A study of the temperature dependence of bienzyme systems and enzymatic chains

It is known that most enzyme-facilitated reactions are highly temperature dependent processes. In general, the temperature coefficient, Q10, of a simple reaction reaches 2.0-3.0. Nevertheless, some enzyme-controlled processes have much lower Q10 (about 1.0), which implies that the process is almost temperature independent, even if individual reactions involved in the process are themselves highly temperature dependent. In this work, we investigate a possible mechanism for this apparent temperature compensation: simple mathematical models are used to study how varying types of enzyme reactions are affected by temperature. We show that some bienzyme-controlled processes may be almost temperature independent if the modules involved in the reaction have similar temperature dependencies, even if individually, these modules are strongly temperature dependent. Further, we show that in non-reversible enzyme chains the stationary concentrations of metabolites are dependent only on the relationship between the temperature dependencies of the first and last modules, whilst in reversible reactions, there is a dependence on every module. Our findings suggest a mechanism by which the metabolic processes taking place within living organisms may be regulated, despite strong variation in temperature

Systems biology of cell behavior

Systems Biology approaches to drug discovery largely focus on the increasing understanding of intracellular and cellular circuits, by computational representation of a molecular system followed by parameter validation against experimental data. This chapter outlines a universal approach to systems biology that allows the linking of intracellular molecular machinery and cellular activity. This procedure is achieved by applying mathematical modeling to molecular modules of a cell in the light of systems biology techniques. © 2010 Springer Science+Business Media, LLC

A calcium dependent de-adhesion mechanism regulates the direction and rate of cell migration: A mathematical model

Cell migration has long been studied by a variety of techniques and many proteins have been implicated in its regulation. Integrins, key proteins that link the cell to the extracellular matrix, are central to adhesion complexes whose turnover defines the rate of cell locomotion. The formation and disassembly of these adhesions is regulated by both intracellular and extracellular factors. In this study we have focused on the Ca2+-dependent protein network (module) that disassembles the adhesion complexes. We have developed a mathematical model that includes the Ca2+-dependent enzymes μ-calpain and phospholipase C (PLC) as well as IP3 receptors and stretch activated Ca2+ channels, all of which have been reported to regulate migration. The model also considers the spatial effects of Ca2+ propagation into lamella. Our model predicts differential activation of calpain at the leading and trailing edges of the cell. Since disassembly of integrin adhesive contacts is proportional to the degree of calpain activation, this leads to cell migration in a preferred direction. We show how the dynamics of Ca2+ spiking affects calpain activation and thus changes the disassembly rate of adhesions. The spiking is controlled by PLC activity and currents through stretch-activated Ca2+ channels. Our model thus combines the effects of various molecular factors and leads to a consistent explanation of the regulation of the rate and direction of cell migration. © 2006 IOS Press. All rights reserved

Elucidating the mechanisms of cooperative calcium-calmodulin interactions: A structural systems biology approach

Background: Calmodulin is an important multifunctional molecule that regulates the activities of a large number of proteins in the cell. Calcium binding induces conformational transitions in calmodulin that make it specifically active to particular target proteins. The precise mechanisms underlying calcium binding to calmodulin are still, however, quite poorly understood. Results: In this study, we adopt a structural systems biology approach and develop a mathematical model to investigate various types of cooperative calcium-calmodulin interactions. We compare the predictions of our analysis with physiological dose-response curves taken from the literature, in order to provide a quantitative comparison of the effects of different mechanisms of cooperativity on calcium-calmodulin interactions. The results of our analysis reduce the gap between current understanding of intracellular calmodulin function at the structural level and physiological calcium-dependent calmodulin target activation experiments. Conclusion: Our model predicts that the specificity and selectivity of CaM target regulation is likely to be due to the following factors: variations in the target-specific Ca2+ dissociation and cooperatively effected dissociation constants, and variations in the number of Ca2+ ions required to bind CaM for target activation. © 2008 Valeyev et al; licensee BioMed Central Ltd

Multiple calcium binding sites make calmodulin multifunctional

Protein-protein or protein-ion interactions with multisite proteins are essential to the regulation of intracellular and extracellular events. There is, however, limited understanding of how ligand-multisite protein interactions selectively regulate the activities of multiple protein targets. In this paper, we focus on the important calcium (Ca2+) binding protein calmodulin (CaM), which has four Ca2+ ion binding sites and regulates the activity of over 30 other proteins. Recent progress in structural studies has led to significant improvements in the understanding of Ca2+-CaM- dependent regulation mechanisms. However, no quantitative model is currently available that can fully explain how the structural diversity of protein interaction surfaces leads to selective activation of protein targets. In this paper, we analyze the multisite protein-ligand binding mechanism using mathematical modelling and experimental data for Ca2+-CaM-dependent protein targets. Our study suggests a potential mechanism for selective and differential activation of Ca2+-CaM targets by the same CaM molecules, which are involved in a variety of intracellular functions. The close agreement between model predictions and experimental dose-response curves for CaM targets available in the literature suggests that such activation is due to the selective activity of CaM conformations in complexes with variable numbers of Ca2+ ions. Although the paper focuses on the Ca2+-CaM pair as a particularly data rich example, the proposed model predictions are quite general and can easily be extended to other multisite proteins. The results of the study may therefore be proposed as a general explanation for multifunctional target regulation by multisite proteins. © The Royal Society of Chemistry

