Regulation of myocardial substrate metabolism during increased energy expenditure: insights from computational studies

In response to exercise, the heart increases its metabolic rate severalfold while maintaining energy species (e.g., ATP, ADP, and Pi) concentrations constant; however, the mechanisms that regulate this response are unclear. Limited experimental studies show that the classic regulatory species NADH and NAD+ are also maintained nearly constant with increased cardiac power generation, but current measurements lump the cytosol and mitochondria and do not provide dynamic information during the early phase of the transition from low to high work states. In the present study, we modified our previously published computational model of cardiac metabolism by incorporating parallel activation of ATP hydrolysis, glycolysis, mitochondrial dehydrogenases, the electron transport chain, and oxidative phosphorylation, and simulated the metabolic responses of the heart to an abrupt increase in energy expenditure. Model simulations showed that myocardial oxygen consumption, pyruvate oxidation, fatty acids oxidation, and ATP generation were all increased with increased energy expenditure, whereas ATP and ADP remained constant. Both cytosolic and mitochondrial NADH/NAD+ increased during the first minutes (by 40% and 20%, respectively) and returned to the resting values by 10-15 min. Furthermore, model simulations showed that an altered substrate selection, induced by either elevated arterial lactate or diabetic conditions, affected cytosolic NADH/NAD+ but had minimal effects on the mitochondrial NADH/NAD+, myocardial oxygen consumption, or ATP production. In conclusion, these results support the concept of parallel activation of metabolic processes generating reducing equivalents during an abrupt increase in cardiac energy expenditure and suggest there is a transient increase in the mitochondrial NADH/NAD+ ratio that is independent of substrate supply.     

Cybernetic modeling of growth in mixed, substitutable substrate environments: Preferential and simultaneous utilization

Growth of microorganisms on substitutable substrate mixtures display diverse growth dynamics characterized by simultaneous or preferential uptake of carbon sources. This article shows that cybernetic modeling concepts which were successful in predicting diauxic growth patterns can be extended to describe simultaneous consumption of substrates. Thus the growth of Escherichia coli on mixtures of glucose and organic acids such as pyruvate, fumarate, and succinate has been described successfully by the cybernetic model presented here showing both diauxic and simultaneous uptake when observed. The model also describes the changes in utilization patterns that occur under changing dilution rates, substrate concentrations, and models of preculturing. The model recognizes the importance of the synthesis of biosynthetic precursors in cell growth through a kinetic structure that is quite general for any mixture of carbon-energy sources. (c) 1996 John Wiley & Sons, Inc.     

Molecular modeling studies of substrate binding by penicillin acylase

Molecular modeling has revealed intimate details of the mechanism of binding of natural substrate, penicillin G (PG), in the penicillin acylase active center and solved questions raised by analysis of available X-ray structures, mimicking Michaelis complex, which substantially differ in the binding pattern of the PG leaving group. Three MD trajectories were launched, starting from PDB complexes of the inactive mutant enzyme with PG (1FXV) and native penicillin acylase with sluggishly hydrolyzed substrate analog penicillin G sulfoxide (1GM9), or from the complex obtained by PG docking. All trajectories converged to a similar PG binding mode, which represented the near-to-attack conformation, consistent with chemical criteria of how reactive Michaelis complex should look. Simulated dynamic structure of the enzyme-substrate complex differed significantly from 1FXV, resembling rather 1GM9; however, additional contacts with residues bG385, bS386, and bN388 have been found, which were missing in X-ray structures. Combination of molecular docking and molecular dynamics also clarified the nature of extremely effective phenol binding in the hydrophobic pocket of penicillin acylase, which lacked proper explanation from crystallographic experiments. Alternative binding modes of phenol were probed, and corresponding trajectories converged to a single binding pattern characterized by a hydrogen bond between the phenol hydroxyl and the main chain oxygen of bS67, which was not evident from the crystal structure. Observation of the trajectory, in which phenol moved from its steady bound to pre-dissociation state, mapped the consequence of molecular events governing the conformational transitions in a coil region a143-a146 coupled to substrate binding and release of the reaction products. The current investigation provided information on dynamics of the conformational transitions accompanying substrate binding and significance of poorly structured and flexible regions in maintaining catalytic framework.     

