With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging field.
The book introduces the basic biological cellular network concepts in the context of cellular functioning, explains the main aspects of the Edinburgh Pathway Editor (EPE) software package, and discusses the process of constructing and verifying kinetic models. It presents the features, user interface, and examples of DBSolve as well as the principles of modeling individual enzymes and transporters. The authors describe how to construct kinetic models of intracellular systems on the basis of models of individual enzymes. They also illustrate how to apply the principles of kinetic modeling to collect all available information on the energy metabolism of whole organelles, construct a kinetic model, and predict the response of the organelle to changes in external conditions. The final chapter focuses on applications of kinetic modeling in biotechnology and biomedicine.
Encouraging readers to think about future challenges, this book will help them understand the kinetic modeling approach and how to apply it to solve real-life problems.
Extensively used throughout the text for pathway visualization and illustration, the EPE software is available on the accompanying CD-ROM. The CD also includes pathway diagrams in several graphical formats, DBSolve installation with examples, and all models from the book with dynamic visualization of simulation results, allowing readers to perform in silico simulations and use the models as templates for further applications.
Moscow State University, Moscow, Russia University of Edinburgh, Scotland, UK
Introduction Systems Biology, Biological Knowledge, and Kinetic Modelling Dependence of enzyme reaction rate on the substrate concentration What are the model limitations? Or, in other words, what can be modeled? Cellular Networks Reconstruction and Static Modelling Pathway reconstruction The high-quality network reconstruction: description of the process Visual notations: three categories Edinburgh Pathway Editor (EPE) Introduction Feature summary of EPE A flexible visual representation Conclusion Construction and Verification of Kinetic Models Introduction Basic principles of kinetic model construction Basic principles of kinetic model verification Study of dynamic and regulatory properties of the kinetic model Introduction to DBSolve Creation and analysis of the models using DBSolve: functional description Enzyme Kinetics Modelling Introduction Basic principles of modeling individual enzymes and transporters "Hyperbolic" enzymes Allosteric enzymes Transporters Kinetic Models of Biochemical Pathways Modelling of the mitochondrial Krebs cycle Modelling of the Escherichia coli branched-chain amino acid biosynthesis Modelling of Mitochondrial Energy Metabolism Oxidative phosphorylation and superoxide production in mitochondria Development of kinetic models Description of individual processes of the model Model predictions Application of the Kinetic Modelling Approach to Problems in Biotechnology and Biomedicine Study of the mechanisms of salicylate-hepatotoxic effect Multiple target identification analysis for antituberculosis drug discovery Application of the kinetic model of E. coli branched-chain amino acid biosynthesis to optimize production of isoleucine and valine Conclusion and Discussion References Index