Note: Oxidative Folding of Peptides and Proteins -- Contents -- Chapter 1 Oxidative Folding of Proteins in vivo -- Chapter 1.1 Thioredoxins and the Regulation of Redox Conditions in Prokaryotes -- 1.1.1 The Thioredoxin Family of Proteins -- 1.1.1.1 The Thioredoxin Fold -- 1.1.1.2 Thioredoxins and the Thioredoxin System -- 1.1.1.3 Glutaredoxins and the Glutaredoxin System -- 1.1.1.4 NrdH and Other Related Proteins -- 1.1.2 Functions of Thioredoxin and Glutaredoxin -- 1.1.2.1 Regulation of Redox Conditions -- 1.1.2.2 Regulation of Metabolic Enzymes -- 1.1.3 Thioredoxins, Glutaredoxins and Protein Folding -- 1.1.3.1 Regulation of Protein Folding via Electrons Provided by Thioredoxins and Glutaredoxins -- 1.1.3.2 Thioredoxins and Glutaredoxins Acting as Protein Disulfide Isomerases or Molecular Chaperones -- 1.1.4 Concluding Remarks -- Acknowledgments -- References -- Chapter 1.2 Disulfide-bond Formation and Isomerization in Prokaryotes -- 1.2.1 Introduction -- 1.2.2 Disulfide-bond Formation -- 1.2.2.1 The Periplasmic Dithiol Oxidase DsbA -- 1.2.2.2 DsbB -- 1.2.3 Disulfide-bond Isomerization -- 1.2.3.1 Disulfide-bond Isomerase DsbC -- 1.2.3.2 Reactivation of DsbC: The Inner Membrane Electron Transporter DsbD -- 1.2.3.3 DsbG, a Structural Homolog of DsbC with Unknown Function -- 1.2.3.4 The Cytochrome c Maturation Factor CcmG is a DsbD Substrate -- 1.2.4 Coexistence of the Oxidative Disulfide-bond Formation and the Reductive Disulfide Isomerization Pathways -- 1.2.5 Concluding Remarks -- Acknowledgements -- References -- Chapter 1.3 The Periplasm of E. coli - Oxidative Folding of Recombinant Proteins -- 1.3.1 Escherichia coli as Host for the Production of Recombinant Proteins - Benefits and Drawbacks -- 1.3.2 Cytoplasm, Periplasm or Cultivation Media - Where to Direct the Target Protein? -- 1.3.3 Physiology and Properties of the Periplasm. , 1.3.4 The Periplasm - How to Get There? -- 1.3.4.1 Signal Sequences -- 1.3.4.2 Secretion of Unfolded Proteins via the Sec Pathway -- 1.3.4.3 Secretion of Folded Proteins via the Tat Pathway -- 1.3.5 Biotechnological Application - the Periplasm as Production Compartment for Recombinant Proteins -- 1.3.5.1 Production of Antibodies and Antibody Fragments -- 1.3.5.2 Secretory Production of Human Proinsulin -- 1.3.5.3 Production of Other Therapeutic Proteins -- 1.3.6 Conclusions and Future Directions -- Acknowledgements -- References -- Chapter 1.4 Oxidative Protein Folding in Mitochondria -- 1.4.1 Introduction -- 1.4.2 Disulfide Bonds in the IMS of Mitochondria -- 1.4.3 Protein Import into the IMS by Oxidative Protein Folding -- 1.4.4 The Redox-dependent Import Receptor Mia40 -- 1.4.5 The FAD-dependent Sulfhydryl Oxidase Erv1 -- 1.4.6 The Mia40-Erv1 Disulfide Relay System -- 1.4.7 Cytochrome c Links the Disulfide Relay System to the Respiratory Chain of Mitochondria -- 1.4.8 Oxidative Protein Folding Drives Import of Sod1 -- 1.4.9 Conclusion and Perspectives -- Acknowledgements -- References -- Chapter 1.5 Oxidative Folding in the Endoplasmic Reticulum -- 1.5.1 Introduction -- 1.5.2 Biochemistry of Disulfide-bond Formation -- 1.5.3 Folding Environment of the ER -- 1.5.4 Thiol Disulfide Oxidoreductase Family -- 1.5.5 Disulfide-bond Oxidation Pathway -- 1.5.5.1 Protein Disulfide Isomerase (PDI) -- 1.5.5.2 Oxidation by Ero1 -- 1.5.5.3 Oxidation by QSOX -- 1.5.6 Disulfide-bond Reduction Pathway -- 1.5.6.1 The Role of Glutathione in the ER -- 1.5.7 Maintaining the Redox