Computational modelling suggests dynamic interactions between Ca ²⁺, IP<inf>3</inf> and G protein-coupled modules are key to robust Dictyostelium aggregation

Under conditions of starvation, Dictyostelium cells begin a programme of development during which they aggregate to form a multicellular structure by chemotaxis, guided by propagating waves of cyclic AMP that are relayed robustly from cell to cell. In this paper, we develop and analyse a new model for the intracellular and extracellular cAMP dependent processes that regulate Dictyostelium migration. The model allows, for the first time, a quantitative analysis of the dynamic interactions between calcium, IP3 and G protein-dependent modules that are shown to be key to the generation of robust cAMP oscillations in Dictyostelium cells. The model provides a mechanistic explanation for the transient increase in cytosolic free Ca2+ concentration seen in recent experiments with the application of the calmodulin inhibitor calmidazolium (R24571) to Dictyostelium cells, and also allows elucidation of the effects of varying both the conductivity of stretch-activated channels and the concentration of external phosphodiesterase on the oscillatory regime of an individual cell. A rigorous analysis of the robustness of the new model shows that interactions between the different modules significantly reduce the sensitivity of the resulting cAMP oscillations to variations in the kinetics of different Dictyostelium cells, an essential requirement for the generation of the spatially and temporally synchronised chemoattractant cAMP waves that guide Dictyostelium aggregation. © The Royal Society of Chemistry 2009

Crosstalk between G-protein and Ca2+ pathways switches intracellular cAMP levels

Cyclic adenosine monophosphate and cyclic guanosine monophosphate are universal intracellular messengers whose concentrations are regulated by molecular networks comprised of different isoforms of the synthases adenylate cyclase or guanylate cyclase and the phosphodiesterases which degrade these compounds. In this paper, we employ a systems biology approach to develop mathematical models of these networks that, for the first time, take into account the different biochemical properties of the isoforms involved. To investigate the mechanisms underlying the joint regulation of cAMP and cGMP, we apply our models to analyse the regulation of cilia beat frequency in Paramecium by Ca2+. Based on our analysis of these models, we propose that the diversity of isoform combinations that occurs in living cells provides an explanation for the huge variety of intracellular processes that are dependent on these networks. The inclusion of both G-protein receptor and Ca 2+-dependent regulation of AC in our models allows us to propose a new explanation for the switching properties of G-protein subunits involved in nucleotide regulation. Analysis of the models suggests that, depending on whether the G-protein subunit is bound to AC, Ca2+ can either activate or inhibit AC in a concentration-dependent manner. The resulting analysis provides an explanation for previous experimental results that showed that alterations in Ca2+ concentrations can either increase or decrease cilia beat frequency over particular Ca2+ concentration ranges. © The Royal Society of Chemistry

A systems model of phosphorylation for inflammatory signaling events

© 2014 Sadreev et al. Phosphorylation is a fundamental biochemical reaction that modulates protein activity in cells. While a single phosphorylation event is relatively easy to understand, multisite phosphorylation requires systems approaches for deeper elucidation of the underlying molecular mechanisms. In this paper we develop a mechanistic model for single- and multisite phosphorylation. The proposed model is compared with previously reported studies. We compare the predictions of our model with experiments published in the literature in the context of inflammatory signaling events in order to provide a mechanistic description of the multisite phosphorylation-mediated regulation of Signal Transducer and Activator of Transcription 3 (STAT3) and Interferon Regulatory Factor 5 (IRF-5) proteins. The presented model makes crucial predictions for transcription factor phosphorylation events in the immune system. The model proposes potential mechanisms for T cell phenotype switching and production of cytokines. This study also provides a generic framework for the better understanding of a large number of multisite phosphorylation-regulated biochemical circuits

A study of the temperature dependence of bienzyme systems and enzymatic chains

It is known that most enzyme-facilitated reactions are highly temperature dependent processes. In general, the temperature coefficient, Q10, of a simple reaction reaches 2.0-3.0. Nevertheless, some enzyme-controlled processes have much lower Q10 (about 1.0), which implies that the process is almost temperature independent, even if individual reactions involved in the process are themselves highly temperature dependent. In this work, we investigate a possible mechanism for this apparent temperature compensation: simple mathematical models are used to study how varying types of enzyme reactions are affected by temperature. We show that some bienzyme-controlled processes may be almost temperature independent if the modules involved in the reaction have similar temperature dependencies, even if individually, these modules are strongly temperature dependent. Further, we show that in non-reversible enzyme chains the stationary concentrations of metabolites are dependent only on the relationship between the temperature dependencies of the first and last modules, whilst in reversible reactions, there is a dependence on every module. Our findings suggest a mechanism by which the metabolic processes taking place within living organisms may be regulated, despite strong variation in temperature

The mechanism of state-public management of vocational education in the region

© 2016, Econjournals. All rights reserved.The relevance of the article is reasoned by the development of civil society and the positioning of vocational education as an open, state-public system. The purpose of the article is to develop a mechanism of state-public management of vocational education in the region. The leading method is the method of action research, allowing obtain new knowledge about state-public management of vocational education in the region and to organize the systematic monitoring of the changes in state-society relations in the management of vocational education. The article reveals the essence and defines the principles of state-public management of vocational education in the region; presents a mechanism of state-public management of vocational education in the region, providing a constructive dialogue between the entities of management process and the formation of a unified regional educational environment. Article submissions may be useful for research and teaching staff of the system of vocational education, specialists of education management bodies and regional authorities