Contributors ................................................. xiii
List of Abbreviations ........................................ xvii
Preface ....................................................... xix
1. Redox Metabolism and Life .................................... 1
By Ruma Banerjee
1.1. Redox Biochemistry and the Evolution of Life ............ 1
1.2. Global Redox Cycles ..................................... 4
1.3. Major Bioenergetic Cycles ............................... 6
1.3.A. Photosynthesis ................................... 6
1.З.В. Aerobic Respiration .............................. 7
2. Antioxidant Molecules and Redox Cofactors ................... 11
Edited by Donald Becker
2.1. Glutathione ............................................ 11
By Joseph J. Barycki
2.1.A. Biological Functions ............................ 13
2.1.В. Biosynthesis .................................... 14
2.l.C. Degradation ..................................... 16
2.1.D. Other Thiol-Based Redox Buffers ................. 21
2.2. Ascorbate .............................................. 22
By Han Asard
2.2.A. Ascorbate Chemistry ............................. 22
2.2.B. Ascorbate Biosynthesis .......................... 23
2.2.C. Ascorbate Recycling ............................. 25
2.2.D. Ascorbate Transport ............................. 26
2.2.E. Importance of Ascorbate in Stress and Disease ... 26
2.3. Other Antioxidants ..................................... 27
By Julie M. Stone and Mark A. Wilson
2.3.A. Lipid-Soluble Antioxidants ...................... 28
2.3.В. Water-Soluble Antioxidants ...................... 31
2.3.С. Antioxidants and Human Health ................... 32
2.4. Redox Coenzymes ........................................ 35
By Ruma Banerjee and Donald F. Becker
2.4.A. Flavin .......................................... 39
2.4.B. NAD ............................................. 40
2.4.C. Quinones ........................................ 42
2.4.D. Pterins and Molybdopterins ...................... 46
2.4.E. Folic Acid ...................................... 46
3. Antioxidant Enzymes ......................................... 49
Edited by Vadim Gladyshev
3.1. ROS-Dependent Enzymes .................................. 50
By Irwin Fridovich and Leslie B. Poole
3.1.A. Catalase ........................................ 50
З.1.В. Superoxide Dismutase ............................ 55
З.1.С. Peroxiredoxins .................................. 59
3.1.D. Alkyl Hydroperoxide Reductases .................. 65
3.2. The Thioredoxin System ................................. 68
By Arne Holmgren
3.2.A. Thioredoxin ..................................... 68
3.2.B. Thioredoxin Reductase ........................... 71
3.3. The Glutathione System ................................. 74
By Marjorie F. Lou
3.3.A. Glutathione Reductase ........................... 75
3.3.B. Glutaredoxin (Thioltransferase) ................. 76
3.4. Repair Enzymes ......................................... 84
By Vadim N. Gladyshev, Sheila S. David, and By
Leslie B. Poole
3.4.A. Methionine Sulfoxide Reductases ................. 84
3.4.B. DNA Repair Enzymes .............................. 87
3.4.C. Sulfiredoxins ................................... 94
3.5. Detoxification Enzymes ................................. 97
By Robert L. Osborne, John H. Dawson, and Shelly
D. Copley
3.5.A. Cytochrome P450 Enzymes: Structure, Function,
and Mechanism ................................... 97
3.5.B. GSH Transferases ............................... 104
3.6. Oxidative Folding ..................................... 113
By Hiroshi Kadokura, Jon Beckwith, and Hiram F.