Metabolism of substrates: energy substrate metabolism during exercise and as modified by training

The question of what is the source of fuel for oxidation by muscle during exercise has been addressed. A review of experiments spanning more than 60 years supports the concept that the major energy source for the metabolism of exercise is the oxidation of fats and carbohydrates. The relative contribution of these major substrates to the total body metabolism depends on factors such as the intensity and duration of the exercise, the diet consumed on the days before the exercise, and the state of physical training. With light prolonged exercise there is a progressively greater use of fat until it can contribute up to 80% of the total caloric expenditure. However, the relative contribution of fat to the metabolism is less and that of carbohydrate greater as exercise intensity increases. Consumption of a diet rich in fat and protein produces a shift toward a greater use of fat with a concomitant reduction of both the intensity and duration of effort that can be sustained. Conversely, ingestion of a carbohydrate-rich diet increases the percentage of carbohydrate used and increases endurance. The concentration of glycogen in muscle is reduced by fat-protein diets and elevated by carbohydrate-rich diets. Endurance training results in a shift of the metabolism toward a greater use of fat during the same absolute and relative exercise loads. This produces a glycogen sparing that is associated with improving endurance capacity.     

Predictive modeling of mixed microbial populations in food products: evaluation of two-species models

Predictive microbiology is an emerging research domain in which biological and mathematical knowledge is combined to develop models for the prediction of microbial proliferation in foods. To provide accurate predictions, models must incorporate essential factors controlling microbial growth. Current models often take into account environmental conditions such as temperature, pH and water activity. One factor which has not been included in many models is the influence of a background microflora, which brings along microbial interactions. The present research explores the potential of autonomous continuous-time/two-species models to describe mixed population growth in foods. A set of four basic requirements, which a model should satisfy to be of use for this particular application, is specified. Further, a number of models originating from research fields outside predictive microbiology, but all dealing with interacting species, are evaluated with respect to the formulated model requirements by means of both graphical and analytical techniques. The analysis reveals that of the investigated models, the classical Lotka-Volterra model for two species in competition and several extensions of this model fulfill three of the four requirements. However, none of the models is in agreement with all requirements. Moreover, from the analytical approach, it is clear that the development of a model satisfying all requirements, within a framework of two autonomous differential equations, is not straightforward. Therefore, a novel prototype model structure, extending the Lotka-Volterra model with two differential equations describing two additional state variables, is proposed to describe mixed microbial populations in foods.     

Stability and distribution of stationary states in glycolysis

The steady-state concentration distributions of glycolytic metabolites are predicted. The dependence of distribution stability on kinetic parameters is evaluated.     

Phosphatidylcholine metabolism in cultured cells: catabolism via glycerophosphocholine

The catabolism of phosphatidylcholine (PtdCho) has been studied in cultured murine neuroblastoma (N1E-115), C6 glioma, rat brain primary glia, and human fibroblast cells. Cells were pulse labelled for 96 h with [methyl-3H]choline followed by a chase for up to 24 h in medium containing 4 mM choline. Measurement of the radioactivity and mass of choline-containing compounds in these cells indicated that the major degradative pathway is PtdCho----lysophosphatidylcholine (lysoPtdCho)----glycerophosphocholine (GroPCho)----choline. At all times during the chase, PtdCho, sphingomyelin and lysoPtdCho comprised 72-92% of the cell-associated radioactivity; the remaining 10-30% was water-soluble and was chiefly GroPCho (30-80%) in all cell lines. In fibroblasts, however, phosphocholine (PCho) was also a major labelled water-soluble component (33-54%). The specific activity of GroPCho closely parallelled that of PtdCho in fibroblasts, but decreased faster than PtdCho in C6 and N1E-115 cells. We postulate that this may be due to distinct pools of PtdCho in the cell with differing rates of turnover. The changes in specific activity of PCho suggest that the major portion is formed by synthesis rather than as a degradative product. However, the inability to reduce the specific activity of this fraction to that of the intracellular choline suggests that a portion may be derived from either PtdCho or GroPCho.     

Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift

Xylose isomerase (E.C. 5.3.1.5) catalyzes the interconversion of aldose and ketose sugars and has an absolute requirement for two divalent cations at its active site to drive the hydride transfer rates of sugar isomerization. Evidence suggests some degree of metal movement at the second metal site, although how this movement may affect catalysis is unknown. The 0.95 A resolution structure of the xylitol-inhibited enzyme presented here suggests three alternative positions for the second metal ion, only one of which appears positioned in a catalytically competent manner. To complete the reaction, an active site hydroxyl species appears appropriately positioned for hydrogen transfer, as evidenced by precise bonding distances. Conversely, the 0.98 A resolution structure of the enzyme with glucose bound in the alpha-pyranose state only shows one of the metal ion conformations at the second metal ion binding site, suggesting that the linear form of the sugar is required to promote the second and third metal ion conformations. The two structures suggest a strong degree of conformational flexibility at the active site, which seems required for catalysis and may explain the poor rate of turnover for this enzyme. Further, the pyranose structure implies that His53 may act as the initial acid responsible for ring opening of the sugar to the aldose form, an observation that has been difficult to establish in previous studies. The glucose ring also appears to display significant segmented disorder in a manner suggestive of ring opening, perhaps lending insight into means of enzyme destabilization of the ground state to promote catalysis. On the basis of these results, we propose a modified version of the bridged bimetallic mechanism for hydride transfer in the case of Streptomyces olivochromogenes xylose isomerase.     

Cellular-based modeling of oscillatory dynamics in brain networks

Oscillatory, population activities have long been known to occur in our brains during different behavioral states. We know that many different cell types exist and that they contribute in distinct ways to the generation of these activities. I review recent papers that involve cellular-based models of brain networks, most of which include theta, gamma and sharp wave-ripple activities. To help organize the modeling work, I present it from a perspective of three different types of cellular-based modeling: 'Generic', 'Biophysical' and 'Linking'. Cellular-based modeling is taken to encompass the four features of experiment, model development, theory/analyses, and model usage/computation. The three modeling types are shown to include these features and interactions in different ways.     

Role of cascades in converting oscillatory signals into stationary step-like responses

In biological signal transduction pathways intermediates are often oscillatory and need to be converted into smooth output signals at the end. We show by mathematical modelling that protein kinase cascades enable converting oscillatory signals into sharp stationary step-like outputs. The importance of this result is demonstrated for the switch-like protein activation by calcium oscillations, which is of biological importance for regulating different cellular processes. In addition, we found that protein kinase cascades cause memory effects in the protein activation, which might be of a physiological advantage since a smaller amount of calcium transported in the cell is required for an effective activation of cellular processes.     

Mathematical modeling for mixed culture growth of two bacterial populations with opposite substrate preferences

An unstructured mathematical model is proposed for mixed culture growth of two different bacterial species that exhibit "opposite" substrate preferences in response to the "same" environmental conditions. The model incorporates enzymatic control mechanisms such as induction, repression, and inhibition in the microorganisms as manifested in their preferential utilization of substrates and microbial interactions such as amensalism and competition. The model predicts cell mass, substrate concentrations, dissolved oxygen tension, as well as key enzyme levels. The predictions of the model are compared with experimental data for pure culture growth and for mixed culture growth on two substrates, glucose and citrate, in a batch reactor.     

