REDOX BIOCHEMISTRY -- CONTENTS -- Contributors -- List of Abbreviations -- Preface -- 1. Redox Metabolism and Life -- 1.1. Redox Biochemistry and the Evolution of Life -- 1.2. Global Redox Cycles -- 1.3. Major Bioenergetic Cycles -- 1.3.A. Photosynthesis -- 1.3.B. Aerobic Respiration -- 2. Antioxidant Molecules and Redox Cofactors -- 2.1. Glutathione -- 2.1.A. Biological Functions -- 2.1.B. Biosynthesis -- 2.1.C. Degradation -- 2.1.D. Other Thiol-Based Redox Buffers -- 2.2. Ascorbate -- 2.2.A. Ascorbate Chemistry -- 2.2.B. Ascorbate Biosynthesis -- 2.2.C. Ascorbate Recycling -- 2.2.D. Ascorbate Transport -- 2.2.E. Importance of Ascorbate in Stress and Disease -- 2.3. Other Antioxidants -- 2.3.A. Lipid-Soluble Antioxidants -- 2.3.B. Water-Soluble Antioxidants -- 2.3.C. Antioxidants and Human Health -- 2.4. Redox Coenzymes -- 2.4.A. Flavin -- 2.4.B. NAD -- 2.4.C. Quinones -- 2.4.D. Pterins and Molybdopterins -- 2.4.E. Folic Acid -- 3. Antioxidant Enzymes -- 3.1. ROS-Dependent Enzymes -- 3.1.A. Catalase -- 3.1.B. Superoxide Dismutase -- 3.1.C. Peroxiredoxins -- 3.1.D. Alkyl Hydroperoxide Reductases -- 3.2. The Thioredoxin System -- 3.2.A. Thioredoxin -- 3.2.B. Thioredoxin Reductase -- 3.3. The Glutathione System -- 3.3.A. Glutathione Reductase -- 3.3.B. Glutaredoxin (Thioltransferase) -- 3.4. Repair Enzymes -- 3.4.A. Methionine Sulfoxide Reductases -- 3.4.B. DNA Repair Enzymes -- 3.4.C. Sulfiredoxins -- 3.5. Detoxification Enzymes -- 3.5.A. Cytochrome P450 Enzymes: Structure, Function, and Mechanism -- 3.5.B. GSH Transferases -- 3.6. Oxidative Folding -- 3.6.A. Disulfide Bond Formation in Bacteria -- 3.6.B. Disulfide Bond Formation in Eukaryotes -- 3.7. Other Antioxidant Enzymes -- 3.7.A. Selenoproteins -- 3.7.B. Heme Oxygenase -- 4. Redox Regulation of Physiological Processes -- 4.1. Reactive Oxygen, Nitrogen, and Thiol-Based Signal Transduction.

4.1.A. Nitric Oxide Signaling -- 4.1.B. Carbon Monoxide Signaling -- 4.1.C. Superoxide and Hydrogen Peroxide -- 4.1.D. Other Novel Redox Molecules -- 4.2. Role of Nitric Oxide Synthases in Redox Signaling -- 4.2.A. Characterization of the Nitric Oxide Synthases -- 4.2.B. Regulation of Nitric Oxide Synthases by Intrinsic Elements -- 4.2.C. Extrinsic Regulation of Nitric Oxide Synthases -- 4.2.D. Interactions of NO with Other Proteins and Enzymes -- 4.3. Redox Regulation of Genes -- 4.3.A. MAP Kinase/Cell Cycle -- 4.3.B. Redox Control of Gene Expression -- 4.3.C. Peptide Editing and Thiol-Mediated Redox Regulation -- 4.4. Redox Regulation of Apoptosis -- 4.4.A. Apoptotic Pathways -- 4.4.B. Reactive Oxygen Species and Apoptosis -- 4.5. Metal Homeostasis -- 4.5.A. Physiological Significance of Metal Metabolism -- 4.5.B. Metal Uptake from the Extracellular Environment -- 4.5.C. Intracellular Metal Distribution by Target-Specific Chaperones -- 4.5.D. Subcellular Membrane Metal Transporters -- 4.5.E. Heme and Iron-Sulfur Cluster Synthesis -- 4.5.F. Cellular Storage -- 4.5.G. Metal Export -- 4.5.H. Regulation of Metal Metabolism -- 4.5.I. Genetic Disorders in Metal Metabolism -- 4.5.J. Perturbation of Metal Homeostasis and Degenerative Disorders -- 4.6. Redox Enzymology -- 4.7. Circadian Clock and Heme Biosynthesis -- 4.7.A. Cyclic Expression of Heme Binding Proteins -- 4.7.B. Circadian Clock Mechanism -- 4.7.C. PAS Is a Heme Binding Domain -- 4.7.D. Expression of Npas2 Is Controlled by mPER2 -- 4.7.E. NPAS2 Regulates Expression of Aminolevulinate Synthase 1 -- 5. Pathological Processes Related to Redox -- 5.1. Protein Modification -- 5.1.A. Protein Oxidation and Aging -- 5.1.B. Mechanisms of Protein Oxidation -- 5.1.C. Peptide Bond Cleavage -- 5.1.D. Oxidation of Amino Acid Residue Side Chains -- 5.1.E. Beta Scission of Amino Acid Side Chains.

