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PubMed1987

Acetylcholine receptor: channel-opening kinetics evaluated by rapid chemical kinetic and single-channel current measurements.

A combination of rapid chemical kinetic (quench-flow) and single-channel current measurements was used to evaluate kinetic parameters governing the opening of acetylcholine-receptor channels in the electric organ (electroplax) of Electrophorus electricus. Chemical kinetic measurements made on membrane vesicles, prepared from the E. electricus electroplax, using carbamoylcholine (200 microM-20 mM) at 12 degrees C, pH 7.0, and in the absence of a transmembrane voltage, yielded values for K1 (dissociation constant for receptor activation), phi (channel closing equilibrium constant), J (specific reaction rate for ion flux), and alpha max (maximum inactivation rate constant) of 1 mM, 3.4, 4 x 10(7) M-1 s-1, and 12 s-1, respectively. The single-channel current recordings were made with cells also from the E. electricus electroplax, at the same temperature and pH as the chemical kinetic measurements, using carbamoylcholine (50 microM-2 mM), acetylcholine (500 nM), or suberyldicholine (20 nM). Single-channel current measurements indicated the presence of a single, unique open-channel state of the E. electricus receptor, in concurrence with previous, less extensive measurements. The rate constant for channel closing (kc) obtained from the mean open time of the receptor channel is 1,100 s-1 for carbamoylcholine, 1,200 s-1 for acetylcholine, and 360 s-1 for suberyldicholine at zero membrane potential; and it decreases e-fold for an 80 mV decrease in transmembrane voltage in each case. The decrease in mean open times of the receptor channel that is associated with increasing the carbamoylcholine concentration is interpreted to be due to carbamoylcholine binding to the regulatory (inhibitory) site on the receptor. An analysis of data obtained with carbamoylcholine showed that the closed times within a burst of channel activity fit a two-exponential distribution, with a concentration-independent time constant considered to be the time constant for carbamoylcholine to dissociate from the regulatory site, and a carbamoylcholine concentration-dependent, but voltage-independent, time constant interpreted to represent the rate constant for channel opening (k0). An analysis of the mean closed time data on the basis of the minimum model gives values for K1 and k0 of 0.6 mM and 440 s-1, respectively, with carbamoylcholine as the activating ligand. The values obtained for K1, phi (= kc/k0), J, and alpha from the single-channel current measurements using electroplax are in good agreement with the values obtained from the chemical kinetic measurements using receptor-rich vesicles prepared from the same cells. These results confirm the assumed basic agreement between two entirely different methodologies and underlie the strategy of using the two techniques to obtain complementary information in time and ligand-concentration regions where only one or the other technique can be used. This agreement between results allows estimates to be made of the ko values, for both acetylcholine and suberyldicholine, from the phi values obtained from the chemical kinetic measurements and the kc values obtained in single-channel current measurements.

Animals↗
PubMed2002

Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates.

The kinetics of interaction of Esigma(70) RNA polymerase (R) with the lambdaP(R) promoter (P) were investigated by filter binding over a broad range of temperatures (7.3-42 degrees C) and concentrations of RNA polymerase (1-123 nM) in large excess over promoter DNA. Under all conditions examined, the kinetics of formation of competitor-resistant complexes (I(2), RP(o)) are single-exponential with first order rate constant beta(CR). Interpretation of the polymerase concentration dependence of beta(CR) in terms of the three step mechanism of open complex formation yields the equilibrium constant K(1) for formation of the first kinetically significant intermediate (I(1)) and the forward rate constant (k(2)) for the conformational change converting I(1) to the second kinetically significant intermediate I(2): R + P-->(K(1))<--I(1)(k(2))-->I(2). Use of rapid quench mixing allows K(1) and k(2) to be individually determined over the entire temperature range investigated, previously not possible at this promoter using manual mixing. Given the large (>60 bp) interface formed in I(1), its relatively small binding constant K(1) at 37 degrees C at this [salt] (approximately 6 x 10(6) M(-1)) strongly argues that binding free energy is used to drive large-scale structural changes in polymerase and/or promoter DNA or other coupled processes. Evidence for coupling of protein folding is provided by the large and negative activation heat capacity of k(a)[DeltaC(o,++)(a)= -1.5(+/-0.2)kcal K(-1)], now shown to originate directly from formation of I(1) [DeltaC(o)(1)= -1.4(+/-0.3)kcal K(-1)] rather than from the formation of I(2) as previously proposed. The isomerization I(1)-->I(2) exhibits relatively slow kinetics and has a very large temperature-independent Arrhenius activation energy [E(act)(2)= 34(+/-2)kcal]. This kinetic signature suggests that formation of the transition state (I(1)-I(2)++ involves large conformational changes dominated by changes in the exposure of polar and/or charged surface to water. Structural and biochemical data lead to the following hypotheses to interpret these results. We propose that formation of I(1) involves coupled folding of unstructured regions of polymerase (beta, beta' and sigma(70)) and bending of promoter DNA (in the -10 region). We propose that interactions with region 2 of sigma(70) and possibly domain 1 of beta induce a kink at the -11/-12 base pairs of the lambdaP(R) promoter which places the downstream DNA (-5 to +20) in the jaws of the beta and beta' subunits of polymerase in I(1). These early interactions of beta and beta' with the DNA downstream of position -5 trigger jaw closing (with coupled folding) and subsequent steps of DNA opening.

