- •Copyright © 2006 by Oxford University Press, Inc.
- •Contents
- •1 Introduction
- •References
- •2.1 Macroscopic, Deterministic Chemical Kinetics
- •2.2 Disordered Kinetics
- •2.3 Fluctuations
- •References
- •3 A Brief Review of Methodology for the Analysis of Biochemical Reactions and Cells
- •3.1 Introduction
- •3.2 Measurement of Metabolite Concentrations
- •3.3 Principles and Applications of Mass Spectrometry
- •3.5 Fluorescent Imaging
- •3.6 Conclusions
- •References
- •4.1 Chemical Neurons and Logic Gates
- •4.2 Implementation of Computers by Macroscopic Chemical Kinetics
- •4.3 Computational Functions in Biochemical Reaction Systems
- •References
- •5.1 Theory
- •5.2 An Example: The Glycolytic Pathway
- •References
- •6 Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network
- •Reference
- •Discussion
- •References
- •References
- •9 Density Estimation
- •9.1 Entropy Metric Construction (EMC)
- •9.2 Entropy Reduction Method (ERM)
- •References
- •10 Applications of Genetic Algorithms to the Determination of Reaction Mechanisms
- •10.1 A Short Primer on Genetic Algorithms
- •10.2 Selection of Regulation of Flux in a Metabolic Model
- •10.3 Evolutionary Development of Biochemical Oscillatory Reaction Mechanisms
- •10.5 Summary
- •References
- •11 Oscillatory Reactions
- •11.1 Introduction
- •11.2 Concepts and Theoretical Constructs
- •11.3 Experiments Leading to Information about the Oscillatory Reaction Mechanism
- •11.4 Examples of Deduction of Reaction Mechanism from Experiments
- •11.5 Limits of Stoichiometric Network Analysis
- •References
- •12.1 Lifetime Distributions of Chemical Species
- •12.2 Response Experiments and Lifetime Distributions
- •12.3 Transit Time Distributions in Complex Chemical Systems
- •12.4 Transit Time Distributions, Linear Response, and Extracting Kinetic Information from Experimental Data
- •12.5 Errors in Response Experiments
- •12.7 Conclusions
- •References
- •13.1 Clustering
- •13.2 Linearization in Various Forms
- •13.3 Modeling of Reaction Mechanisms
- •13.4 Boolean Networks
- •13.5 Correlation Metric Construction for Genetic Networks
- •13.6 Bayesian Networks
- •13.7 Some Other Illustrative Approaches
- •References
- •Index
96 DETERMINATION OF COMPLEX REACTION MECHANISMS
time-resolved measurements of chemical and biochemical concentrations such as CZE and parallel gene expression monitoring from DNA chips.
For an application of this method to a genome study, see section 13.5. Other applications of our correlation function method to a part of glycolysis are given in [12] and [13].
Acknowledgment This chapter is based in part on the article “A test case of correlation metric construction of a reaction pathway from measurements” by Adam Arkin, Peidong Shen, and John Ross [1], with some changes in wording.
References
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[2]Stryer, L. Biochemistry, 3rd ed.; Freeman: New York, 1988.
[3]Arkin, A.; Ross, J. Computational functions in biochemical reaction networks. Biophys. J. 1994, 67, 560–578.
[4]Hocker, C. G.; Epstein, I. R.; Kustin, K.; Tornheim, K. Glycolytic pH oscillations in a flow reactor. Biophys. Chem. 1994, 51, 21–35.
[5]Oefner, P. J. Surface-charge reversed capillary zone electrophoresis of inorganic and organic anions. Electrophoresis 1995, 16, 46–56.
[6]Shen, P.; Hauri, D.; Ross, J.; Oefner, P. J. Analysis of glycolysis metabolites by capillary zone electrophoresis with indirect UV detection. J. Capillary Electrophor. 1996, 3, 155–163.
[7]Card, D. A.; Folmer, D. E.; Sato, S.; Buzza, S. A.; Castleman, A. W., Jr. Covariance mapping of ammonia clusters: evidence of the connectiveness of clusters with coulombic explosion. J. Phys. Chem. 1997, 101, 3417–3423.
[8]Kemp, R. G. Rabbit liver phosphofructokinase: comparison of some properties with those of muscle phosphofructokinase. J. Biol. Chem. 1971, 246, 245–252.
[9]Colombo, G. P.; Tate, W.; Girotti, A. W.; Kemp, R. G. Interaction of inhibitors with muscle phosphofructokinase. J. Biol. Chem. 1975, 250, 9404–9412.
[10]Schaftingen, E. V.; Jett, M. F.; Hue, L. H.; Hers, G. Control of liver 6-phosphofructokinase by fructose 2,6-bisphosphate and other effectors. Proc. Natl. Acad. Sci. USA 1981, 78, 3483–3486.
[11]Uyeda, K.; Furuya, E.; Luby, L. J. The effect of natural and synthetic D-fructose 2,6- bisphosphate on the regulatory kinetic properties of liver and muscle phosphofructokinases.
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[12]Steuer, R.; Kurths, J.; Fiehn, O.; Weckwerth, W. Observing and interpreting correlations in metabolic networks. Bioinformatics 2003, 19, 1019–1026.
[13]Kaufmann, K. J.; Pajerowski, J. D.; Jamshidi, N.; Paulson, B. O.; Edwards, J. S. Description and analysis of metabolic connectivity and dynamics in the human blood cell. Biophys. J. 2002, 83, 646–662.