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D Garfinkel

Publications and source records attributed to D Garfinkel.

At least 37 records · Page 2Linked to original sources
PubMed1987

Kinetic properties of hexokinase as assembled with a microcomputer data base.

We have constructed a relational data base containing the kinetic properties of the isoenzymes of hexokinase using the Knowledgeman data-base program on an IBM PC microcomputer. The natural subunit of this data base is the refereed publication, 165 of which were included. Reported values for the Mr (approx. 97,000) are in good agreement, but this agreement becomes progressively worse as one examines the Km values for glucose and ATP and the Ki for glucose 6-phosphate, where the reported values are spread over three orders of magnitude. Some quantities are very thinly or unreliably determined. Experimental conditions, especially free Mg2+ concentration, are rarely close to physiological. Reasons for the spread or uncertainty of numbers, and the distinctions that can be made between isoenzymes despite this spread, are discussed.

Adenosine Triphosphate↗
PubMed1987

Altered therapeutic range for quinidine after myocardial infarction and cardiac surgery.

Although most assays for measuring drug levels in serum determine the total concentration, effects from a drug are determined better by measuring the concentration of unbound (free) drug in serum. When the free fraction of a drug is constant, the total drug concentration may act as a good guide in predicting drug activity. However, if the free fraction is altered from normal, the serum concentration of the total drug may be misinterpreted. Quinidine has a high binding affinity for alpha-1-acid glycoprotein. We present the case of a woman who had a myocardial infarction; after cardiac surgery, she was found to have high concentrations of alpha-1-acid glycoprotein (228 mg/dL) and a low free fraction of quinidine (0.032). At that time the patient had a total concentration of quinidine of 33.9 mumol/L (11 micrograms/mL) but showed no signs or symptoms of toxicity because the concentration of free quinidine was not high. Physicians should be aware of the limitations of assays in determining the unbound concentration of drugs in serum. This awareness is particularly crucial with drugs that bind well to serum proteins, especially when pathologic conditions change the extent of binding.

Aged↗
PubMed1987

Modeling and artificial intelligence approaches to enzyme systems.

Modeling is a means of formulating and testing complex hypotheses. Useful modeling is now possible with biological laboratory microcomputers with which experimenters feel comfortable. Artificial intelligence (AI) is sufficiently similar to modeling that AI techniques, now becoming usable on microcomputers, are applicable to modeling. Microcomputer and AI applications to physiological system studies with multienzyme models and with kinetic models of isolated enzymes are described. Using an IBM PC microcomputer, we have been able to fit kinetic enzyme models; to extend this process to design kinetic experiments by determining the optimal conditions; and to construct an enzyme (hexokinase) kinetics data base. We have also used a PC to do most of the constructing of complex multienzyme models, initially with small simple BASIC programs; alternative methods with standard spreadsheet or data base programs have been defined. Formulating and solving differential equations in appropriate representational languages, and sensitivity analysis, are soon likely to be feasible with PCs. Much of the modeling process can be stated in terms of AI expert systems, using sets of rules for fitting and evaluating models and designing further experiments. AI techniques also permit critiquing and evaluating the data, experiments, and hypotheses being modeled, and can be extended to supervise the calculations involved.

Artificial Intelligence↗
PubMed1986

Is aging inevitable? The intracellular zinc deficiency hypothesis of aging.

A review of the literature suggests that an intracellular zinc deficiency may be the primary cause of the aging process. Zinc-metalloenzymes play an important role in many aspects of cellular metabolism including DNA replication, repair and transcription. The main enzymes affected by zinc deficiency may be specific for each cell type. Depending on which zinc enzymes are "overvulnerable", zinc deficiency may result in accumulation of useless (or toxic) materials, malproduction of essential proteins, a neoplastic change or cell death, thus explaining the variability in aging patterns in different cell types. There is no simple and reliable index of zinc status in humans and a therapeutic trial may be needed to establish zinc deficiency. Finding a zinc-compound which can enter the cell and avoid the development of intracellular zinc deficiency may retard the aging process and postpone age-related diseases.

Aging↗
PubMed1986

Magnesium in cardiac energy metabolism.