Bacteriophage lambda↗
PubMed2001

Mycobacterium tuberculosis mycothione reductase: pH dependence of the kinetic parameters and kinetic isotope effects.

The recent identification of the enzyme in Mycobacterium tuberculosis that catalyzes the NADPH-dependent reduction of the unique low molecular weight disulfide mycothione, mycothione reductase, has led us to examine the mechanism of catalysis in greater detail. The pH dependence of the kinetic parameters V and V/K for NADPH, NADH, and an active analogue of mycothione disulfide, des-myo-inositol mycothione disulfide, has been determined. An analysis of the pH profiles has allowed the tentative assignment of catalytically significant residues crucial to the mechanism of disulfide reduction, namely, the His444-Glu449 ion pair and Cys39. Solvent kinetic isotope effects were observed on V and V/K(DIMSSM), yielding values of 1.7 +/- 0.2 and 1.4 +/- 0.2, respectively, but not on V/K(NADPH). Proton inventory studies (V versus mole fraction of D(2)O) were linear, indicative of a single proton transfer in a solvent isotopically sensitive step. Steady-state primary deuterium kinetic isotope effects on V have been determined using NADPH and NADH, yielding values of 1.27 +/- 0.03 and 1.66 +/- 0.14, respectively. The pre-steady-state primary deuterium kinetic isotope effect on enzyme reduction has values of 1.82 +/- 0.04 and 1.59 +/- 0.06 for NADPH and NADH, respectively. The steady-state primary deuterium kinetic isotope effect using NADH coincide with that obtained under single turnover conditions, suggesting the complete expression of the intrinsic primary kinetic isotope effect. Rapid reaction studies on the reductive half-reaction using NADPH and NADH yielded maximal rates of 129 +/- 2 and 20 +/- 1 s(-1), respectively, while similar studies of the oxidation of the two-electron reduced enzyme by mycothiol disulfide yielded a maximum rate of 190 +/- 10 s(-1). These data suggest a unique flavoprotein disulfide mechanism in which the rate of the oxidative half-reaction is slightly faster than the rate of the reductive half-reaction.

Deuterium↗
PubMed2006

Mechanistic implications of pseudo zero order kinetics in kinetic resolutions.

This work provides simulations as well as experimental results from kinetic resolutions to demonstrate that a constant product enantioselectivity versus conversion profile in kinetic resolution is not a general consequence of pseudo zero order kinetics in [substrate] but occurs only under specific mechanistic constraints. For such a profile to be observed, the reaction must follow a mechanism exhibiting saturation kinetics for only one enantiomeric [substrate] on the only one of the two parallel pathways. For a single catalyst species, this will be limited to situations of near-perfect selectivity. Combining kinetic profiles with the enantioselectivity/conversion relationship in kinetic resolution can help to distinguish between proposed mechanisms and provide information about relative binding constants, the reactivity of intermediate species, and turnover by more than one active catalyst species.

Alcohols↗
PubMed2001

Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading.

In the context of cell signaling, kinetic proofreading was introduced to explain how cells can discriminate among ligands based on a kinetic parameter, the ligand-receptor dissociation rate constant. In the kinetic proofreading model of cell signaling, responses occur only when a bound receptor undergoes a complete series of modifications. If the ligand dissociates prematurely, the receptor returns to its basal state and signaling is frustrated. We extend the model to deal with systems where aggregation of receptors is essential to signal transduction, and present a version of the model for systems where signaling depends on an extrinsic kinase. We also investigate the kinetics of signaling molecules, "messengers," that are generated by aggregated receptors but do not remain associated with the receptor complex. We show that the extended model predicts modes of signaling that exhibit kinetic discrimination for some range of parameters but for other parameter values show little or no discrimination and thus escape kinetic proofreading. We compare model predictions with experimental data.

