Comparative aspects of the apparent Michaelis constant for neutral amino acid transport in several animal tissues

The apparent Michaelis constant, Km, for transport of a number of neutral amino acids has been compared between intestine, heart, brain and erythrocytes among a variety of animals using values available in the literature. Neutral amino acids with side chains containing 3, 4, 7 and 9 carbon atoms had approximately equal mean Km values when tested for intestinal transport among a variety of species; alanine appeared to have a mean Km value that was larger than those found for the first group, and glycine had a significantly greater mean Km than all of the other compounds tested. Km values for phenylalanine and tryptophan measured in rat heart were found to be close to the means measured for these substrates in intestine. The mean Km values measured in mammalian brain for each of the neutral amino acid substrates were found not be significantly different from each other. When the means of Km values for the neutral amino acids tested were compared between intestine and brain, only the glycine means were shown to differ significantly between the organs. Based on data for several mammalian species, brain appears to have a greater average apparent affinity for glycine than does intestine. In the human erythrocytes and in a few other mammalian species, Km values for all neutral amino acids tested with exception of glycine were found to be similar in magnitude to each other and to the Km averages of neutral amino acids found in intestine for the series containing 3-9 carbon atoms. The Km value for glycine in the human erythrocyte was noted to be substantially lower in value than the averages for glycine in brain or intestine. Avian red blood cells appear to have high apparent affinity for neutral amino acid transport when compared with red cells of several mammalian species.     

Urease activity and its Michaelis constant for soil systems

Summary Urea hydrolysis was measured in two separate sets of experiments. (1) Nine soil (0–15 cm) samples were treated with 200 g of urea-N g^–1 dry soil and incubated (at 37°C) at 50 per cent of the water holding capacity. Samples were periodically analysed for the remaining urea-N. The urease activity (time in hoursrequired to hydrolyse half the applied urea-N) was determined to be 5.8 to 15.2 hours in the various soils, which appeared to associate principally with the organic carbon content of the soils (r=–0.80^**). (2) Three soils were treated with 25 to 2000 g urea-N g^–1 dry soil amounting to 0.9 to 72.0 mM urea in 11 soil: solution. The system was buffered at pH 7.2 and agitated for 5h when the remaining urea-N was determined. The values of Km and Vmax were computed by two methods (i) from the integrated form of the Michaelis-Menten equation based on the results of the first study, and (ii) from the Michaelis-Menton equation based on urea hydrolysis in the second study. The integrated method appeared to be more suitable for enzyme kinetic studies in soil systems where the Km and V_max values bore close relationship (r=–0.88^**).     

Estimation of Michaelis constant and maximum velocity from the direct linear plot

When estimates of Michaelis-Menten parameters are obtained from kinetic observations taken in pairs, as in the direct linear plot, bias can arise in the final estimates if any pairs lead to negative values of the maximum velocity V. This bias can be removed by treating such negative values as if they were large and positive, and by treating the corresponding values of Km in the same way.     

Measurement of Michaelis constant for human erythrocyte transketolase and thiamin diphosphate

Human erythrocyte transketolase could be resolved from thiamin diphosphate (TDP) by acidification of the ammonium sulfate precipitate to pH 3.5, but not by other tested procedures. Resolution was 98% by chemical measurement of residual thiamin and 95% by residual enzyme activity. Reconstitution of the resolved preparation by incubation with TDP was dependent upon TDP concentration, duration, temperature, and the presence of dithiothreitol. At low TDP concentrations, 1 h was required for maximum activation; kinetic analysis then yielded an apparent Km value for TDP of 65 nM (SD 14 nM) from 100 erythrocyte lysates and similar values for reconstituted resolved preparations previously purified 400-fold and 10,000-fold. Velocity data obtained by transketolase assays in which the TDP was added to resolved preparations simultaneously with substrates yielded an apparent Km value for TDP of 2.3 microM (SD 1.6 microM) from 114 erythrocyte lysates and similar values for purified preparations. The recovery of activity following resolution and reconstitution ranged from 21 to 60% from lysates and 38 to 70% from purified preparations. Residual ammonium sulfate up to 4.9 mM decreased the apparent Km value for TDP, while a concentration of 11.3 mM increased the value in a manner competitive with TDP and with an apparent Ki value of 2.3 mM. The spectrophotometric assay of transketolase activity was greatly affected by storage of frozen solutions of the substrate ribose 5-phosphate.     

