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E-raamat: Kinetic Modelling in Systems Biology

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(Moscow State University, Moscow, Russia), (University of Edinburgh, Scotland, UK)
  • Formaat: 360 pages
  • Ilmumisaeg: 24-Oct-2008
  • Kirjastus: Chapman & Hall/CRC
  • Keel: eng
  • ISBN-13: 9781420011661
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Kinetic Modelling in Systems BiologySuurem pilt
  • Formaat: 360 pages
  • Ilmumisaeg: 24-Oct-2008
  • Kirjastus: Chapman & Hall/CRC
  • Keel: eng
  • ISBN-13: 9781420011661
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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.





Downloadable Resources FeaturesExtensively used throughout the text for pathway visualization and illustration, the EPE software is available on the accompanying downloadable resources. The downloadable resources also include 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.

Arvustused

This book will help the reader to understand the kinetic modeling approach, apply it to solve real-life problems, and give the opportunity to think about future challenges. It also illustrates how to apply the principles of kinetic modeling to perform various functions. ISCB News #49, June 2010

About the Authors, xvii
Introduction, xix
CHAPTER 1 Systems Biology, Biological Knowledge and Kinetic Modelling 1
DEPENDENCE OF ENZYME REACTION RATE ON THE SUBSTRATE CONCENTRATION
3
WHAT ARE THE MODEL LIMITATIONS? OR, IN OTHER WORDS, WHAT CAN BE MODELLED?
8
CHAPTER 2 Cellular Networks Reconstruction and Static Modelling 13
PATHWAY RECONSTRUCTION
13
THE HIGH-QUALITY NETWORK RECONSTRUCTION: DESCRIPTION OF THE PROCESS
14
VISUAL NOTATIONS: THREE CATEGORIES
17
Communication between Diagrams
22
Tools and Methods for Static Modelling
24
Databases, Ontology and Standards for Pathway Reconstruction
25
SBML
27
SBGN: A Visual Notation for Network Diagrams
28
CHAPTER 3 Edinburgh Pathway Editor 29
INTRODUCTION
30
FEATURE SUMMARY OF EPE
31
A FLEXIBLE VISUAL REPRESENTATION
35
CONCLUSION
47
CHAPTER 4 Construction and Verification of Kinetic Models 49
INTRODUCTION
49
BASIC PRINCIPLES OF KINETIC MODEL CONSTRUCTION
50
Development of a System of Ordinary Differential Equations Describing the Dynamics of a Metabolic System
51
Derivation of Rate Law of Enzymatic Reactions
58
BASIC PRINCIPLES OF KINETIC MODEL VERIFICATION
60
Verification of Kinetic Model Using in Vitro Experimental Data Measured for Purified Enzymes
60
Verification of the Kinetic Model Using in Vitro and in Vivo Experimental Data Measured for a Biochemical System
61
STUDY OF DYNAMIC AND REGULATORY PROPERTIES OF THE KINETIC MODEL
63
CHAPTER 5 Introduction to DBSolve 65
CREATION AND ANALYSIS OF THE MODELS USING DBSOLVE. FUNCTIONAL DESCRIPTION
66
A General Look at the Interface
67
Description of the Example
67
The 'Metabolic Network' Tab: Creation of ODE System (Simple Method)
69
Creation of the ODE System Using RCT Format (The Alternative Method)
71
DBSolve Editors: RHS, Initial Values, Pools
72
RHS Editor
72
Initial Values
73
Pools
73
ODE Tab: Solving the ODE System. Model Integration or in Silico Experiments
73
Explicit Tabbed Page. Calculating Dependencies Determined Explicitly
77
The Implicit Solver Tabbed Page. The Study of the System in a Steady State
79
Experimental Data Tab: Creation of the Table with Experimental Data
81
The Fitter Tabbed Page: Automatic Parameter Fitting
84
Options Tab
86
Advanced User Tab
87
Example of Fitting
87
The 'Options' Tabbed Page
90
Some Examples from the CD
92
CHAPTER 6 Enzyme Kinetics Modelling 95
INTRODUCTION
95
BASIC PRINCIPLES OF MODELLING OF INDIVIDUAL ENZYMES AND TRANSPORTERS
96
Methods to Derive Rate Equation on the Basis of Enzyme Catalytic Cycle
97
Quasi-Equilibrium Approach
98
Quasi-Steady-State Approach
100
Combined Quasi-Equilibrium, Quasi-Steady-State Approach
102
How to Express Parameters of the Catalytic Cycle in Terms of Kinetic Parameters
107
Examples of Rate Equations Expressed in Terms of Kinetic Parameters
109
Random Bi Bi Mechanism
109
Ordered Uni Bi Mechanism
110
Ping Pong Bi Bi Mechanism
111
'HYPERBOLIC' ENZYMES
113