Animals↗
PubMed2006

Use of Intralipid for kinetic analysis of HDL apoC-III: evidence for a homogeneous kinetic pool of apoC-III in plasma.

Apolipoprotein C-III (apoC-III) is an important regulator of lipoprotein metabolism. Radioisotope and stable isotope kinetic studies show differing results in relation to the kinetics of apoC-III in HDL. Kinetic analysis of HDL apoC-III may be difficult because of its low concentration, as well as the presence of other apoproteins at higher concentration, in the HDL fraction. We used Intralipid(R) (IL), known to preferentially extract apoC proteins from plasma, as a means of extracting apoC-III from HDL before apoprotein separation by isoelectric focusing gel electrophoresis for the measurement of tracer enrichment. Protein purity was assessed by an isoleucine-to-leucine (Ile/Leu) ratio, as apoC-III contains no isoleucine. We compared apoC-III kinetics in 14 men using a bolus infusion of deuterated leucine. The Ile/Leu ratio for IL-extracted HDL (IL-HDL) apoC-III (3.0 +/- 0.7%) was not different from that of VLDL apoC-III (2.6 +/- 0.6%) but was significantly lower than that of untreated HDL apoC-III (9.0 +/- 2.9%) (P < 0.001). The isotopic enrichment curves and fractional catabolic rates (FCRs) for IL-HDL apoC-III were not different from those of VLDL apoC-III. In contrast, HDL apoC-III had significantly lower isotopic enrichments and FCRs than IL-HDL apoC-III (P < 0.001). In conclusion, this simple IL method can be used to isolate apoC-III from HDL with minimal interference from other HDL apoproteins, and it demonstrates that the kinetics of apoC-III in VLDL and HDL are similar, supporting the concept of a single kinetically homogeneous pool of apoC-III in plasma.

Apolipoprotein C-III↗
PubMed2005

Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis.

Depending on the nucleotide sequence, the temperature, and other conditions, RNA hairpin-folding kinetics can be very complex. The complexity with a wide range of cooperative and noncooperative kinetic behaviors arises from the interplay between the formation of the loops, the disruption of the misfolded states, and the formation of the rate-limiting base stacks. With a rate constant model and a kinetic-cluster theory, we explore the broad landscape for RNA hairpin-folding kinetics. The model is validated through direct tests against several experimental measurements. The general kinetic folding mechanisms and the predicted great variety of folding kinetics are directly applicable and quantitatively testable in experiments. The results from this study suggest that 1), previous experimental findings based on the individual hairpins revealed only a small fraction of much broader and more complex RNA hairpin-folding landscapes; 2), even for structures as simple as hairpins, universal folding timescales and pathways do not exist; and 3), to treat the loop size as the sole factor to determine the hairpin-folding rate is an oversimplification.

Base Pairing↗
PubMed1998

Kinetic-Diffusion-Controlled Adsorption and Desorption Kinetics on Planar Surfaces.

The adsorption and desorption kinetics of water-soluble associative polymers with different molecular weights on the silicon wafers were studied by ellipsometry. The parameters characterizing the adsorption and desorption processes such as (a) the maximum amount of adsorbate adsorbed, Gammainfinity, (b) the equilibrium constant, K(p), (c) the activation energy of adsorption, (-DeltaH), (d) the rate constants for adsorption and desorption processes, Kad, Kdes, (e) the coefficient of diffusion, D0, (f) the activation energy of the effective diffusion, Q, and (g) the time needed to attain the equilibrium states for the adsorption and desorption processes were calculated from the experimental ellipsometric data. It is shown that the adsorption kinetics for mixtures over a wide range of concentrations is governed by: (I) the kinetic adsorption at the interface, (II) the kinetic adsorption at the interfaces as well as simultaneous diffusion, and/or (III) diffusion. The existence of regimes (I), (II), and (III) for adsorption and desorption kinetics are justified by using the experimental data for the adsorption and desorption kinetics of water-soluble associative polymers with different molecular weights of 12, 62, and 120 kg/mol. Copyright 1998 Academic Press.

Journal Article↗
PubMed1980

Hydroboration kinetics: Unusual kinetics for the reaction of 9-borabicyclo[3.3.1]nonane with representative alkenes.

