- •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
Index
Page numbers in italic refer to figures; page numbers in boldface signify entries in tables.
activated complex theory, 8 activity coefficients, 8 AND gate, 37, 43 Arrhenius equation, 7–8 autocatalysis, 125 autocatalytic species, 132 autocorrelation function, 25
Belousov–Zhabotinsky (BZ) reaction, 125–127
bifurcation analysis, 129–131, 129, 130 bifurcation diagrams, 115, 143–147, 145, 146 binary coding, 104–105
biochemical reaction network (BRN), 40 bioinformatics, 207–209
Bayesian networks, 215–220, 216, 217, 218, 219
Boolean networks, 211–213, 213 clustering, 208, 209
correlation metric construction for genetic networks, 213–215, 214, 215
linearization, 209–210, 210
modeling reaction mechanisms, 210–211,
212
other approaches, 220–221
bistable reaction systems and bistable electronic switches, 37–38
blue fluorescent protein (BFP), 23
capillary electrophoresis (CE), 13–15 capillary isoelectric focusing (CIEF), 14 capillary zone electrophoresis (CZE), 14 catalyst, definition, 3
causal connectivity, definition, 3 cellular dynamics, 12
chemical neurons, 34–37, 36 chlorite–iodide reaction, 129–131, 129, 130,
160
bifurcation diagrams, 163–164, 163 concentration shift destabilization,
161–162, 162, 162
concentration shift regulation, 161, 161 model, 164–165, 165
phase shift of oscillations, 164 qualitative pulsed species response,
160–161, 161 classical identification, 4–6
complex systems, deducing reaction mechanisms, 2
223
224 INDEX
computations by macroscopic kinetic systems, 34
chemical neurons and logic gates, 34–37, 36 computational functions, 40–44, 41 implementation of computers, 37–40,
38, 39 concentration
correlation function method, 2 relative change, 47
stationary state, 47
continuous-flow stirred tank reactor (CSTR), 37–39, 38, 39, 59
control, definition, 3 controllability, 5 Coomassie Blue stain, 21
correlation metric construction (CMC) experimental test, 87–96, 88, 90
matrix summary of distance matrix, 92 MDS diagram, 93
time-lagged correlation function, 91 genetic networks, 213–215, 214, 215 theory of statistical construction of reaction
mechanisms, 65–85, 68, 72, 77, 78, 81
cross-correlation function, 25 cross-shaped diagram, 131, 144 cyan fluorescent protein (CFP), 23 cycle species, 132
cyclic pathways, 135–136 cyclin-dependent kinase (CDK), 212
density estimation
entropy metric construction (EMC), 97–102, 100, 101
deterministic kinetics, 7–8 disappearance processes, 193 disordered kinetics, 9
DNA microarrays, 18–20, 19 Drazer–Zanette experiment, 176–180, 181
Easterby’s equation, 187 electro-osmotic flow (EOF), 13–14 electrospray ionization (ESI), 16 elementary reaction, definition, 3 entropy, 98
entropy metric construction (EMC), 97–102,
100, 101
entropy reduction method (ERM), 102 enzyme binding and rate coefficients (EBR),
114–115 exit species, 132
feedback mechanisms, 125 feedback species, 133 fluctuations, 9
fluorescence localization after photobleaching (FLAP), 24
fluorescence loss in photobleaching (FLIP), 24 fluorescence recovery after photobleaching
(FRAP), 24 fluorescent dyes, 21 fluorescent imaging, 23
fluorescence correlation spectroscopy (FCS), 25–26, 25
fluorescence resonance energy transfer (FRET), 26–27
fluorescence speckle microscopy (FSM), 24 future trends, 27
photobleaching and photoactivation, 23–24 total internal reflection fluorescence
microscopy (TIRFM), 25
Fourier Transform Ion Cyclotron Resonance (FT-ICR) MS, 17
fructose 6-phosphate/fructose 1,6-biphosphate cycle, 40–43, 42
gas chromatography-mass spectrometry (GC-MS), 13
genetic algorithm method, 2
genetic algorithms (GAs), 104–105, 122 basic techniques
crossover, 105 elitism, 105 mutation, 105
roulette wheel selection, 105 termination, 106
evolutionary development of biochemical oscillatory reaction mechanisms, 112–118, 117, 118
enzyme binding constants, 114
flux regulation selection, 106–112, 106 limiting network diagrams, 111 noncompetitive binding, 107
systematic determination of reaction mechanism and rate coefficients, 119–122
genome, 207 gluconeogenesis, 43 glycolysis, 4, 42–43, 113
experimental test of correlation metric construction (CMC), 87–96, 88, 90
matrix summary of distance matrix, 92 MDS diagram, 93
time-lagged correlation function, 91
experimental test of pulse perturbation method, 58–64, 59, 60, 61, 63
pathway, 53–56, 54, 55, 56 green fluorescent protein (GFP), 23 Green functions, 185, 193
high-performance anion-exchange chromatography (HPAEC), 12, 13
high-pressure liquid chromatography (HPLC), 12–13
proteome analysis, 21
Hopf bifurcation, 129, 130, 131, 143 horseshoe effect, 83 hydrophilic-interaction chromatography
(HILIC), 13
input negative feedback, 137 inverse self-regulation, 142
iodate–arsenous acid reaction, 37, 38, 39 ion trap mass analysers, 17