Self-organizing maps: stationary states,metastability and convergence rate

We investigate the effect of various types of neighborhood function on the convergence rates and the presence or absence of metastable stationary states of Kohonen's self-organizing feature map algorithm in one dimension. We demonstrate that the time necessary to form a topographic representation of the unit interval [0, 1] may vary over several orders of magnitude depending on the range and also the shape of the neighborhood function, by which the weight changes of the neurons in the neighborhood of the winning neuron are scaled. We will prove that for neighborhood functions which are convex on an interval given by the length of the Kohonen chain there exist no metastable states. For all other neighborhood functions, metastable states are present and may trap the algorithm during the learning process. For the widely-used Gaussian function there exists a threshold for the width above which metastable states cannot exist. Due to the presence or absence of metastable states, convergence time is very sensitive to slight changes in the shape of the neighborhood function. Fastest convergence is achieved using neighborhood functions which are "convex" over a large range around the winner neuron and yet have large differences in value at neighboring neurons.     

Thermodynamic and kinetic studies of a stoichiometric model of energetic metabolism under starvation conditions

Abstract A stoichiometric model of anaerobic glycolysis is presented and the influence on its dynamics by the ATP-consuming membrane transport processes and substrate input rate are studied. The model is represented by a system of four ODE (ordinary differential equations), mass conservation equations and functions of state variables, such as thermodynamic efficiency. A low substrate input rate provokes damped oscillations while a high enrgy load determines sustained oscillations in all the metabolites and in thermodynamic efficiency. Due to the lack of linearity between fluxes and forces in the oscillatory region it may be stated that oscillations appear when the system is kinetically controlled.     

Pyridine metabolism in tea plants: salvage, conjugate formation and catabolism

Pyridine compounds, including nicotinic acid and nicotinamide, are key metabolites of both the salvage pathway for NAD and the biosynthesis of related secondary compounds. We examined the in situ metabolic fate of [carbonyl-¹⁴C]nicotinamide, [2-¹⁴C]nicotinic acid and [carboxyl-¹⁴C]nicotinic acid riboside in tissue segments of tea (Camellia sinensis) plants, and determined the activity of enzymes involved in pyridine metabolism in protein extracts from young tea leaves. Exogenously supplied ¹⁴C-labelled nicotinamide was readily converted to nicotinic acid, and some nicotinic acid was salvaged to nicotinic acid mononucleotide and then utilized for the synthesis of NAD and NADP. The nicotinic acid riboside salvage pathway discovered recently in mungbean cotyledons is also operative in tea leaves. Nicotinic acid was converted to nicotinic acid N-glucoside, but not to trigonelline (N-methylnicotinic acid), in any part of tea seedlings. Active catabolism of nicotinic acid was observed in tea leaves. The fate of [2-¹⁴C]nicotinic acid indicates that glutaric acid is a major catabolite of nicotinic acid; it was further metabolised, and carbon atoms were finally released as CO₂. The catabolic pathway observed in tea leaves appears to start with the nicotinic acid N-glucoside formation; this pathway differs from catabolic pathways observed in microorganisms. Profiles of pyridine metabolism in tea plants are discussed.     

Beneficial effects of supplemental buffer and substrate on energy metabolism during small bowel storage

Successful preservation of small bowel (SB) is closely correlated with the maintenance of cellular energetics. This study was designed to assess the ability of a modified UW solution supplemented with buffer and glucose to facilitate ATP production during cold storage. In part A, rats SB (n = 4) were flushed vascularly as follows: Group 1, UW solution (control); Group 2, HUW solution (UW+90 mM histidine). Inclusion of histidine resulted in a >3-fold increase in buffering capacity over the pH range 7.4-6.8. Positive effects of histidine on ATP and energy charge were apparent after 4-10h storage. Examination of the key regulatory enzyme, Phosphofructokinase (PFK), reflected a sustained activation was over 1-4h in the HUW group only. In part B, groups were vascularly flushed as follows: Group 1, HUW solution (control); Group 2, Group 1+20mM glucose; and Group 3, Group 2+luminal flush. Elevated ATP and total adenylates over 2-10h in Group 3 compared to control were a direct consequence of improved glycolytic activity. This data supports the hypothesis that tissue energetics can be significantly improved during cold storage using a histidine-buffered UW solution supplemented with carbohydrate substrate.     