Kinetic Model of Histidinol Dehydrogenase from Escherichia coli
113
Available Experimental Data
113
Construction of the Catalytic Cycle
114
Derivation of Rate Equations
118
Estimation of Kinetic Parameters of the Rate Equations Using in Vitro Experimental Data
121
Kinetic Model of Escherichia coli Isocitrate Dehydrogenase and Its Regulation by Isocitrate Dehydrogenase Kinase/Phosphatase
124
Available Experimental Data
126
Kinetic Model of Isocitrate Dehydrogenase
126
Kinetic Model of IDH Kinase/Phosphatase
128
Model Predictions
136
Kinetic Model of β-Galactosidase from Escherichia coli Cells
139
Catalytic Cycle of β-Galactosidase Construction
139
Derivation of the Rate Equation of β;-Galactosidase
141
Identification of the Parameters of the β-Galactosidase Rate Equation
147
Model Predictions
147
Kinetic Model of Imidazologlycerol-Phosphate Synthetase from Escherichia coli
150
Experimental Data
150
Catalytic Cycle
153
Derivation of the Rate Equations
153
Evaluation of Parameters of the Rate Equations
158
Application of the Model to Predict How the Synthetase and Glutaminase Activities of Imidazologlycerol-Phosphate Synthetase Depend on Concentrations of the Substrates and Effectors
166
ALLOSTERIC ENZYMES
168
Principles Used for Description of the Functioning of Allosteric Enzymes
168
Kinetic Model of Phosphofructokinase-1 from Escherichia coli
170
Available Experimental Data
172
Reconstruction of a Catalytic Cycle of Phosphofructokinase-1
173
Derivation of a Rate Equation
175
Verification of the Model against Experimental Data
178
Predictions of the Model
180
TRANSPORTERS
187
Kinetic Model of Mitochondrial Adenine Nucleotide Translocase
187
Experimental Data for Model Verification
188
Antiporter Functioning Mechanism
188
Kinetic Scheme
189
Derivation of Rate Equation
190
Dependence of Kinetic Constants on Membrane Potential
194
Estimation of Parameters
198
Model Verification
200
Model Predictions
202
CHAPTER 7 Kinetic Models of Biochemical Pathways 207
MODELLING OF THE MITOCHONDRIAL KREBS CYCLE
208
Model Development
208
Description of Individual Enzymes of the Krebs Cycle
210
α-Ketoglutarate Dehydrogenase
212
Aspartate-Glutamate Carrier (AGC)
214
Aspartate Aminotransferase (AspAT)
219
Succinate Thiokinase (STK)
221
Succinate Dehydrogenase
225
Fumarase (FUM)
227
Malate Dehydrogenase (MDH)
228
α–Ketoglutarate-Malate Carrier (KMC)
229
Estimation of Model Parameters from in Vivo Data
231
MODELING OF THE ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID BIOSYNTHESIS
233
Model Development
233
Derivation of the Rate Equations
235
Detailed Description of Pathway Steps
237
Influxes
237
Threonine Dehydratase (TDH)
239
Acetolactate Synthase (AHAS)
239
Acetohydroxy Acid Isomeroreductase (IR)
241
Dihydroxy-Acid Dehydratase (DHAD)
243
Branched-Chain Amino Acid Transaminase (BCAT)
245
NADP Recycling and Effluxes
246
Evaluation of Maximal Reaction Rates
246
CHAPTER 8 Modelling of Mitochondrial Energy Metabolism 249
OXIDATIVE PHOSPHORYLATION AND SUPEROXIDE PRODUCTION IN MITOCHONDRIA
249
DEVELOPMENT OF KINETIC MODELS
251
DESCRIPTION OF INDIVIDUAL PROCESSES OF THE MODEL
262
MODEL PREDICTIONS
269
CHAPTER 9 Application of the Kinetic Modelling Approach to Problems in Biotechnology and Biomedicine 277
STUDY OF THE MECHANISMS OF SALICYLATE HEPATOTOXIC EFFECT
277
Kinetic Description of the Influence of Salicylates on the Krebs Cycle
278
Impacts of Different Mechanisms of Salicylate Inhibition on the Total Adverse Effect on the Krebs Cycle
283
Prediction of Possible Ways to Recover Krebs Cycle Functionality
285
MULTIPLE TARGET IDENTIFICATION ANALYSIS FOR ANTI-TUBERCULOSIS DRUG DISCOVERY
287
Construction of a Kinetic Model of the Glyoxylate Shunt in Mycobacterium tuberculosis
288
Application of the Model to Identify Potential Targets for Therapeutic Drug Intervention
292
APPLICATION OF THE KINETIC MODEL OF ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID BIOSYNTHESIS TO OPTIMISE PRODUCTION OF ISOLEUCINE AND VALINE
293
Prediction of Possible Genetic Changes That Should Maximise Isoleucine and Valine Production
294
Conclusion and Discussion 299
REFERENCES 303
INDEX 323
Demin, Oleg; Goryanin, Igor
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