Metabolic Networks: a Signal-Oriented Approach to Cellular Models
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Joseph W. Lengeler
Abstract
Complete genomes, far advanced proteomes, and even ‘metabolomes’ are available for at least a few organisms, e. g., Escherichia coli. Systematic functional analyses of such complete data sets will produce a wealth of information and promise an understanding of the dynamics of complex biological networks and perhaps even of entire living organisms. Such complete and holistic descriptions of biological systems, however, will increasingly require a quantitative analysis and the help of mathematical models for simulating whole systems. In particular, new procedures are required that allow a meaningful reduction of the information derived from complex systems that will consequently be used in the modeling process. In this review the biological elements of such a modeling procedure will be described. In a first step, complex living systems must be structured into well-defined and clearly delimited functional units, the elements of which have a common physiological goal, belong to a single genetic unit, and respond to the signals of a signal transduction system that senses changes in physiological states of the organism. These functional units occur at each level of complexity and more complex units originate by grouping several lower level elements into a single, more complex unit. To each complexity level corresponds a global regulator that is epistatic over lower level regulators. After its structuring into modules (functional units), a biological system is converted in a second step into mathematical sub-models that by progressive combination can also be assembled into more aggregated model structures. Such a simplification of a cell (an organism) reduces its complexity to a level amenable to present modeling capacities. The universal biochemistry, however, promises a set of rules valid for modeling biological systems, from unicellular microorganisms and cells, to multicellular organisms and to populations.
Copyright © 2000 by Walter de Gruyter GmbH & Co. KG
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- The Mitochondrial Protein Import Motor
- The Immunoglobulin κ Gene Families of Human and Mouse: a Cottage Industry Approach
- Protein-Protein Interactions in Receptor Activation and Intracellular Signalling
- Molecular Genetic Analysis of Glucocorticoid Signaling Using the Cre/loxP System
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- Thyroid Hormone Receptors Bind to an Element in the Connexin43 Promoter
- Analysis of the Deubiquitinating Enzymes of the Yeast Saccharomyces cerevisiae
- Helical Tubes of FtsZ from Methanococcus jannaschii
- Surface Topography of Microtubule Walls Decorated with Monomeric and Dimeric Kinesin Constructs
- Histone Deacetylase Activity Is Required for the Induction of the MyoD Muscle Cell Lineage in Xenopus
- The Effect of Heat Shock on 20S/26S Proteasomes
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Articles in the same Issue
- Alexander J. Varshavsky Felix Hoppe-Seyler Lecturer 2000
- The Ubiquitin System and the N-End Rule Pathway
- Paper of the Year 1999: Award to Igor Stagljar
- A Clockwork Organ
- The Transgeneticists Toolbox: Novel Methods for the Targeted Modification of Eukaryotic Genomes
- Interdependence of Filamentous Actin and Microtubules for Asymmetric Cell Division
- Genetic Analysis of Mammalian Cyclin-Dependent Kinases and Their Inhibitors
- Phosphorylcholine Substituents in Nematodes: Structures, Occurrence and Biological Implications
- Selenium in Biology: Facts and Medical Perspectives
- The Role of Se, Mo and Fe in the Structure and Function of Carbon Monoxide Dehydrogenase
- Molecular Basis for Interactions of the DnaK Chaperone with Substrates
- Protein Import: the Hitchhikers Guide into Chloroplasts
- Pathway Analysis and Metabolic Engineering in Corynebacterium glutamicum
- Metabolic Networks: a Signal-Oriented Approach to Cellular Models
- Representing and Analysing Molecular and Cellular Function Using the Computer
- Protein Aggregation and Pathogenesis of Huntingtons Disease: Mechanisms and Correlations
- The Mitochondrial Protein Import Motor
- The Immunoglobulin κ Gene Families of Human and Mouse: a Cottage Industry Approach
- Protein-Protein Interactions in Receptor Activation and Intracellular Signalling
- Molecular Genetic Analysis of Glucocorticoid Signaling Using the Cre/loxP System
- Macromolecular Intelligence in Microorganisms
- Thyroid Hormone Receptors Bind to an Element in the Connexin43 Promoter
- Analysis of the Deubiquitinating Enzymes of the Yeast Saccharomyces cerevisiae
- Helical Tubes of FtsZ from Methanococcus jannaschii
- Surface Topography of Microtubule Walls Decorated with Monomeric and Dimeric Kinesin Constructs
- Histone Deacetylase Activity Is Required for the Induction of the MyoD Muscle Cell Lineage in Xenopus
- The Effect of Heat Shock on 20S/26S Proteasomes
- Sec61p Is the Main Ribosome Receptor in the Endoplasmic Reticulum of Saccharomyces cerevisiae
