Computer analysis of sub-parameters of depurination and depolymerization rate constants in Feulgen DNA hydrolysis

Feulgen DNA hydrolysis curves derived from cytofluorometry at various temperatures and HCl concentrations were computer analyzed with least squares fit to Bateman function. By comparing the depurination (k1) and depolymerization (k2) rate constants at different hydrolysis conditions, it was found that the two parameters of temperature and HCl concentration can be expressed as k = AN2 X exp (-B/T), where A and B are constants, N is the HCl concentrations, and T is the absolute temperature. From the analysis of Feulgen hydrolysis curves with 2N HCl at various temperatures, it was calculated that A = 5.3590 X 10(14) and B = 12133.543, for k1, and A = 6.2401 X 10(14) and B = 12181.660, for k2 for mouse 4C hepatocytes fixed with absolute methanol. Computer generated theoretical hydrolysis curves using the above k1 and k2 values were compared with experimental curves at various temperatures and HCl-concentrations. The two types of hydrolysis curves coincided with each other when 1-3 N HCl was used at temperatures between 30-40 degrees C. The peak times of hydrolysis curves at different conditions determined by experimental analysis and theoretical estimations also coincided reasonably well with each other. The physico-chemical phenomena underlying the equation designating k1 and k2 values are discussed.     

Study of the mode of action of a polygalacturonase from the phytopathogen Burkholderia cepacia

We have recently isolated and heterologously expressed BcPeh28A, an endopolygalacturonase from the phytopathogenic Gram-negative bacterium Burkholderia cepacia. Endopolygalacturonases belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. The mode of action of BcPeh28A on different substrates has been investigated and its enzymatic mechanism elucidated. The hydrolysis of polygalacturonate indicates that BcPeh28A is a non-processive enzyme that releases oligomers with chain lengths ranging from two to eight. By inspection of product progression curves, a kinetic model has been generated and extensively tested. It has been used to derive the kinetic parameters that describe the time course of the formation of six predominant products. Moreover, an investigation of the enzymatic activity on shorter substrates that differ in their overall length and methylation patterns sheds light on the architecture of the BcPeh28A active site. Specifically the tolerance of individual sites towards methylated saccharide units was rationalized on the basis of the hydrolysis of hexagalacturonides with different methylation patterns.     

The use of a DNA acid-hydrolysis profile for detecting the characteristics of the DNA of malignant tumor cells]

Literature on application of DNA acid hydrolysis curves to cytochemical studies of tumours and invariable homologous tissues is reviewed. It is shown that multiapex DNA acid hydrolysis curves typical of tumours reflect physical and chemical characteristics of DNP malignant cells.     

Age-related changes in chromatin of liver cell nuclei of different ploidity.

A comparison of the Feulgen hydrolysis curves and the chromatin compactness of the liver cell nuclei of young and old rats was made. It was found that the rate of DNA depurination and chromatin compactness are higher in the liver cell nuclei of old rats, both in di-and tetraploidal cells. The effect of fixation upon the course of the hydrolysis curves is discussed.     

Age-related changes in chromatin of liver cell nuclei of different ploidity

Summary A comparsion of the Feulgen hydrolysis curves and the chromatin compactness of the liver cell nuclei of young and old rats was made. It was found that the rate of DNA depurination and chromatin compactness are higher in the liver cell nuclei of old rats, both in di-and tetraploidal cells. The effect of fixation upon the course of the hydrolysis curves is discussed.This investigation was supported by grant 474/VI Committee of Cell Pathology, Polish Academy of Sciences     

Cytochemical analysis of the chromatin of liver cell nuclei and nuclei of oval cells by means of the Feulgen hydrolysis curve in rats treated by thioacetamide

The present study is an analysis of the Feulgen hydrolysis characteristics in nuclei of liver cells and oval cells in rats treated by thioacetamide (TAA) and of liver cells in control rats. The curves show a double-peaked pattern. A slower hydrolysis is noted in the first peak after TAA treatment. This suggests an alteration of the acid-labile part of the chromatin. The curve obtained in the oval cells is different from the one in the liver cells. The implications of these differences are discussed with respect to development of cholangiocarcinomas.     

