa value of 4.43. However, the maximum kcat was observed at neutral pH (pH congruent to 6) and the pKa was 4.49. These apparently different pH profiles for kcat/Km and kcat of this enzyme were due to the decreasing Km value in the acid pH region. The pressure and temperature dependences of these kinetic parameters were also measured. N-Benzoylglycyl-L-phenyllactate (Bz-Gly-OPhLac) gave dependences similar to those of the peptide substrate, suggesting that there is no distinct difference in the catalytic mechanism between the peptide and the ester hydrolyses.

Carboxypeptidases↗

PubMedDate not supplied

Myocardial bethanidine kinetics after single-dose intravenous infusion: correlation with plasma kinetics in closed-chest dogs.

Myocardial and plasma bethanidine kinetics were determined in five dogs after an intravenous dose of 6 mg/kg/10 min. Serial myocardial drug concentrations were determined from endomyocardial samples obtained by transvenous biopsies between 15 min and 72 h. Tissue and plasma samples were assayed by gas-liquid chromatography. Bethanidine was rapidly concentrated in myocardium within 15 min. Tissue/plasma drug ratios averaged 131 +/- 35 between 15 min and 2 h and 53 +/- 10 between 6 and 48 h. Parallel biexponential decay then occurred for both tissue and plasma compartments; the terminal half-life approximated 16 h. Based on differences in rates of myocardial drug kinetics, the cardiac antifibrillatory effects of bethanidine may occur more rapidly than those of bretylium.

Animals↗

PubMed1998

Biomechanics of the knee during closed kinetic chain and open kinetic chain exercises.

PURPOSE: Although closed (CKCE) and open (OKCE) kinetic chain exercises are used in athletic training and clinical environments, few studies have compared knee joint biomechanics while these exercises are performed dynamically. The purpose of this study was to quantify knee forces and muscle activity in CKCE (squat and leg press) and OKCE (knee extension). METHODS: Ten male subjects performed three repetitions of each exercise at their 12-repetition maximum. Kinematic, kinetic, and electromyographic data were calculated using video cameras (60 Hz), force transducers (960 Hz), and EMG (960 Hz). Mathematical muscle modeling and optimization techniques were employed to estimate internal muscle forces. RESULTS: Overall, the squat generated approximately twice as much hamstring activity as the leg press and knee extensions. Quadriceps muscle activity was greatest in CKCE when the knee was near full flexion and in OKCE when the knee was near full extension. OKCE produced more rectus femoris activity while CKCE produced more vasti muscle activity. Tibiofemoral compressive force was greatest in CKCE near full flexion and in OKCE near full extension. Peak tension in the posterior cruciate ligament was approximately twice as great in CKCE, and increased with knee flexion. Tension in the anterior cruciate ligament was present only in OKCE, and occurred near full extension. Patellofemoral compressive force was greatest in CKCE near full flexion and in the mid-range of the knee extending phase in OKCE. CONCLUSION: An understanding of these results can help in choosing appropriate exercises for rehabilitation and training.

Adult↗