Free intracellular magnesium ion, which influences many metabolic processes, is the subject of ongoing research. Its concentration has been difficult to measure because the available methods, including dye injection, microelectrodes, and nuclear magnetic resonance measurements, are invasive or indirect. Concentrations ranging from 0.1 mM in frog muscle to 6 mM in barnacle muscle have been reported. We describe recent experimental evidence regarding the concentration of free intracellular magnesium and consider the limitations of these methods. A substantial body of evidence, including our models of cardiac energy metabolism and its magnesium-related processes, indicates that intracellular concentrations of free magnesium are low (ca. 0.4 mM) and vary with time and conditions.

Animals↗
PubMed1985

Kinetic analysis of monocarboxylate uptake into perfused rat hearts.

To test a prediction that trans-sarcolemmal lactate movement is carrier mediated, 14C-labelled lactate or pyruvate and 3H-mannitol were transiently infused (2 min) into aerobically perfused rat hearts that had been depleted of intracellular monocarboxylates by a 30 min pre-perfusion in the absence of substrates. Uptake was calculated from the difference between the level of 14C-substrate predicted from the extracellular distribution of 3H-mannitol and the actual level (corrected for 14CO2 contamination) measured in successive 20 s samples of effluent perfusate. Computer optimization analysis of the initial influx revealed that monocarboxylate transport is not simply a question of diffusion. On the contrary, saturation and cross-inhibition (Ki, lactate 0.14 +/- 0.04 mM; Ki, pyruvate 2.2 +/- 0.4 mM; Ki, acetoacetate 6.2 +/- 0.9 mM; and Ki, 3-hydroxybutyrate 20 +/- 6.0 mM) suggest that trans-sarcolemmal monocarboxylate movements are reversibly mediated by a high activity (Vmax 34 +/- 7 mumol/min/g wet wt), low affinity lactate (Km 6 +/- 2 mM) permease. Further, studies into the effects of pH indicate that transport requires prior protonation of the carrier (pKa 7.1) and that lactate movements are driven by the displacement of the trans-sarcolemmal lactate and proton gradient from the Donnan equilibrium.

Animals↗
PubMed1985

Magnesium regulation of the glycolytic pathway and the enzymes involved.

Past work, including our computer simulation of cardiac energy metabolism, indicates that magnesium is an important coherent controller of glycolysis and the Krebs cycle. Many of the glycolytic enzymes are sensitive to Mg2+. The most important effect is due to MgATP2-being a cofactor for a number of these enzymes while other chelation forms are inactive or inhibitory. The means by which Mg2+ and Mg2+ chelates of adenine nucleotides regulate the most important glycolytic enzymes--hexokinase, phosphofructokinase, aldolase, phosphoglycerate kinase, and pyruvate kinase--are described in detail. Creatine kinase, which is important in energy metabolism and highly sensitive to both metal ions and pH, is also discussed. It is necessary to properly control the composition of assay mixtures (particularly with regard to metal ions) in order to determine what actually regulates the activity of an enzyme.

Adenosine Diphosphate↗
PubMed1985

Monocarboxylate-uptake kinetics in perfused rat heart.

While there is considerable evidence to suggest that lactate and pyruvate transport across the cell membrane is controlled, virtually nothing is known about the mechanisms. To test a prediction that sarcolemmal monocarboxylate transport is mediated by a specific carrier, we have examined the kinetics of pyruvate and lactate uptake into aerobically perfused rat hearts. In preparations depleted of intracellular lactate and pyruvate by a 30-min pre-perfusion in the absence of substrates, various concentrations of [14C]lactate or pyruvate (0.02 Ci/mole), together with [3H]mannitol (50 nCi/ml), were transiently (2 min) infused into the mainstream perfusate immediately above the heart. Uptake was calculated from the difference between the level of 14C-labeled substrate predicted from the extracellular distribution of [3H]mannitol and the actual level (corrected for 14CO2 contamination) measured in successive 20-sec samples of effluent perfusate. Computer optimization analysis of the initially rapid (first 60 sec) uptake rates revealed that monocarboxylate transport is not simply a question of diffusion. On the contrary, the observation of typical saturation kinetics (Vmax 7.7-8.4 mumoles/min per g wet wt.) and cross-inhibition (Ki pyr, 2.3 +/- 0.5 mM; Ki lac, 0.16 +/- 0.02 mM) suggest that transsarcolemmal movement of monocarboxylate may be mediated by a high-affinity lactate (km 3.9 +/- 0.9 mM), low-affinity pyruvate (Km 8.6 +/- 1.1 mM), translocase.