A standard formula for the determination of the initial rate of hydrolysis of carboxymethylcellulose

The integrated rate equation of Huang, originally used to describe the hydrolysis of insoluble acid treated cellulose, is shown equally applicable in describing the hydrolysis of carboxymethylcellulose (CMC) using a dilution series of Cellulomonas sp. ATCC 21399 crude cellulase as enzyme preparation. Interpretation of the progress curves of hydrolysis of CMC according to the integrated rate equation is used to calculate a standard formula for the conversion of the rate of hydrolysis into the initial velocity of hydrolysis. The validity of the standard formula is tested, using enzyme preparations from Cellulomonas grown under varied conditions, and enzyme preparations containing purified endoglucanases from Cellulomonas.     

Kinetics of the hydrolysis of lean meat protein by alcalase: Derivation of two alternative rate equations and their fit to experimental data

Two rate equations have been developed to model the hydrolysis of ground lean meat protein by Alcalase. The first equation was based on classical Michaelis-Menten kinetics and the second on the adsorption of enzyme to the protein prior to reaction. It was assumed that this adsorption could be modelled by a Langmuir-type adsorption isotherm. Each equation considered the enzyme to be competitively inhibited by reaction product, and considered enzyme inactivation to be first order. Both rate equations have been fitted to experimental data obtained from the hydrolysis of meat protein by Alcalase. Initial rate data indicated that the adsorption model was more appropriate. However, both equations gave satisfactory fits to 11 reaction progress curves determined over a wide range of enzyme and substrate concentrations.     

A mathematical model for the receptor mediated cellular regulation of the low density lipoprotein metabolism

A prototype mathematical model for Brown and Goldstein's pioneering studies on the LDL receptor mediated pathway for the regulation of the cellular content of cholesterol has been developed in this paper. In order to analyze the essential features of this complex system quantitatively and still reflect the framework of the total system, six important processes are considered in the model. They are: (1A, B) the hydrolysis and synthesis of the LDL receptor; (2) the binding of LDL to its receptors; (3) the hydrolysis of LDL; (4) the storage of cholesteryl esters; (5) the regulation of de novo synthesis of cholesterol; and (6) the efflux of free cholesterol to the external medium. All these processes form a system to let the cells take up enough cholesterol from the external medium for their utilization and yet avoid the excessive accumulation of the lipid within the cells. The validity of the model is tested by showing that it can predict many of experimental curves obtained for human fibroblasts in tissue culture studies. The main purpose of the model is to determine how the free cholesterol level in the cell is related to the external LDL concentration and the regulatory capacity of the cells to adapt to a changing LDL environment. In addition, the model reveals an important behavior of SMC, i.e., for a slowly increasing LDL concentration in the extracellular medium, the rate of intracellular degradation of LDL will first increase and then become saturated. It is proposed based on these results that the saturation of LDL degradation by SMCs and the subsequent increase in subendothelial LDL levels in regions of high macromolecular permeability might play a vital role in the formation of the early foam cell lesion.     

Acid hydrolysis characteristics of spleen colony cells under Feulgen staining

A cytophotometrical determination of DNA content was performed in cells of murine spleen colonies originating from bone marrow and in lymphocytes of axillary lymph nodes under various temperatures (22, 25 and 37 degrees C) of hydrolysis (5N HCl). It is shown that acid hydrolysis at 20 and 25 degrees C is most-preferable for proliferated cells of spleen clones and for non-proliferated lymphocytes. It is concluded that hydrolysis curves for clonal cell nuclei in different phases of mitotic cycle practically coincided.     

Chain-length dependence of the kinetics of the hyaluronan hydrolysis catalyzed by bovine testicular hyaluronidase

Hyaluronan (HA) has various biological functions that are strongly dependent on its chain length. In some cases, as in inflammation and angiogenesis, long and short chain-size HA effects are antagonistic. HA hydrolysis catalyzed by hyaluronidase (HAase) is believed to be involved in the control of the balance between longer and shorter HA chains. Our studies of native HA hydrolysis catalyzed by bovine testicular HAase have suggested that the kinetic parameters depend on the chain size. We thus used HA fragments with a molar mass ranging from 8x10(2) g mol(-1) to 2.5x10(5) g mol(-1) and native HA to study the influence of the chain length of HA on the kinetics of its HAase-catalyzed hydrolysis. The initial hydrolysis rate strongly varied with HA chain length. According to the Km and Vm/Km values, the ability of HA chains to form an efficient enzyme-substrate complex is maximum for HA molar masses ranging from 3x10(3) to 2x10(4) g mol(-1). Shorter HA chains seem to be too short to form a stable complex and longer HA chains encounter difficulties in forming a complex, probably because of steric hindrance. The hydrolysis Vm values strongly suggest that as the chain length decreases the HAase increasingly catalyses transglycosylation rather than hydrolysis. Finally, two HA chain populations, corresponding to HA chain molar masses lower and higher than approximately 2x10(4) g mol(-1), are identified and related to the bi-exponential character of the model we have previously proposed to fit the experimental points of the kinetic curves.     