Endogenous substrate for energy metabolism and ultrastructural correlates in spermatozoa of the sea urchin Diadema setosum

Energy metabolism in spermatozoa of the sea urchin Diadema setosum of the order Diadematoida was examined. The spermatozoa contained not only several kinds of phospholipids and cholesterol, but also triglyceride (TG). Glycogen and glucose were present at extremely low levels. Following dilution of dry sperm and incubation in seawater, the TG content decreased rapidly. Other lipids, however, remained at constant levels, except for a slight increase in the level of free fatty acid. High lipase activity was demonstrated in the spermatozoa. ¹⁴C-labeled fatty acid was oxidized to ¹⁴CO₂. Ultrastructural study also showed that lipid globules were present at the bottom of the midpiece. After incubation in seawater, morphological changes in the lipid globules were observed and some vacuoles appeared. Thus, the results obtained strongly suggest that D. setosum spermatozoa obtain energy through oxidation of fatty acid from TG stored in the lipid globules at the midpieces. © 1995 Wiley-Liss, Inc.     

Hysteresis, alternative stationary states and auto-oscillations in an open futile cycle one of the reactions of which is substrate inhibited]

In connection with the problem of regulation of futile (energy-dissipating) cycles in cell metabolism, a kinetic model has been investigated of an open cycle S1 (see article) S2, in which one of the enzymes (E-) is inhibited by the excess of its substrate S2. The quasi-stationary net velocity of the utilization of substrate S1 in the cycle as a function of its concentration is shown to be of a hysteretic character. Owing to this the alternative stationary states and self-oscillations may occur in the cycle. Under certain conditions the transition from one alternative state to another may reverse the direction of the net flux of conversion from S1 to S2 or vice versa. The self-oscillations are associated with a periodical change in the net flux direction. It is suggested the participation of glycogen (starch) in the self-oscillatory mechanism of the futile cycle formed by the phosphofructokinase and fructose bisphosphatase reactions may give rise to oscillations with the period of 10(3)-10(4) min, which may serve as the basis for the cell clock.     

Enhanced polyamine catabolism alters homeostatic control of white adipose tissue mass, energy expenditure, and glucose metabolism

Peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1 alpha) is an attractive candidate gene for type 2 diabetes, as genes of the oxidative phosphorylation (OXPHOS) pathway are coordinatively downregulated by reduced expression of PGC-1 alpha in skeletal muscle and adipose tissue of patients with type 2 diabetes. Here we demonstrate that transgenic mice with activated polyamine catabolism due to overexpression of spermidine/spermine N(1)-acetyltransferase (SSAT) had reduced white adipose tissue (WAT) mass, high basal metabolic rate, improved glucose tolerance, high insulin sensitivity, and enhanced expression of the OXPHOS genes, coordinated by increased levels of PGC-1 alpha and 5'-AMP-activated protein kinase (AMPK) in WAT. As accelerated polyamine flux caused by SSAT overexpression depleted the ATP pool in adipocytes of SSAT mice and N(1),N(11)-diethylnorspermine-treated wild-type fetal fibroblasts, we propose that low ATP levels lead to the induction of AMPK, which in turn activates PGC-1 alpha in WAT of SSAT mice. Our hypothesis is supported by the finding that the phenotype of SSAT mice was reversed when the accelerated polyamine flux was reduced by the inhibition of polyamine biosynthesis in WAT. The involvement of polyamine catabolism in the regulation of energy and glucose metabolism may offer a novel target for drug development for obesity and type 2 diabetes.