Influences of nonuniform activity distributions on the apparent maximum reaction rate and apparent Michaelis constant of immobilized enzyme reactions

The influences of nonuniform activity distribution within a porous solid support on the apparent kinetic parameters, V_m^app and K_m^app, of immobilized enzyme reactions following the Michaelis-Menten kinetics were theoretically investigated. As the enzyme is distributed to the neighborhood of the external surface of the support, V_m^app and K_m^app approach their respective intrinsic values over a wide range of substrate concentration. There is a close relationship between the nonuniform distribution and internal diffusional resistance. Changes in these two factors provide similar effects on V_m^app and K_m^app. As long as the immobilized enzyme reaction follows Michaelis-Menten kinetics, the nonuniform activity distribution never makes K_m^app less than its intrinsic value.     

pH-Stat titration method for dihydrofolate reductase activity measurements: application to determination of substrate Michaelis constant and antifolate inhibition constant

A pH-Stat titration method was developed for measuring dihydrofolate reductase (DHFR) activity; this method permits detection of very low DHFR activities corresponding to 100 pmol of substrate reduced per minute. This value is about ten times lower than those observed using the classical spectrophotometric method. This sensitivity makes it possible to measure the DHFR in crude tissue extracts. With beef liver DHFR, Michaelis constants for the cofactor NADPH and the natural substrate determined by this method were 1.9 +/- 0.3 X 10(-5) and 8.5 +/- 0.5 X 10(-7) M, respectively. The inhibition constant of methotrexate, a competitive inhibitor of dihydrofolate, was 3.4 +/- 1.3 X 10(-11) M.     

Nonfixed relationship of the Michaelis constant and maximum velocity with their corresponding rate constants

The Michaelis constant (K(m)) and V(mas) (E0k(cat)) values for two mutant sets of enzymes were studied from the viewpoint of their definition in a rapid equilibrium reaction model and in a steady state reaction model. The "AMP set enzyme" had a mutation at the AMP-binding site (Y95F, V67I, and V67I/L76V), and the "ATP set enzyme" had a mutation at a possible ATP-binding region (Y32F, Y34F, and Y32A/Y34A). Reaction rate constants obtained using steady state model analysis explained discrepancies found by the rapid equilibrium model analysis. (i) The unchanged number of bound AMPs for Y95F and the wild type despite the markedly increased K(m) values for AMP of the AMP set of enzymes was explained by alteration of the rate constants of the AMP step (k(+2), k(-2)) to retain the ratio k(+2)/k(-2). (ii) A 100 times weakened selectivity of ATP for Y34F in contrast to no marked changes in K(m) values for both ATP and AMP for the ATP set of enzymes was explained by the alteration of the rate constants of the ATP steps. A similar alteration of the K(m) and k(cat) values of these enzymes resulted from distinctive alterations of their rate constants. The pattern of alteration was highly suggestive. The most interesting finding was that the rate constants that decided the K(m) and k(cat) values were replaced by the mutation, and the simple relationships between K(m), k(cat), and the rate constants of K(m)1 = k(+1)/k(-1) and k(cat) = k(f) were not valid. The nature of the K(m) and k(cat) alterations was discussed.     

The effects of temperature and pH on the apparent Michaelis constant of glutathione reductase from maize (Zea mays L.)

The interacting effects of temperature and pH on the kinetics of glutathione reductase from maize have been studied in detail. The apparent K_m for oxidized glutathione (GSSG) measured with desalted crude extracts increased in an exponential manner with rising temperature as a single variable. Increasing pH as a single variable also resulted in higher values of apparent K_m for GSSG. When pH was allowed to vary with temperature, a curve which combined the pH and temperature responses was observed. Temperature had the stronger influence and this combined curve was displaced from the temperature curve due to the effect of pH. The pH to which the assay buffer was adjusted at 30°C had an influence on the pattern of the results in this type of experiment. The response of apparent K_m for NADPH, and of apparent K_m for GSSG using partially-purified extracts, were also examined. The variation with temperature, at constant pH, was again exponential. The pattern of change of apparent K_m with temperature is strongly dependent on experimental conditions. Affinity/temperature relationships deduced from such data would only reflect enzyme function in vivo if the physiological environment could be reproduced exactly in the assay mixture.     

Causes of variability in estimates of mutational variance from mutation accumulation experiments

Characteristics of the new phenotypic variation introduced via mutation have broad implications in evolutionary and medical genetics. Standardized estimates of this mutational variance, V_M, span 2 orders of magnitude, but the causes of this remain poorly resolved. We investigated estimate heterogeneity using 2 approaches. First, meta-analyses of ∼150 estimates of standardized V_M from 37 mutation accumulation studies did not support a difference among taxa (which differ in mutation rate) but provided equivocal support for differences among trait types (life history vs morphology, predicted to differ in mutation rate). Notably, several experimental factors were confounded with taxon and trait, and further empirical data are required to resolve their influences. Second, we analyzed morphological data from an experiment in Drosophila serrata to determine the potential for unintentional heterogeneity among environments in which phenotypes were measured (i.e. among laboratories or time points) or transient segregation of mutations within mutation accumulation lines to affect standardized V_M. Approximating the size of an average mutation accumulation experiment, variability among repeated estimates of (accumulated) mutational variance was comparable to variation among published estimates of standardized V_M. This heterogeneity was (partially) attributable to unintended environmental variation or within line segregation of mutations only for wing size, not wing shape traits. We conclude that sampling error contributed substantial variation within this experiment, and infer that it will also contribute substantially to differences among published estimates. We suggest a logistically permissive approach to improve the precision of estimates, and consequently our understanding of the dynamics of mutational variance of quantitative traits.     

