Metabolic Futile Cycles and Their Functions: A Systems Analysis of Energy and Control

It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on open-system thermodynamics and metabolic control analysis. It is shown that the {\it stoichiometric sensitivity} of an intermediary metabolite concentration with respect to changes in steady-state flux is governed by the effective equilibrium constant of the intermediate formation, and the equilibrium can be regulated by a futile cycle. The direction of the shift in the effective equilibrium constant depends on the direction of operation of the futile cycle. High stoichiometric sensitivity corresponds to ultrasensitivity of an intermediate concentration to net flow through a pathway; low stoichiometric sensitivity corresponds to super-robustness of concentration with respect to changes in flux. Both cases potentially play important roles in metabolic regulation. Futile cycles actively shift the effective equilibrium by expending energy; the magnitude of changes in effective equilibria and sensitivities is a function of the amount of energy used by a futile cycle. This proposed mechanism for control by futile cycles works remarkably similarly to kinetic proofreading in biosynthesis. The sensitivity of the system is also intimately related to the rate of concentration fluctuations of intermediate metabolites. The possibly different roles of the two major mechanisms for cellular biochemical regulation, namely reversible chemical modifications via futile cycles and shifting equilibrium by macromolecular binding, are discussed.Comment: 11 pages, 5 figure

Systems approaches to modelling pathways and networks.

Peer reviewedPreprin

ИЗУЧЕНИЕ ВОЗМОЖНОСТИ РЕГУЛЯЦИИ АНГИОГЕНЕЗА IN VITRO С ПОМОЩЬЮ РЕКОМБИНАНТНЫХ ФРАГМЕНТОВ ИНГИБИТОРОВ АНГИОГЕНЕЗА ЭНДОСТАТИНА, ТУМСТАТИНА И PEDF

Neovascular diseases of visual organ such as age-related macular degeneration, retinopathy of prematurity, diabetic retinopathy, thrombosis of central retina vein and its branches, neovascular glaucoma, choroid and retina tumors have the leading positions in the list of ophtalmopatologies that result in blindness and incapacity. The variety of angiostatic medications of applied ophtalmology is scant. The aim of work was to study the possibile approaches to angiogenesis regulation in vitro with the help of recombinant fragments of natural inhibitors of angiogenesis such as endostatin, tumstatin and PEDF (pigment epithelial derived factor), and also their ability to be the base of potentially feasible and pharmacologically active substances. It is determined that endostatin, tumstatin and PEDF, as well as the comparison medication Bevacizumab in vitro have pro- or antiangiogenic influence. The direction of the biological effect depends on the cultivation conditions, peptide concentration in the cultural fluid and stage of angiogenesis. Неоваскулярные заболевания органа зрения, такие как возрастная макулярная дегенерация, ретинопатия недоношенных, диабетическая ретинопатия, тромбозы центральной вены сетчатки и ее ветвей, неоваскулярная глаукома, опухоли хориоидеи и сетчатки, занимают лидирующие позиции в перечне офтальмопатологии, приводящей к слепоте и инвалидизации, а также к социальной и психологической дезадаптации. Арсенал ангиостатических препаратов в практической офтальмологии скуден. Цель настоящей работы заключалась в изучении возможности регуляции ангиогенеза in vitro с помощью рекомбинантных фрагментов природных ингибиторов ангиогенеза эндостатина, тумстатина и PEDF (pigment epithelial derived factor) и применения их в качестве потенциально возможных фармакологически активных субстанций. Установлено, что in vitro эндостатин, тумстатин и PEDF, как и препарат сравнения бевацизумаб, оказывают про- или антиангиогенное действие. Направленность биологического эффекта зависит от условий культивирования, концентрации пептида в культуральной жидкости и этапа ангиогенеза.

Parametric pattern selection in a reaction-diffusion model

We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate) where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways

An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism

Methionine (Met) is an essential amino acid that is needed for the synthesis of S-adenosylmethionine (AdoMet), the major biological methylating agent. Methionine used for AdoMet synthesis can be replenished via remethylation of homocysteine. Alternatively, homocysteine can be converted to cysteine via the transsulfuration pathway. Aberrations in methionine metabolism are associated with a number of complex diseases, including cancer, anemia, and neurodegenerative diseases. The concentration of methionine in blood and in organs is tightly regulated. Liver plays a key role in buffering blood methionine levels, and an interesting feature of its metabolism is that parallel tracks exist for the synthesis and utilization of AdoMet. To elucidate the molecular mechanism that controls metabolic fluxes in liver methionine metabolism, we have studied the dependencies of AdoMet concentration and methionine consumption rate on methionine concentration in native murine hepatocytes at physiologically relevant concentrations (40–400 µM). We find that both [AdoMet] and methionine consumption rates do not change gradually with an increase in [Met] but rise sharply (∼10-fold) in the narrow Met interval from 50 to 100 µM. Analysis of our experimental data using a mathematical model reveals that the sharp increase in [AdoMet] and the methionine consumption rate observed within the trigger zone are associated with metabolic switching from methionine conservation to disposal, regulated allosterically by switching between parallel pathways. This regulatory switch is triggered by [Met] and provides a mechanism for stabilization of methionine levels in blood over wide variations in dietary methionine intake

Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system

<p>Abstract</p> <p>Background</p> <p>A central question for the understanding of biological reaction networks is how a particular dynamic behavior, such as bistability or oscillations, is realized at the molecular level. So far this question has been mainly addressed in well-mixed reaction systems which are conveniently described by ordinary differential equations. However, much less is known about how molecular details of a reaction mechanism can affect the dynamics in diffusively coupled systems because the resulting partial differential equations are much more difficult to analyze.</p> <p>Results</p> <p>Motivated by recent experiments we compare two closely related mechanisms for the product activation of allosteric enzymes with respect to their ability to induce different types of reaction-diffusion waves and stationary Turing patterns. The analysis is facilitated by mapping each model to an associated complex Ginzburg-Landau equation. We show that a sequential activation mechanism, as implemented in the model of Monod, Wyman and Changeux (MWC), can generate inward rotating spiral waves which were recently observed as glycolytic activity waves in yeast extracts. In contrast, in the limiting case of a simple Hill activation, the formation of inward propagating waves is suppressed by a Turing instability. The occurrence of this unusual wave dynamics is not related to the magnitude of the enzyme cooperativity (as it is true for the occurrence of oscillations), but to the sensitivity with respect to changes of the activator concentration. Also, the MWC mechanism generates wave patterns that are more stable against long wave length perturbations.</p> <p>Conclusions</p> <p>This analysis demonstrates that amplitude equations, which describe the spatio-temporal dynamics near an instability, represent a valuable tool to investigate the molecular effects of reaction mechanisms on pattern formation in spatially extended systems. Using this approach we have shown that the occurrence of inward rotating spiral waves in glycolysis can be explained in terms of an MWC, but not with a Hill mechanism for the activation of the allosteric enzyme phosphofructokinase. Our results also highlight the importance of enzyme oligomerization for a possible experimental generation of Turing patterns in biological systems.</p

On the dynamics of the adenylate energy system: homeorhesis vs homeostasis.

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life