ionic strength, 8 isobaric tags, 22
isotope-coded affinity tags (ICAT), 22
Jacobian matrix elements (JMEs), 128–129
Kalman filtering, 5 kinetic processes
disordered kinetics, 9 fluctuations, 9
macroscopic, deterministic kinetics, 7–8
Langmuir adsorption isotherms, 176
lifetime distributions of species, 171–173, 205 response experiments, 173–182
errors, 192–197, 194, 195 LISREL, 5
logic gates, 34–37, 36, 40–43, 42
marked species, 198 mass action law, 46
mass action rate expressions, 7 mass spectrometry (MS)
principles and applications, 15–16 detectors, 17–18
HPLC detectors, 13 mass analyzers, 16–17
mass-to-charge ratio (m/z) of ions, 16 matrix-assisted laser desorption/ionization
(MALDI), 16 metabolome, 12 methodologies, 11, 27
INDEX 225
fluorescent imaging, 23–27 genome-wide analyses of mRNA and
proteins, 18
DNA microarrays, 18–20, 19 proteome analysis, 20–23, 22 mass spectrometry (MS), 15–16
detectors, 17–18
mass analyzers, 16–17
metabolite concentration measurements, 11–12
capillary electrophoresis (CE), 13–15, 15 high-pressure liquid chromatography
(HPLC), 12–13 metric, requirements, 98
micellar electrokinetic capillary chromatography (MECC), 14
molality, 8 mRNA, 207
linearization, 209–210, 210 multidimensional scaling (MDS), 73–82, 75,
76, 78, 81 glycolysis, 93
multivariate systems, 5–6
NAND gate, 66, 78
network performance evaluation, 109–110 neural networks, 40
NFT mechanism, 119–120 nonlinear systems, 5 NOR gate, 42
normal self-regulation, 142 normalized correlation functions, 67 Nyquist critical frequency, 6
observability, 5 OR gate, 43
oscillatory reactions, 2, 125–127 concepts and theoretical constructs,
127–128
bifurcation analysis, 129–131, 129, 130 categorization of oscillatory reaction,
136–137
Jacobian matrix elements (JMEs), 128–129
role of species, 131–133
stoichiometric network analysis (SNA), 133–136, 134, 136
deduction of mechanism examples, 151 chlorite–iodide reaction, 160–165 peroxidase–oxidase (PO) reaction,
151–160, 152
226 INDEX
oscillatory reactions (continued) experiments providing mechanism
information, 138 amplitude relations, 138, 140
bifurcation diagrams, 143–147, 145, 146 characterization of species, 138, 139 concentration shift destabilization, 143 concentration shift regulation, 141–142 delay experiments, 148
external periodic perturbation, 150 other methods, 151
phase relations, 139–141
phase response experiments, 149–150 pulsed species response, 147–148, 147 quenching, 148–149
stabilization of unstable steady state, 150 limits of stoichiometric network analysis,
166
output negative feedback, 137
ozone, formation and decomposition by light in upper atmosphere, 2
pair correlation function, 97 pair probability distribution, 99 parallel computing, 40
pattern recognition, 39 pentose cycle, 4
peroxidase–oxidase (PO) reaction, 151–152, 156–157, 157
concentration shift destabilization, 154–155, 155
concentration shift regulation, 153–154,
154, 154
model, 157–160, 158, 159
phase shifts of oscillations, 152, 153 qualitative pulsed species response, 155,
155
quench experiments, 156, 156
relative amplitudes of oscillations, 152, 153 phase response curve (PRC), 149
phase transition curve (PTC), 149 phenotype, 11 phosphorylation/dephosphorylation cycle, 41 photoactivation, 23–24
photobleaching, 23–24 Polanyi relations, 177
polyacrylamide gel electrophoresis, 21 primary salt effect, 8
proteome analysis, 20–23, 22 pulse method, 2
pulse perturbations
experimental test, 58–64, 59, 60, 61, 63 glycolytic pathway, 53–56, 54, 55, 56 theory, 46–53, 47, 48, 50, 51, 52
quadrupole mass analyzers, 16 quenching, 148–149
rate coefficients, 8 reachability, 5
reaction–diffusion systems, 197–204 reaction mechanisms, definition, 3 reaction pathway, definition, 3 reactions, 1
recovery species, 133
red fluorescent protein (RFP), 23 relative change in concentration, 47 replication processes, 193 reverse-phase (RP) HPLC, 13 RNA, 207. See also mRNA
saddle-node bifurcations, 130 selected ion monitoring (SIM), 16 SEPATH, 5
sign-symbolic shift matrix, 139, 140, 141, 142 silver staining, 21
single nucleotide polymorphisms (SNP), 18 stationary state concentrations, 47 statistical construction of reaction
mechanisms, 65–85, 68, 72, 77, 78, 81 stochastic elements in reactions, 5 stoichiometric equations, 1
stoichiometric network analysis (SNA), 131, 133–136, 134, 136
limits, 166
susceptibility functions, 185
time-lagged correlation function, 67, 69, 70, 73
glycolysis, 91
time-of-flight (TOF) mass analyzers, 16–17 total internal reflection fluorescence
microscopy (TIRFM), 25 tracers, 170
transformation processes, 193 transit time distributions, 182–188
extracting kinetic information from experimental data, 188–192
Turing machines, 40
yellow fluorescent protein (YFP), 23
Zeldovich–Roginskii model, 178