The kinetics of hydroboration of alkenes with 9-borabicyclo[3.3.1]nonane dimer, (9-BBN)(2), exhibit interesting characteristics. With more reactive alkenes, such as 1-hexene, 2-methyl-1-pentene, 3,3-dimethyl-1-butene, and cyclopentene, the reaction exhibits first-order kinetics, first order in (9-BBN)(2) and zero order in alkene. On the other hand, with less reactive alkenes, such as cyclohexene, 1-methylcyclohexene, and 2,3-dimethyl-2-butene, the reaction exhibits three-halves-order kinetics, first order in alkene and one-half order in (9-BBN)(2). These kinetics can be accounted for in terms of the following mechanism:(9-BBN)(2) right arrow over left arrow 2 9-BBN9-BBN + alkene --> B-alkyl-9-BBNIn the case of the more reactive alkenes, the rate-determining step is the dissociation of the dimer. With less reactive alkenes, the reaction of the alkene with the monomer becomes the rate-determining step. For certain alkenes, such as 2-methyl-2-butene and cis-3-hexene, neither of the two steps is a decisive rate-determining step. Therefore, the reaction exhibits kinetic behavior between that of first- and three-halves-order kinetics.

Journal Article↗
PubMed2006

A kinetic study of lipase-catalyzed reversible kinetic resolution involving verification at miniplant-scale.

Lipase-catalyzed kinetic resolution of racemates is a popular method for synthesis of chiral synthons. Most of these resolutions are reversible equilibrium limited reactions. For the first time, an extensive kinetic model is proposed for kinetic resolution reactions, which takes into account the full reversibility of the reaction, substrate inhibition by an acyl donor and an acyl acceptor as well as alternative substrate inhibition by each enantiomer. For this purpose, the reversible enantioselective transesterification of (R/S)-1-methoxy-2-propanol with ethyl acetate catalyzed by Candida antarctica lipase B (CAL-B) is investigated. The detailed model presented here is valid for a wide range of substrate and product concentrations. Following model discrimination and the application of Haldane equations to reduce the degree of freedom in parameter estimation, the 11 free parameters are successfully identified. All parameters are fitted to the complete data set simultaneously. Six types of independent initial rate studies provide a solid data basis for the model. The effect of changes in substrate and product concentration on reaction kinetics is discussed. The developed model is used for simulations to study the behavior of reaction kinetics in a fixed bed reactor. The typical plot of enantiomeric excess versus conversion of substrate and product is evaluated at various initial substrate mixtures. The model is validated by comparison with experimental results obtained with a fixed bed reactor, which is part of a fully automated state-of-the-art miniplant.

Enzymes, Immobilized↗
PubMed1997

Isotope ratio mass spectrometry, compared with conventional mass spectrometry in kinetic studies at low and high enrichment levels: application to lipoprotein kinetics.

The aim of the present study was to compare the performances of gas chromatography/mass spectrometry (GC/MS) and gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) in stable isotope kinetic studies. In the analysis of cholesterol and leucine, GC/C/IRMS gave precise and linear results over a large scale of 13C enrichment (-22 to +760 delta/1000 for cholesterol, -26 to +600 delta/1000 for leucine). Compared with GC/MS, GC/C/IRMS was much more accurate and reproducible, especially at low [13C]-cholesterol enrichment (-12 delta/1000), with cholesterol samples ranging from 0.11 to 17 ng. Cholesterol ester kinetics in rabbit plasma low-density lipoproteins was studied after injection of 3 mg [3,4-(13)C]cholesterol. A smooth and regular kinetic curve was obtained with GC/C/IRMS; results were much less reproducible with GC/MS. Finally, the performances of GC/C/IRMS were demonstrated in the simultaneous kinetic study of three human plasma apolipoproteins during a primed constant infusion of 0.7 mg.kg-1.h-1 L-[l-13C]leucine. Kinetic curves were obtained in very-low-density lipoproteins and low-density lipoproteins for apolipoprotein B100, and in high-density lipoproteins for apolipoproteins AI and AIL.

Adult↗
PubMed2000

Kinetic mechanism of the single-stranded DNA recognition by Escherichia coli replicative helicase DnaB protein. Application of the matrix projection operator technique to analyze stopped-flow kinetics.