Determination of saltiness from the laws of thermodynamics--estimating the gas constant from psychophysical experiments

One can relate the saltiness of a solution of a given substance to the concentration of the solution by means of one of the well-known psychophysical laws. One can also compare the saltiness of solutions of different solutes which have the same concentration, since different substances are intrinsically more salty or less salty. We develop here an equation that relates saltiness both to the concentration of the substance (psychophysical) and to a distinguishing physical property of the salt (intrinsic). For a fixed standard molar entropy of the salt being tasted, the equation simplifies to Fechner's law. When one allows for the intrinsic 'noise' in the chemoreceptor, the equation generalizes to include Stevens's law, with corresponding decrease in the threshold for taste. This threshold reduction exemplifies the principle of stochastic resonance. The theory is validated with reference to experimental data.     

Parameter estimates from mark-recapture experiments on two populations subject to migration and death

A model is developed for a triple catch marking experiment on two areas with migration between the two areas and death or emigration occurring. Estimates of the parameters of the model are derived. Some of these estimates are shown to be suitable even under certain restrictions on migration (e.g. animals may be restricted to a single transfer in the course of the experiment). Variances of the estimates were not derived but some rules were developed, based on computer simulations, to guide the experimenter in planning experiments and in judging the precision of his estimates.     

The variability in circadian phase and amplitude estimates derived from sequential constant routines.

Both the constant routine (CR) and the dim light melatonin onset have been suggested as reliable methods to determine circadian phase from a single circadian cycle. However, both techniques lack published studies quantifying the intercycle variability in their phase resolution. To address this question eight healthy male subjects participated in two CRs, 7 days apart. Circadian phase was determined using 3-min samples of core body temperature and two hourly urinary sulphatoxy melatonin excretion rates. Phase and amplitude were estimated using simple (24 h) and complex (24 + 12 h) cosinor models of temperature data and the onset, offset, and a distance-weighted-least-squares (DWLS) fitted acrophase for the melatonin metabolite. The variability in phase estimates was measured using the mean absolute difference between successive CRs. Using the simple 24 h model of temperature data, the mean absolute phase difference was 51 min (SD = 35 min). Using the complex model, the mean absolute phase difference was 62 min (SD = 35 min). Using the DWLS fitted acrophase for the melatonin metabolite, the mean absolute phase difference between CR1 and CR2 was 40 min (SD = 26 min). The results indicate that for CRs a week apart, the mean absolute difference in an individual's phase estimate can vary by 40-60 min depending on the choice of dependent measure and analytic technique. In contrast to the intraindividual variability, the group results showed considerably less variability. The mean algebraic difference between CRs, using temperature- or melatonin-derived estimates, was less than 5 min, and well within the range of normal measurement error.     

Laccase from prokaryotes: a new source for an old enzyme

Laccases (benzenediol: oxygen oxidoreductase, EC 1.10.3.2) are multi-copper-containing enzymes capable of catalyzing the oxidation of a wide range of phenolic and non phenolic aromatic compounds. The available data indicates that laccases from prokaryotes are promising biological tools for green chemistry based applications, especially in decolorization of industrial textile dye effluents which constitute a major threat to soil and ground water reservoirs worldwide. Another appropriate application of prokaryotic laccases is bio-bleaching of different kind of pulps where there is indiscriminate use of hazardous chlorine based chemicals for brightness of the paper. In recent years, researchers have shown interest in the identification and characterization of laccases from prokaryotic sources. This catalyst is not commonly reported from this kingdom, although prokaryotes have immense environmental adaptability and biochemical versatility. Moreover, true laccases or laccase-like enzymes exist in many gram-negative, gram-positive bacteria and actinomycetes. Corresponding genes have been identified and functionally expressed in genetically developed hosts. This review summarizes the research efforts to characterize laccases and their properties from different prokaryotic sources, including bacteria and actinomycetes.     

Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments

MOTIVATION: There has been much interest in using patterns derived from surface-enhanced laser desorption and ionization (SELDI) protein mass spectra from serum to differentiate samples from patients both with and without disease. Such patterns have been used without identification of the underlying proteins responsible. However, there are questions as to the stability of this procedure over multiple experiments. RESULTS: We compared SELDI proteomic spectra from serum from three experiments by the same group on separating ovarian cancer from normal tissue. These spectra are available on the web at http://clinicalproteomics.steem.com. In general, the results were not reproducible across experiments. Baseline correction prevents reproduction of the results for two of the experiments. In one experiment, there is evidence of a major shift in protocol mid-experiment which could bias the results. In another, structure in the noise regions of the spectra allows us to distinguish normal from cancer, suggesting that the normals and cancers were processed differently. Sets of features found to discriminate well in one experiment do not generalize to other experiments. Finally, the mass calibration in all three experiments appears suspect. Taken together, these and other concerns suggest that much of the structure uncovered in these experiments could be due to artifacts of sample processing, not to the underlying biology of cancer. We provide some guidelines for design and analysis in experiments like these to ensure better reproducible, biologically meaningfully results. AVAILABILITY: The MATLAB and Perl code used in our analyses is available at http://bioinformatics.mdanderson.org