Animals↗
PubMed1984

Calculation of free-Mg2+ concentration in adenosine 5'-triphosphate containing solutions in vitro and in vivo.

We have attempted to resolve the differences between the levels of free Mg2+ in muscle calculated by Wu et al. [Wu, S. T., Pieper, G. M., Salhany, J. M., & Eliot, R. S. (1981) Biochemistry 20, 7399-7403] (2.5 mM in guinea pig heart) and by Gupta and Moore [Gupta, R. K., & Moore, R. D. (1980) J. Biol. Chem. 255, 3987-3993] (0.6 mM in frog skeletal muscle) on the basis of substantially identical measurements by 31P NMR of the phosphate peaks in the spectrum of MgATP2-. The differences depend on the methods of calculation, including which reactions in which multiple equilibria are being considered. Biochemists and physical chemists customarily use different working definitions of the stability constant for MgATP2- in particular. Wu et al. used in their calculations, without reconciliation, methods involving three different operational definitions of the chelation equilibria involved. An algorithm for calculating Mg2+ and total ATP, which can be carried out with a hand calculator, is described here. With it, we calculated Mg2+ levels that agree with those determined by Gupta et al. [Gupta, R. K., Benkovic, J. L., & Rose, Z. B. (1978) J. Biol. Chem. 253, 6165-6171] with their in vitro systems. We therefore agree with the finding of Gupta and Moore that the Mg2+ level in skeletal and cardiac muscle is 0.6 mM.

Adenosine Triphosphate↗
PubMed1984

A computer program for analyzing enzyme kinetic data using graphical display and statistical analysis.

A computer program, PENNZYME (M. C. Kohn, L. E. Menten, and D. Garfinkel, Comput. Biomed. Res. 12, 461, 1979), that fits trial rate laws to enzyme and transport steady-state kinetic data by nonlinear regression has been enhanced. The new version includes a set of mnemonic commands which can be displayed in a menu at the user's option. Graphic displays of measured data and computed curves, as well as deviations between them (residual plots) have been added to aid the user in determining if a model is free of bias or systematic error. Other features include the ability to display the variance-covariance matrix of the parameters, to hold individual parameters constant during an optimization, and to optimize error models for the experimental data by the extended-least-squares technique.

Computers↗
PubMed1984

Nucleotide sequence of the tms genes of the pTiA6NC octopine Ti plasmid: two gene products involved in plant tumorigenesis.

The nucleotide sequence of the tumor morphology locus, tms, from pTiA6NC has been determined. The sequence analysis indicates that each of two polyadenylylated transcripts encoded by this locus contains an open reading frame; the predicted transcript 1 gene product has a molecular size of 83,769 daltons, and the predicted transcript 2 gene product, of 49,588 daltons. The precise start and stop positions of the transcript 2 RNA have been mapped with S1 nuclease. Several insertion mutations have been constructed. One of these localizes the transcript 2 promoter within the 72 base pairs 5' to transcription initiation. Significant homology was observed between the protein encoded by transcript 1 and the adenine binding region of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens, suggesting that the transcript 1 protein binds adenine either as substrate or cofactor.

Amino Acid Sequence↗
PubMed1984

Fitting physiological models to data.

Methods of fitting models to experimental data obtained from biological systems are reviewed. The Michaelis-Menten model is used as the working example of a familiar and well-studied biological model. Criteria for selecting models include goodness of fit, freedom from systematic errors, and simplicity. A given model is usually fitted and the optimal parameters determined by minimization of an objective function, usually the sum of the squared errors. Freedom from systematic errors is best judged graphically. The important mathematical methods of fitting models are derived from the calculus and include linear and quadratic programming. The latter leads to minimization of the sum of squares of errors. Optimal search procedures, which also perform this minimization, are surveyed. Other properties of models, such as the proper number of parameters and whether linearization is appropriate, are discussed. The specialized problems of biological models and data are considered.

Models, Biological↗