Kinetics of the Escherichia coli primary replicative helicase DnaB protein binding to a single-stranded DNA, in the presence of the ATP non-hydrolyzable analog AMP-PNP, have been performed, using the fluorescence stopped-flow technique. This is the first direct determination of the mechanism of the ssDNA recognition by a hexameric helicase. Binding of the fluorescent etheno-derivative of a ssDNA to the enzyme is characterized by a strong increase of the nucleic acid fluorescence, which provides an excellent signal to quantitatively study the mechanism of ssDNA recognition by the helicase. The kinetic experiments have been performed with a ssDNA 20-mer, depsilonA(pepsilonA)(19), that encompasses the entire, total ssDNA-binding site of the helicase and with the 10-mer depsilonA(pepsilonA)(9), which binds exclusively to the ssDNA strong subsite within the total ssDNA-binding site. Association of the DnaB helicase with the 20-mer is characterized by three relaxation times, which indicates that the binding occurs by the minimum three-step mechanism where the bimolecular binding step is followed by two isomerization steps. This mechanism is described by the equation: Helicase+ssDNAk1/(k1)<-->(k-1)(H-ssDNA)1(k2)<-->(k-2)(H-ssDNA)2 (k3)<-->(k-3)(H-ssDNA)3. The value of the bimolecular rate constant, k(1), is four to six orders of magnitude lower than the value expected for the diffusion-controlled reaction. Moreover, quantitative amplitude analysis suggests that the major conformational change of the ssDNA takes place in the formation of the (H-ssDNA)(1). These results indicate that the determined first step includes formation of the collision and an additional transition of the protein-ssDNA complex, most probably the local opening of the protein hexamer. The data indicate that the binding mechanism reflects the interactions of the ssDNA predominantly through the strong ssDNA-binding subsite. The analysis of the stopped-flow kinetics has been performed using the matrix-projection operator technique, which provides a powerful method to address stopped-flow kinetics, particularly, the amplitudes. The method allowed us to determine the specific fluorescence changes accompanying the formation of all the intermediates. The sequential nature of the determined mechanism indicates the lack of the kinetically significant conformational equilibrium of the DnaB hexamer as well as a transient dissociation of the hexamer prior to the ssDNA binding. The significance of these results for the functioning of the DnaB helicase is discussed.

Bacterial Proteins↗
PubMed1983

Glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides: revised kinetic mechanism and kinetics of ATP inhibition.

The kinetic mechanisms of the NAD- and NADP-linked reactions catalyzed by glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides were examined using product inhibition, dead-end inhibition and alternate substrate experiments. The results are consistent with a steady-state random mechanism for the NAD-linked and an ordered, sequential mechanism with NADP+ binding first for the NADP-linked reaction. Thus, the enzyme can bind NADP+, NAD+, and glucose 6-phosphate, but the enzyme-glucose 6-phosphate complex can react only with NAD+, not with NADP+. This affects the rate equation for the NADP-linked reaction by introducing a term for a dead-end enzyme-glucose 6-phosphate complex. The kinetic mechanisms represent revisions of those proposed previously (C. Olive, M.E. Geroch, and H.R. Levy, 1971, J. Biol. Chem. 246, 2047-2057) and provide a kinetic basis for the regulation of coenzyme utilization of the enzyme by glucose 6-phosphate concentration (H.R. Levy, and G.H. Daouk, 1979, J. Biol. Chem. 254, 4843-4847) and NADPH/NADP+ concentration ratios (H.R. Levy, G.H. Daouk, and M.A. Katopes, 1979, Arch, Biochem. Biophys. 198, 406-413). The kinetic mechanisms were found to be the same at pH 6.2 and pH 7.8. The kinetics of ATP inhibition of the NAD- and NADP-linked reactions were examined at pH 6.2 and pH 7.8. The results are interpreted in terms of ATP addition to binary enzyme-coenzyme and enzyme-glucose 6-phosphate complexes.

Adenosine Triphosphate↗
PubMed1983

Kinetic analysis of bacterial clearance in mice using the ESTRIPc and KINET microcomputer programs.

Two BASIC microcomputer programs, ESTRIPc and KINET, were used to analyze the kinetics of bacterial clearance from the blood and mesenteric lymph nodes of mice. Because of the similarities between the clearance of bacteria and the clearance of drugs from tissue, blood pharmacokinetic techniques were applied to the analysis of bacterial clearance data. The ESTRIPc program, developed for pharmacokinetic analysis and modified for the study of bacterial clearance, was employed to fit the experimental data of bacterial survival versus time to a polyexponential equation with 1, 2, or 3 terms. The KINET program, written specifically for kinetic analysis of bacterial clearance, uses the biexponential equation constants derived with ESTRIPc to calculate half-life values, rate constants, and other useful kinetic parameters. The combined use of these programs permits precise comparisons of the clearance rates of different bacterial species from the blood or tissues of experimental animals.

