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
Metabolic network structure determines key aspects of functionality and regulation
TL;DR: A theoretical method for simultaneously predicting key aspects of network functionality, robustness and gene regulation from network structure alone is devised by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes).
Journal ArticleDOI
Optimality and evolutionary tuning of the expression level of a protein
Erez Dekel,Uri Alon +1 more
TL;DR: Protein expression from the lac operon seems to be a solution of a cost–benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments.
Journal ArticleDOI
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions
TL;DR: This review focuses on the interaction of plants and root associated bacteria enhancing plant mineral nutrition, summarizing the current knowledge in several research fields that can converge to improve the understanding of the molecular mechanisms underpinning this phenomenon.
Journal ArticleDOI
Statistical strategies for avoiding false discoveries in metabolomics and related experiments
David Broadhurst,Douglas B. Kell +1 more
TL;DR: A list of some of the simpler checks that might improve one’s confidence that a candidate biomarker is not simply a statistical artefact is provided, and a series of preferred tests and visualisation tools that can assist readers and authors in assessing papers are suggested.
Journal ArticleDOI
Gene regulatory network inference: Data integration in dynamic models—A review
TL;DR: This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods and approaches are discussed that enable the modelling of the dynamics of Gene regulatory systems.
References
More filters
Journal ArticleDOI
Reaction-rate theory: fifty years after Kramers
TL;DR: In this paper, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry.
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
Comparison of experimental binding data and theoretical models in proteins containing subunits.
Journal ArticleDOI
Potential, impedance, and rectification in membranes
TL;DR: A theoretical picture has been presented based on the use of the general kinetic equations for ion motion under the influence of diffusion and electrical forces and on a consideration of possible membrane structures that shows qualitative agreement with the rectification properties and very good agreementwith the membrane potential data.
Book
Linear Multivariable Control: A Geometric Approach
TL;DR: In this article, the authors present an approach to controlability, feedback assignment, and pole shifting in a single linear functional model, where the observer is assumed to be a dynamic observer.