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M C Kohn

Publications and source records attributed to M C Kohn.

At least 55 records · Page 3Linked to original sources
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↗
PubMed1983

Computer modeling of muscle phosphofructokinase kinetics.

The kinetics of the phosphofructokinase reaction were studied by computer modeling. A general random order, two-state allosteric model, of which the Monod--Wyman--Changeux model is a limiting case, was found to most accurately reproduce the experimental observations of Pettigrew & Frieden (1979 a,b). A simplified model with Hill coefficients was found to fit almost as well. In these models substrates bind preferentially to and stabilize the enzyme in the R state, and ATPH3-, the inhibitory species, binds preferentially to and stabilizes the enzyme in the T state. Enzymatic activity is regulated by conversion from the R to the T state, which is effected by protonation, especially of the uncomplexed enzyme, but the experimental data are inadequate for accurate estimation of the pKa of the enzyme. Random order binding of substrates is an important cause of sigmoidal kinetics. Additional experiments that would aid in the discrimination among rival models are described.

Adenosine Triphosphate↗
PubMed1983

Sensitivity to values of the rate constants in a neurochemical metabolic model.

Equations were derived for the instantaneous relative sensitivities of reaction rates (controllability indices) and metabolite concentrations (response indices) to perturbations in the values of rate constants and were used to analyze the behavior of a model of in vivo glutamate metabolism in rat brain. Controllabilities of reversible reactions were found to increase as the values of the corresponding rate constants (i.e., the rate of approach to equilibrium) increased. Response indices generally declined with the metabolic distance between the metabolite and the rate constant, but they were unexpectedly high for reversible reactions with high controllabilities. The transient response of a given metabolite is most sensitive to reactions involving metabolites which are changing most rapidly relative to their respective pool sizes. Rapidly reversible reactions are most important for communication between metabolite pools.

Animals↗
PubMed1983

A graph-theoretical analysis of metabolic regulation.

A graph theoretical method is proposed for modeling metabolic networks including enzymic cascades and synergistic binding of ligands to enzymes. Formal operations on the graph of a given network leads to the identification of feedback metabolites and the enzymes which regulate the feedback. These systemic properties are thus isolated from the purely local regulation of individual enzymes. The method was applied to a model of glycogen metabolism. At low cyclic AMP and insulin levels feedback control of the system is predicted to be largely with the glycogen branching and debranching enzymes, which set the amount of glycogen in the metabolically available outer branches.

Cyclic AMP↗
PubMed1983

Computer simulation of metabolism in palmitate-perfused rat heart. II. Behavior of complete model.

Intermediary metabolism in rat hearts perfused with 11 mM glucose plus 1 mM palmitate was simulated by a computer model. Several enzyme submodels in a previous version of the isolated rat heart computer model were improved, and a new fatty acid oxidation pathway model was added. Compartmentation of metabolites in a pseudo-stationary state was calculated, and its implications are discussed, e.g., citrate level may not regulate glycolysis because it is mostly mitochondrial. Citrate synthetase, controlled largely by its inhibitors, is of key importance in regulating fatty acid metabolism. The response of aconitase to the mitochondrial Mg2+ level is of major importance in setting both the mitochondrial citrate and isocitrate levels. Pyruvate dehydrogenase is about 96% in the inactive phosphorylated form, and the active form is also 15% inhibited by products, severely limiting pyruvate oxidation and causing preferential utilization of palmitate as the metabolic fuel. The simulation is consistent with a creatine phosphate shuttle which delivers high energy phosphate to the site of its utilization for mechanical work.

Animals↗
PubMed1983

Computer simulation of metabolism in palmitate-perfused rat heart. III. Sensitivity analysis.

The behavior of a computer model of metabolism in glucose- and palmitate-perfused rat hearts was interpreted by sensitivity analysis to explain why the heart preferentially utilizes fatty acids as fuel even in the presence of substantial exogenous glucose. The sensitivity functions identified those metabolites and enzymes which were most important in regulating the metabolic rate and determined which enzymes set the levels of the critical metabolites. Control of the mitochondrial redox potential and the distribution of coenzyme A thioesters regulated the rate of fatty acid utilization while strong inhibition of citrate synthetase resulted in accumulation of acetyl CoA and suppression of pyruvate oxidation. Glycolysis was limited by the cytosolic ATP/ADP ratio set largely by the creatine shuttle. Metabolic control appears to be widely distributed rather than localized at "key" enzymes. Metabolite levels are usually set by enzymes controlled by modifiers whereas metabolic flux is regulated by the enzymes that produce ligands for the modifier-controlled enzymes.

Animals↗
PubMed1983

Computer simulation of metabolism in palmitate-perfused rat heart. I. Palmitate oxidation.

A computer model of the fatty acid oxidation pathway in perfused rat heart was constructed. It includes uptake, activation, and beta-oxidation of fatty acids, triglyceride synthesis and hydrolysis, and carnitine-dependent transport of acyl groups across the mitochondrial membrane under pseudosteady state conditions. Fatty acid utilization may be limited by beta-oxidation in hypoxia or ischemia but probably not in aerobic conditions. Nonesterified fatty acids bound to proteins are found to be metabolically available. The model predicts that stearate, but not palmitate, can support the highest observed respiration rate for perfused rat heart without supplementation by other substrates. Fatty acids are preferentially oxidized rather than being stored as triglycerides because the cystosolic acyl CoA level is lower than the Km for triglyceride synthesis. It is suggested that feedback inhibition of triglyceride lipase regulates utilization of triglycerides as fuel in aerobic hearts.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed1979

Computer simulation of the fructose bisphosphatase/phosphofructokinase couple in rat liver.