Kinetics of the Hydrolysis of 8-Bromo-Cyclic GMP by the Light-Activated Phosphodiesterase of Toad Rods

The hypothesis that cyclic GMP is the internal transmitter of retinal rod phototransduction, when combined with the observations that 8-bromo-cyclic GMP opens the cyclic GMP-dependent outer segment conductance and that rods into which 8-bromo-cyclic GMP has been injected still respond to light, predicts that the light-activated phosphodiesterase (EC 3.1.4.17) must catalyze the hydrolysis of 8-bromo-cyclic GMP. This hypothesis was tested by measuring light-activated toad rod disk membrane phosphodiesterase with a pH assay technique. Phosphodiesterase-catalyzed hydrolysis of 8-bromo-cyclic GMP was confirmed: at pH 8.0, total proton production after flash activation was identical to total amount of 8-bromo-cyclic GMP added as substrate. Photoactivated phosphodiesterase was remarkably less efficient in catalyzing the hydrolysis of 8-bromo-cyclic GMP than of cyclic GMP: Vmax for 8-bromo-cyclic GMP was 0.063 M/M rhodopsin/s, whereas that for cyclic GMP was 11 M/M rhodopsin/s--170 times greater. The Km for 8-bromo-cyclic GMP was 160 microM, and for cyclic GMP, 590 microM. 8-bromo-cyclic GMP competitively inhibited phosphodiesterase-catalyzed hydrolysis of cyclic GMP with a Ki of 1.2 mM. Complete reaction progress curves were analyzed for obedience to Michaelis-Menten kinetics: cyclic GMP hydrolysis, 8-bromo-cyclic GMP hydrolysis, and cyclic GMP hydrolysis in the presence of 8-bromo-cyclic GMP as competitive inhibitor were found to follow the integrated form of the Michaelis-Menten equation over the time course of the reactions, assuming phosphodiesterase was activated as a step. The kinetic parameters extracted from reaction progress curves were consistent with those derived from analysis of the initial velocity.(ABSTRACT TRUNCATED AT 250 WORDS)     

Modeling the activity burst in the initial phase of cellulose hydrolysis by the processive cellobiohydrolase Cel7A

The hydrolysis of cellulose by processive cellulases, such as exocellulase TrCel7A from Trichoderma reesei, is typically characterized by an initial burst of high activity followed by a slowdown, often leading to incomplete hydrolysis of the substrate. The origins of these limitations to cellulose hydrolysis are not yet fully understood. Here, we propose a new model for the initial phase of cellulose hydrolysis by processive cellulases, incorporating a bound but inactive enzyme state. The model, based on ordinary differential equations, accurately reproduces the activity burst and the subsequent slowdown of the cellulose hydrolysis and describes the experimental data equally well or better than the previously suggested model. We also derive steady-state expressions that can be used to describe the pseudo-steady state reached after the initial activity burst. Importantly, we show that the new model predicts the existence of an optimal enzyme-substrate affinity at which the pseudo-steady state hydrolysis rate is maximized. The model further allows the calculation of glucose production rate from the first cut in the processive run and reproduces the second activity burst commonly observed upon new enzyme addition. These results are expected to be applicable also to other processive enzymes.     