Gilbert
3.6.A. Disulfide Bond Formation in Bacteria ........... 113
3.6.B. Disulfide Bond Formation in Eukaryotes ......... 120
3.7. Other Antioxidant Enzymes ............................. 127
By Vadim N. Gladyshev and Stephen W. Ragsdale
3.7.A. Selenoproteins ................................. 127
3.7.B. Heme Oxygenase ................................. 131
4. Redox Regulation of Physiological Processes ................ 135
Edited by Martin Dickman
4.1. Reactive Oxygen, Nitrogen, and Thiol-Based Signal
Transduction .......................................... 136
By Ilsa I. Rovira and Toren Finkel
4.1.A. Nitric Oxide Signaling ......................... 136
4.1.B. Carbon Monoxide Signaling ...................... 141
4.1.C. Superoxide and Hydrogen Peroxide ............... 143
4.I.D. Other Novel Redox Molecules .................... 147
4.2. Role of Nitric Oxide Synthases in Redox Signaling ..... 148
By Bettie Sue Masters
4.2.A. Characterization of the Nitric Oxide
Synthases ...................................... 149
4.2.B. Regulation of Nitric Oxide Synthases by
Intrinsic Elements ............................. 150
4.2.C. Extrinsic Regulation of Nitric Oxide
Synthases ...................................... 152
4.2.D. Interactions of NO with Other Proteins and
Enzymes ........................................ 152
4.3. Redox Regulation of Genes ............................. 154
By Martin B. Dickman
4.3.A. MAP Kinase/Cell Cycle .......................... 154
4.3.B. Redox Control of Gene Expression ............... 155
4.3.C. Peptide Editing and Thiol-Mediated Redox
Regulation ..................................... 156
4.4. Redox Regulation of Apoptosis ......................... 158
By Martin B. Dickman
4.4.A. Apoptotic Pathways ............................. 158
4.4.B. Reactive Oxygen Species and Apoptosis .......... 159
4.5. Metal Homeostasis ..................................... 162
By Jaekwon Lee
4.5.A. Physiological Significance of Metal
Metabolism ..................................... 163
4.5.B. Metal Uptake from the Extracellular
Environment .................................... 164
4.5.C. Intracellular Metal Distribution by Target-
Specific Chaperones ............................ 165
4.5.D. Subcellular Membrane Metal Transporters ........ 167
4.5.E. Heme and Iron-Sulfur Cluster Synthesis ......... 168
4.5.F. Cellular Storage ............................... 168
4.5.G. Metal Export ................................... 168
4.5.H. Regulation of Metal Metabolism ................. 169
4.5.I. Genetic Disorders in Metal Metabolism .......... 171
4.5.J. Perturbation of Metal Homeostasis and
Degenerative Disorders ......................... 172
4.6. Redox Enzymology ...................................... 173
By Stephen W. Ragsdale
4.7. Circadian Clock and Heme Biosynthesis ................. 177
By Cheng Chi Lee
АЛЛ. Cyclic Expression of Heme Binding Proteins ............ 177
4.7.B. Circadian Clock Mechanism ...................... 178
4.7.C. PAS Is a Heme Binding Domain ................... 179
4.7.D. Expression of Npas2 Is Controlled by mPER2 ..... 180
4.7.E. NPAS2 Regulates Expression of Aminolevulinate
Synthase 1 ..................................... 180
5. Pathological Processes Related to Redox .................... 183
Edited by Ruma Banerjee
5.1. Protein Modification .................................. 184
By Earl R. Stadtman
5.1.A. Protein Oxidation and Aging .................... 184
5.1.B. Mechanisms of Protein Oxidation ................ 184
5.1.C. Peptide Bond Cleavage .......................... 187
5.I.D. Oxidation of Amino Acid Residue Side Chains .... 188
5.1.E. Beta Scission of Amino Acid Side Chains ........ 189
5.1.F. Generation of Protein Carbonyl Derivatives ..... 189
5.1.G. Formation of Protein Cross-Linked
Derivatives .................................... 193
5.1.H. Role of Protein Oxidation in Aging ............. 193
5.2. Oxidative Stress in the Eye: Age-Related Cataract
and Retinal Degeneration .............................. 194
By Marjorie F. Lou and John W. Crabb
5.2.A. Oxidative Stress and Cataract .................. 195
5.2.B. Oxidative Stress and Retinal Pathology ......... 199
5.3. Redox Mechanisms in Cardiovascular Disease: Chronic
Heart Failure ......................................... 204
By George J. Rozanski
5.3.A. Excitation-Contraction Coupling in Cardiac
Myocytes ....................................... 204
5.3.B. Role of Oxidative Stress in Chronic Heart
Failure ........................................ 206