5.1.F. Generation of Protein Carbonyl Derivatives -- 5.1.G. Formation of Protein Cross-Linked Derivatives -- 5.1.H. Role of Protein Oxidation in Aging -- 5.2. Oxidative Stress in the Eye: Age-Related Cataract and Retinal Degeneration -- 5.2.A. Oxidative Stress and Cataract -- 5.2.B. Oxidative Stress and Retinal Pathology -- 5.3. Redox Mechanisms in Cardiovascular Disease: Chronic Heart Failure -- 5.3.A. Excitation-Contraction Coupling in Cardiac Myocytes -- 5.3.B. Role of Oxidative Stress in Chronic Heart Failure -- 5.3.C. Redox Modulation of Ca(2+) Handling Proteins -- 5.3.D. Hypertrophy and Cell Death -- 5.3.E. Extracellular Matrix Remodeling -- 5.4. Role of Reactive Oxygen Species in Carcinogenesis -- 5.4.A. ROS Act as Growth Signaling Messengers -- 5.4.B. Phosphatases Are Prime Targets for ROS During Growth Stimulation -- 5.4.C. Uncontrolled Production of ROS is Carcinogenic -- 5.4.D. ROS Can Induce Carcinogenic DNA and Protein Adducts -- 5.4.E. ROS Can Affect DNA Methylation and Gene Expression -- 5.4.F. Mitochondrial DNA Mutations Are Induced by ROS -- 5.4.G. Clinical Trials on Antioxidant Supplementation Against Cancer -- 5.5. Oxidative Stress and the Host-Pathogen Interaction -- 5.5.A. Neutrophils and the Innate Immune Response -- 5.5.B. Bacterial Targets of Oxidative Damage -- 5.5.C. Regulating the Oxidative Stress Response -- 5.5.D. The Oxidative Stress Response -- 5.5.E. Evasion of the Innate Immune Response -- 6. Specialized Methods -- 6.1. Mass Spectrometry Applications for Redox Biology -- 6.1.A. Mass Spectrometer -- 6.1.B. Applications of Mass Spectrometry -- 6.1.C. Hydrogen Exchange Mass Spectrometry -- 6.2. Electron Paramagnetic Resonance (EPR) for the Redox Biochemist -- 6.2.A. Introduction to Magnetic Resonance Spectroscopy -- 6.2.B. Basic EPR Theory -- 6.2.C. Appearance of the EPR Spectrum -- 6.2.D. The EPR Experiment.

6.2.E. The Conventional EPR Spectrometer: Detection of the Signal -- 6.2.F. Sensitivity and Saturation in EPR -- 6.2.G. Measuring the Concentration of Spins -- 6.2.H. Nuclear Hyperfine and Spin-Spin Interactions -- 6.3. Redox Potentiometry -- 6.3.A. Midpoint Potential -- 6.3.B. Redox-Linked Processes -- 6.3.C. Potentiometric Technique -- 6.4. Bioinformatics Methods to Study Thiol-Based Oxidoreductases -- 6.4.A. Identification of Redox-Active Cysteines in Proteins -- 6.4.B. Cysteine-Based Redox Motifs -- 6.4.C. Conserved Cysteines in Metal-Binding Proteins -- 6.4.D. Secondary Structure Context of Redox-Active Cysteines -- 6.4.E. Structure Modeling -- 6.4.F. Comparative Sequence Analysis of Thiol-Based Oxidoreductases -- 6.5. Electrophysiology -- 6.5.A. Electrophysiology Part I: Ion Channel Physiology -- 6.5.B. Electrophysiology Part II -- 6.6. Methods to Detect Reactive Metabolites of Oxygen and Nitrogen -- 6.6.A. Detection of the Superoxide Anion Radical -- 6.6.B. Detection of Hydrogen Peroxide -- 6.6.C. F2-Isoprostanes as Indicators of Lipid Peroxidation In Vivo -- 6.6.D. Measurement of the GSSG/GSH Redox Couple in Cells and Tissue -- 6.6.E. Methods to Detect NO and Its Oxidized Metabolites In Vitro and In Vivo -- 6.6.F. Detection of S-Nitrosothiols by Colorimetric and Fluorimetric Methods -- 6.6.G. Is the Presence of 3-Nitrotyrosine a Specific Footprint for Peroxynitrite? -- Index.