Open AccessBook
The Regulation of Cellular Systems
TLDR
The basic equations of metabolic control analysis are rewritten in terms of co-response coefficients and internal response coefficients to describe the interaction of optimization methods and the interrelation with evolution.Abstract:
Introduction Fundamentals of biochemical modeling Balance equations Rate laws Generalized mass-action kinetics Various enzyme kinetic rate laws Thermodynamic flow-force relationships Power-law approximation Steady states of biochemical networks General considerations Stable and unstable steady states Multiple steady states Metabolic oscillations Background Mathematical conditions for oscillations Glycolytic oscillations Models of intracellular calcium oscillations A simple three-variable model with only monomolecular and bimolecular reactions Possible physiological significance of oscillations Stoichiometric analysis Conservation relations Linear dependencies between the rows of the stoichiometry matrix Non-negative flux vectors Elementary flux modes Thermodynamic aspects A generalized Wegscheider condition Strictly detailed balanced subnetworks Onsager's reciprocity reactions for coupled enyme reactions Time hierarchy in metabolism Time constants The quasi-steady-state approximation The Rapid equilibrium approximation Modal analysis Metabolic control analysis Basic definitions A systematic approach Theorems of metabolic control analysis Summation theorems Connectivity theorems Calculation of control coefficients using the theorems Geometrical interpretation Control analysis of various systems General remarks Elasticity coefficients for specific rate laws Control coefficients for simple hypothetical pathways Unbranched chains A branched system Control of erythrocyte energy metabolism The reaction system Basic model Interplay of ATP production and ATP consumption Glycolytic energy metabolism and osmotic states A simple model of oxidative phosphorylation A three-step model of serine biosynthesis Time-dependent control coefficients Are control coefficients always parameter independent? Posing the problem A system without conserved moieties A system with a conserved moiety A system including dynamic channeling Normalized versus non-normalized coefficients Analysis in terms of variables other than steady-state concentrations and fluxes General analysis Concentration ratios and free-energy-differences as state variables Entropy production as response variable Control of transient times Control of oscillations A second-order approach A quantitative approach to metabolic regulations Co-response coefficients Fluctuations of internal variables versus parameter perturbations Internal response coefficients Rephrasing the basic equations of metabolic control analysis in terms of co-response coefficients and internal response coefficients Control within and between subsystems Modular approach Overall elasticities Overall control coefficients Flux control insusceptibility Control exerted by elementary steps in enzyme catalysis Control analysis of metabolic channeling Comparison of metabolic control analysis and power-law formalism Computational aspects Application of optimization methods and the interrelation with evolution Optimization of the catalytic properties of single enzymes Basic assumptions Optimal values of elementary rate constants Optimal Michaelis constants Optimization of multienzyme systems Maximization of steady-state flux Influence of osmotic constraints and minimization of intermediate concentrations Minimization of transient times Optimal stoichiometries.read more
Citations
More filters
Journal ArticleDOI
The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)
TL;DR: In this paper, the authors describe the rules of the ring, the ring population, and the need to get off the ring in order to measure the movement of a cyclic clock.
Journal ArticleDOI
Modeling and simulation of genetic regulatory systems: a literature review.
TL;DR: This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equation, stochastic equations, and so on.
Journal ArticleDOI
COPASI---a COmplex PAthway SImulator
Stefan Hoops,Sven Sahle,Ralph Gauges,Christine Lee,Jürgen Pahle,Natalia Simus,Mudita Singhal,Liang Xu,Pedro Mendes,Ursula Kummer +9 more
TL;DR: COPASI is presented, a platform-independent and user-friendly biochemical simulator that offers several unique features, and numerical issues with these features are discussed; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in Stochastic simulation.
Journal ArticleDOI
Complete nitrification by Nitrospira bacteria
Holger Daims,Elena V. Lebedeva,Petra Pjevac,Ping Han,Craig W. Herbold,Mads Albertsen,Nico Jehmlich,Márton Palatinszky,Julia Vierheilig,A. G. Bulaev,Rasmus Hansen Kirkegaard,Martin von Bergen,Thomas Rattei,Bernd Bendinger,Per Halkjær Nielsen,Michael Wagner +15 more
TL;DR: The discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers, and the genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation.
Journal ArticleDOI
Analysis of optimality in natural and perturbed metabolic networks
TL;DR: The method of minimization of metabolic adjustment (MOMA), whereby the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type is tested, is tested and found to be useful in understanding the evolutionary optimization of metabolism.
References
More filters
Journal ArticleDOI
Is metabolic channelling the complicated solution to the easy problem of reducing transient times
Journal ArticleDOI
Characteristic reaction paths of biochemical reaction systems with time scale separation.
James C. Liao,Edwin N. Lightfoot +1 more
TL;DR: General theorems are developed predicting the existence of characteristic reaction paths as asymptotic limits whenever there is effective time scale separation, and available evidence suggests that these conditions will occur for the majority of reaction networks.
Journal ArticleDOI
Extending the quasi-steady state concept to analysis of metabolic networks
James C. Liao,Edwin N. Lightfoot +1 more
TL;DR: The approach suggested appears to provide an effective means for describing system dynamics and determining the behavior of an individual enzyme in an intact system by making a first-order allowance for interaction with the system as a whole.
Journal ArticleDOI
Substrate channeling among glycolytic enzymes: fact or fiction.
H. Gutfreund,P.B. Chock +1 more
Journal ArticleDOI
An attempt to generalize the control coefficient concept
TL;DR: In this article, the authors extended the notion of control strength inside a metabolic pathway to the case of a periodic flux and simulated a subsystem of the glycolysis where a periodic behaviour exists and calculated the control strength on the period and on the amplitude of the ATP concentration.