Animals↗
PubMed2006

New multi-step kinetics using common affinity biosensors saves time and sample at full access to kinetics and concentration.

Today, affinity-based biosensorics is a standard technology in quantitative biomolecular interaction analysis, but suffers from low sample throughput and sometimes from inaccessible kinetics. A new methodology for such biosensors is introduced here that cuts down measurement time dramatically and increases confidentiality of results. In contrast to traditional applications, the ligand immobilized on the sensor chip is exposed to the binding analyte at a rapid stepwise change of the analyte concentration without the need for regenerations between analyte additions. In the application presented here, each addition of the analyte is succeeded by a buffer flow, yielding alternating association and dissociation phases in a "zigzag" style. This binding curve pattern is analyzed by means of novel fitting algorithms, which render detailed kinetics rate constants at a high level of self-consistency, and hence, validity due to multiple cross-checks. In comparison with traditional sequential kinetics analysis, this new multi-step kinetics approach returns practically identical (or improved) kinetics constants--at valuable savings in time/material since regeneration steps, ligand re-captures, or titration equilibrations are unnecessary.

Algorithms↗
PubMed2005

Comparison between semiautomated kinetic perimetry and conventional Goldmann manual kinetic perimetry in advanced visual field loss.

PURPOSE: To compare quantitatively visual field (VF) results obtained using a new standardized semiautomated kinetic perimetry (SKP) with those obtained by conventional Goldmann manual kinetic perimetry (MKP) in patients with advanced VF loss. DESIGN: Prospective, single-center, observational comparative case series. SUBJECTS AND METHODS: Seventy-seven eligible patients (36 suffering from advanced retinal nerve fiber layer loss, 20 with concentric constriction of the VF, and 21 with hemianopia) were included in the study. One eye of each patient was examined on the same day with MKP and SKP. Three isopters, identical in both tests, were chosen to assess the extent of the VF loss. To compare the location and size of the corresponding isopters obtained with MKP and SKP, intersection areas of superimposed isopters were expressed as a percentage of union areas. MAIN OUTCOME MEASURES: The area and position of isopters for a defined stimulus condition obtained with both methods were compared. Test duration and patients' preference were also evaluated. RESULTS: Isopters obtained with Goldmann MKP enclosed areas smaller by 20% (confidence interval [CI], 12%-27%). The mean intersection area of Goldmann and SKP VFs was 1763.1 square degrees (CI, 1558.6-1967.7) smaller than the union for stimulus III4e over all groups of patients. Semiautomated kinetic perimetry was preferred by 60% of patients with concentric constriction of the VF. Median duration of the examination was 15 minutes and did not differ significantly between the 2 methods. CONCLUSIONS: Our results indicate that SKP isopter shape and size were very comparable to those obtained on the same eyes with MKP. Semiautomated kinetic perimetry may represent a more standardized method of kinetic perimetry, which still takes advantage of perimetrist-patient interaction to diagnose and monitor advanced VF loss in clinical practice.

Adolescent↗
PubMed1999

General method of analysis of kinetic equations for multistep reversible mechanisms in the single-exponential regime: application to kinetics of open complex formation between Esigma70 RNA polymerase and lambdaP(R) promoter DNA.

A novel analytical method based on the exact solution of equations of kinetics of unbranched first- and pseudofirst-order mechanisms is developed for application to the process of Esigma70 RNA polymerase (R)-lambdaPR promoter (P) open complex formation, which is described by the minimal three-step mechanism with two kinetically significant intermediates (I1, I2), [equation: see text], where the final product is an open complex RPo. The kinetics of reversible and irreversible association (pseudofirst order, [R] >> [P]) to form long-lived complexes (RPo and I2) and the kinetics of dissociation of long-lived complexes both exhibit single exponential behavior. In this situation, the analytical method provides explicit expressions relating observed rate constants to the microscopic rate constants of mechanism steps without use of rapid equilibrium or steady-state approximations, and thereby provides a basis for interpreting the composite rate constants of association (ka), isomerization (ki), and dissociation (kd) obtained from experiment for this or any other sequential mechanism of any number of steps. In subsequent papers, we apply this formalism to analyze kinetic data obtained in the reversible and irreversible binding regimes of Esigma70 RNA polymerase (R)-lambdaP(R) promoter (P) open complex formation.

Bacteriophage lambda↗
PubMed2004

Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics.

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured.

Bayes Theorem↗