Spectral and kinetic studies of phosphate and magnesium ion binding to yeast inorganic pyrophosphatase

Inorganic pyrophosphatase must bind two phosphate molecules in order to catalyze pyrophosphate synthesis. In this report it is shown that Pi causes marked effect on the absorption spectrum of baker's yeast inorganic pyrophosphatase and this effect can be used to analyze Pi binding to this enzyme. A series of absorbance versus Pi concentration curves in the presence of 0.5-20 mM free Mg2+ were obtained at pH 7.2 and computer-fitted to 19 models. The dissociation constant of magnesium phosphate (8.5 +/- 0.4 mM) used in this analysis was measured with a Mg2+-sensitive electrode. The best model implies successive binding of two magnesium phosphate molecules or random-order binding of magnesium phosphate and free phosphate molecules. The first route predominates at physiological concentrations of Mg2+. The Pi-inhibition pattern of pyrophosphate hydrolysis confirmed that Pi adds to the active site and provided further evidence for the existence of an activating Pi-binding site. The possibility is raised that the pathways of pyrophosphate synthesis and hydrolysis by inorganic pyrophosphatase may differ in the sense that the binding of the fourth metal ion/subunit may facilitate the synthesis and inhibit the hydrolysis.     

Computer analysis of Feulgen hydrolysis kinetics.

A least squares fit of Feulgen hydrolysis time curves to the Bateman function is performed using an especially adapted parameter transformation together with a standard conjugate gradients iteration procedure. The method has been applied to a large number of measured data, and the use and limits of the computer evaluation are discussed.     

Application of artificial neural networks to modelling of starch hydrolysis by glucoamylase

The applicability of neural networks to the dynamic modelling of starch hydrolysis by Aspergillus niger glucoamylase is studied. The advantage of this technique is the possibility of predicting the reaction curves without a detailed kinetic model. Two independent neural models were proposed to predict the concentration of the products and conversion degree of the substrate at the end of the reaction (Model 1) as well as the reaction courses in the first stage when the sharp changes in the reaction rate are observed (Model 2). The results of simulations prove the ability of neural-network models to describe the complex kinetics of starch hydrolysis by glucoamylase.     

Computer analysis of Feulgen hydrolysis kinetics

Summary A least squares fit of Feulgen hydrolysis time curves to the Bateman function is performed using an especially adapted parameter transformation together with a standard conjugate gradients iteration procedure. The method has been applied to a large number of measured data, and the use and limits of the computer evaluation are discussed.     

Isolation and properties of 2 forms of cyclic nucleotide phosphodiesterase from the rat brain under normal conditions and after irradiation

It is established that the functional activity of two phosphodiesterase forms--phosphodiesterase I (Ca2+-calmodulin-sensitive) and phosphodiesterase II (Ca2+-calmodulin-insensitive), isolated from grey matter of the irradiated rat brain varies essentially in comparison with that of the normal rats. In the early period of acute radiation injury both phosphodiesterase I sensitivity to calmodulin and phosphodiesterase II special activity under hydrolysis of 3', 5'-GMP decrease but phosphodiesterase I special activity under hydrolysis of 3', 5'-GMP increases. The investigation of temperature dependence of phosphodiesterase I and phosphodiesterase II activations revealed changes in character of curves, the temperature optimum under irradiation being unchanged and inflections appearing on the Arrhenius curves.     

A comparison of two Hill-type skeletal muscle models on the construction of medial gastrocnemius length-tension curves in humans in vivo

Human length-tension curves are traditionally constructed using a model that assumes passive tension does not change during contraction (model A) even though the animal literature suggests that passive tension can decrease (model B). The study's aims were threefold: 1) measure differences in human medial gastrocnemius length-tension curves using model A vs. model B, 2) test the reliability of ultrasound constructed length-tension curves, and 3) test the robustness of fascicle length-generated length-tension curves to variations between the angle and fascicle length relationship. An isokinetic dynamometer manipulated and measured ankle angle while ultrasound was used to measure medial gastrocnemius fascicle length. Supramaximal tibial nerve stimulation was used to evoke resting muscle twitches. Length-tension curves were constructed using model A {angle-torque [A-T((A))], length-torque [L-T((A))]} or model B {length-torque [L-T((B))]} in three conditions: baseline, heel-lift (where the muscle was shortened at each angle), and baseline repeated 2 h later (+2 h). Length-tension curves constructed from model B differed from those produced via model A, indicated by a significant increase in maximum torque (≈23%) when using L-T((B)) vs. L-T((A)). No parameter measured was different between baseline and +2 h for any method, indicating good reliability when using ultrasound. Length-tension curves were unaffected by the heel-lift condition when using L-T((A)) or L-T((B)) but were affected when using A-T((A)). Since the muscle model used significantly alters human length-tension curves, and given animal data indicate model B to be more accurate when passive tension is present, we recommend that model B should be used when constructing medial gastrocnemius length-tension curves in humans in vivo.