5.3.C. Redox Modulation of Ca2+ Handling Proteins ..... 206
5.3.D. Hypertrophy and Cell Death ..................... 209
5.3.E. Extracellular Matrix Remodeling ................ 209
5.4. Role of Reactive Oxygen Species in Carcinogenesis ..... 212
By Suresh Veeramani and Ming-Fong Lin
5.4.A. ROS Act as Growth Signaling Messengers ......... 212
5.4.B. Phosphatases Are Prime Targets for ROS
During Growth Stimulation ...................... 212
5.4.C. Uncontrolled Production of ROS is
Carcinogenic ................................... 214
5.4.D. ROS Can Induce Carcinogenic DNA and Protein
Adducts ........................................ 215
5.4.E. ROS Can Affect DNA Methylation and Gene
Expression ..................................... 216
5.4.F. Mitochondrial DNA Mutations Are Induced by
ROS ............................................ 216
5.4.G. Clinical Trials on Antioxidant
Supplementation Against Cancer ................. 216
5.5. Oxidative Stress and the Host-Pathogen Interaction .... 218
By Greg A. Somerville
5.5.A. Neutrophils and the Innate Immune Response ..... 219
5.5.B. Bacterial Targets of Oxidative Damage .......... 220
5.5.С Regulating the Oxidative Stress Response ........ 221
5.5.D. The Oxidative Stress Response .................. 223
5.5.E. Evasion of the Innate Immune Response .......... 223
6. Specialized Methods ........................................ 227
Edited by Stephen Ragsdale
6.1. Mass Spectrometry Applications for Redox Biology ...... 228
By Ashraf Raza and John R. Engen
6.1 .A. Mass Spectrometer .................................. 228
6.1.В. Applications of Mass Spectrometry .............. 231
6.l.C. Hydrogen Exchange Mass Spectrometry ............ 236
6.2. Electron Paramagnetic Resonance (EPR) for the Redox
Biochemist ............................................ 237
By Stephen W. Ragsdale and Javier Seravalli
6.2.A. Introduction to Magnetic Resonance
Spectroscopy ................................... 237
6.2.B. Basic EPR Theory ............................... 239
6.2.С Appearance of the EPR Spectrum .................. 240
6.2.D. The EPR Experiment ............................. 240
6.2.E. The Conventional EPR Spectrometer: Detection
of the Signal .................................. 241
6.2.F. Sensitivity and Saturation in EPR .............. 244
6.2.G. Measuring the Concentration of Spins ........... 244
6.2.H. Nuclear Hyperfine and Spin-Spin Interactions ... 246
6.3. Redox Potentiometry ................................... 247
By Donald F. Becker
6.3.A. Midpoint Potential ............................. 247
6.3.B. Redox-Linked Processes ......................... 248
6.3.C. Potentiometric Technique ....................... 249
6.4. Bioinformatics Methods to Study Thiol-Based
Oxidoreductases ....................................... 251
By Dmitri E. Fomenko and Vadim N. Gladyshev
6.4.A. Identification of Redox-Active Cysteines in
Proteins ....................................... 251
6.4.B. Cysteine-Based Redox Motifs .................... 253
6.4.C. Conserved Cysteines in Metal-Binding
Proteins ....................................... 253
6.4.D. Secondary Structure Context of Redox-Active
Cysteines ...................................... 253
6.4.E. Structure Modeling ............................. 255
6.4.E. Comparative Sequence Analysis of Thiol-Based
Oxidoreductases ................................ 255
6.5. Electrophysiology ..................................... 256
By Mark P. Thomas and Harold D. Schultz
6.5.A. Electrophysiology Part I: Ion Channel
Physiology ..................................... 256
6.5.В. Electrophysiology Part II ...................... 263
6.6. Methods to Detect Reactive Metabolites of Oxygen
and Nitrogen .......................................... 272
By Matthew B. Grisham
6.6. A. Detection of the Superoxide Anion Radical .......... 273
6.6.B. Detection of Hydrogen Peroxide ................. 274
6.6.C. F2-Isoprostanes as Indicators of Lipid
Peroxidation In Vivo ........................... 276
6.6.D. Measurement of the GSSG/GSH Redox Couple in
Cells and Tissue ............................... 277
6.6.E. Methods to Detect NO and Its Oxidized
Metabolites In Vitro and In Vivo ............... 277
6.6.F. Detection of 5-Nitrosothiols by Colorimetric
and Fluorimetric Methods ....................... 281
6.6.G. Is the Presence of 3-Nitrotyrosine
a Specific Footprint for Peroxynitrite? ........ 283
Index ......................................................... 285
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