Recycling of fructose 6-phosphate and fructose 1,6-bisphosphate in the rat liver under gluconeogenic and glycolytic conditions was investigated with a computer model containing representations of the kinetic properties of phosphofructokinase and fructose 1,6-bisphosphatase under realistic physiological conditions. The two enzyme submodels were constructed from data for the isolated enzymes in vitro by formal optimization. Tissue metabolite concentrations were corrected for cytosolic/mitochondrial compartmentation and effects of chelation and protonation equilibria. This model, which mostly considers the behavior of livers from starved rats, predicts negligible recycling under physiologically realistic conditions. Metabolic regulation of fructose 6-phosphate, the magnesium ion concentration and the distribution of adenine nucleotides appear to prevent operation of a 'futile cycle' in vivo. Rate-limiting chemical species were identified by sensitivity analysis.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. I. Model construction.

A computer model of energy metabolism was constructed for the pyruvate-perfused rat heart subjected to a sudden increase in work load. The model construction techniques are explained and justified. Hypotheses defining a plausible sequence of physiological events resulting in the observed behavior of the organ were arrived at from the measured metabolite time profiles. There is a lag in increasing pyruvate utilization following the work-jump. A transient increase in fatty acid oxidation is required to account for the observed respiration rate. The observed increase in lactate production of this preparation is due to a transient "burst" of glycogenolysis after which the remaining lactate is imported from the interstitium and oxidized, reversing lactate dehydrogenase and hence the alpha-ketoglutarate-malate portion of the malate-aspartate shuttle.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. II. Krebs cycle.

A realistic metabolic model of the tricarboxylic acid cycle in the perfused rat heart was constructed to help explain the sequence of biochemical events regulating the metabolism of exogenous pyruvate following a large increase in work load. The unchelated Mg2+ level was the most important controlling factor. The resulting mixture of chelated and unchelated nucleotides and tribasic acids effected coordinated control of citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA synthetase, fumarase, and nucleoside diphosphokinase, because Mg2+-chelates are generally substrates whereas unchelated species are inhibitors. Succinate dehydrogenase is largely controlled by the ubiquinone redox potential. The fluxes through alpha-ketoglutarate and malate dehydrogenases are largely dependent on thepyridine nucleotide redox potential, but the succinyl CoA-to-CoASH ratio strongly affects the former enzyme as well. The model predicts an accumulation of succinate during the transition to higher work output.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. III. Pyruvate dehydrogenase.

A physiologically and biochemically realistic model of the regulation of pyruvate dehydrogenase complex (PDH) was constructed for the perfused rat heart. It includes conversion between inactive (phospho) and active (dephospho) forms by a specific protein kinase (PDHK) and phosphoprotein phosphatase (PDHP). The activity of the tightly bound PDHK is influenced by synergistic activation/inhibition by acetyl CoA/CoASH and NADH/NAD. PDHK in this simulation was more sensitive to the fraction of ADP that was Mg2+-chelated than to the ATP-to-ADP ratio. Ca2+ stimulates binding of Mg2+-dependent PDHP to the complex; the bound enzyme was considered to be the active species. The fraction of PDH in the active form, rather than substrate and inhibitor levels, determines PDH activity under these conditions. This fraction depends on the present value and recent history of the difference between PDHK and PDHP activities. Both of these are active continuously and continuously control PDH.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. IV. Model behavior.

The behavior of a computer model of energy metabolism was determined for perfused rat hearts utilizing pyruvate as sole exogenous fuel and subjected to a rapid increase in work load. Computer-generated metabolite profiles, which are solutions of the differential equations for 1 min elapsed time, closely match 12 experimental curves (involving 120 concentration measurements) and exhibit the following properties. The computed cytosolic pyruvate level oscillates due to large changes in the rates of the processes that produce and consume this metabolite. Cytosolic Mg2+ seems to act as a coordinated controller of glycolytic enzymes; its transient increase permits a transient increase of glycolysis without an accumulation of glucose 6-phosphate. Lactate is exported to the interstitium by a lactate permease and then reimported and oxidized. As a result, the malate-aspartate shuttle reverses direction, and the Krebs cycle is "unspanned."

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. V. Physiological implications.

The results of a simulation of metabolism in the pyruvate-perfused rat heart subjected to a sudden increase in work load are interpreted to provide a coherent explanation for the observed physiology. Respiration is most closely correlated with the mitochondrial phosphate potential, calculated from the MgATP and MgADP levels. No correlation between respiration and the pH gradient across the mitochondrial membrane was found. The transient falls in pH in the cytosol and perhaps the mitochondria are due largely to carbonic and lactic acidosis and appear to be only weakly coupled. The heart maintains a high ATP level during the transition to increased work by utilizing its energy reserves in order of decreasing availability in response to physiological signals mediated by Mg2+, Ca2+, and cAMP.

Animals↗