Balance of the ER -- 1.5.8 Substrate Recognition by PDI and its Homologs -- 1.5.9 Conclusion -- References -- Chapter 1.6 The Ero1 Sulfhydryl Oxidase and the Oxidizing Potential of the Endoplasmic Reticulum -- 1.6.1 Introduction. , 1.6.2 Mechanism for Generation and Transfer of Disulfides by Ero1 -- 1.6.2.1 A Route for Intramolecular Electron Transfer Supported by the Ero1 Structure -- 1.6.2.2 Oxidation of PDI by Ero1 -- 1.6.2.3 Comparison of Ero1 with the DsbB Intramembrane Sulfhydryl Oxidoreductase of Bacteria -- 1.6.2.4 Comparison of Ero1 to Erv Sulfhydryl Oxidases -- 1.6.3 Destination of Reducing Equivalents Derived from Cysteine Thiol Oxidation by Ero1 -- 1.6.4 Regulation of Ero1 and the Maintenance of Redox Homeostasis in the ER -- 1.6.5 Ero1 Orthologs -- 1.6.6 Summary -- References -- Chapter 1.7 Eukaryotic Protein Disulfide-isomerases and their Potential in the Production of Disulfide-bonded Protein Products: What We Need to Know but Do Not! -- 1.7.1 Introduction -- 1.7.2 Evidence that PDI is Rate or Yield Limiting in the Production of High-value Proteins -- 1.7.2.1 Oxidative Folding in vitro -- 1.7.2.2 Optimizing Production of Disulfide-bonded Proteins in Escherichia coli -- 1.7.2.3 Optimizing Production of Disulfide-bonded Proteins in Saccharomyces cerevisiae -- 1.7.2.4 Optimizing Production of Disulfide-bonded Proteins in Mammalian and Insect Cells -- 1.7.3 What Limits our Ability to Enhance the Usefulness of PDI in the Production of High-value Proteins? -- 1.7.3.1 Functional Organization of Chaperones and Folding Factors in the ER -- 1.7.3.2 Functional Significance of the Existence of Multiple Members of the PDI Family -- 1.7.3.3 Functional Organization of the Flow of Redox Equivalents to Newly Synthesized Proteins in the ER: Linear Electron Transfer Chain or Network? -- 1.7.3.4 Dynamic Description of the Action of PDI on Protein Substrates -- Acknowledgements -- References -- Chapter 1.8 Cellular Responses to Oxidative Stress -- 1.8.1 Oxidative Stress: An Imbalance in Favor of Pro-oxidants -- 1.8.1.1 Reactive Oxygen Species. , 1.8.1.2 The Deleterious Effects of Oxidative Stress -- 1.8.1.3 Cellular Responses to Oxidative Stress -- 1.8.1.4 Cysteines: The Building Blocks of ROS-sensing Nano-switches -- 1.8.2 OxyR: A Redox-regulated Transcription Factor -- 1.8.2.1 Discovery of an H2O2-response Regulator in E. coli -- 1.8.2.2 The OxyR Regulon -- 1.8.2.3 Redox Regulation of OxyR's Function -- 1.8.2.4 Biotechnological Application of OxyR -- 1.8.3 Hsp33: A Chaperone Specialized for Oxidative Stress Protection -- 1.8.3.1 The Redox-regulated Chaperone Holdase Hsp33 -- 1.8.3.2 Mechanism of Hsp33's Redox Regulation -- 1.8.3.3 Hsp33: Central Member of a Multichaperone Network -- 1.8.4 Oxidative Stress and Redox Regulation: Turning Lemons into Lemonade -- References -- Chapter 2 Oxidative Folding of Proteins in vitro -- Chapter 2.1 The Role of Disulfide Bonds in Protein Folding and Stability -- 2.1.1 Introduction -- 2.1.2 Stabilization of Proteins by Disulfide Bonds -- 2.1.3 Disulfide Bonds in Protein Folding Reactions -- 2.1.4 Conclusions -- References -- Chapter 2.2 Strategies for the Oxidative in vitro Refolding of Disulfide-bridge-containing Proteins -- 2.2.1 Introduction -- 2.2.2 Chemical Systems for the in vitro Formation of Disulfide Bridges -- 2.2.2.1 Transition Metal-catalyzed Air Oxidation -- 2.2.2.2 Thiol-Disulfide Exchange Systems -- 2.2.2.3 Mixed Disulfides -- 2.2.2.4 Enzymatic Catalysis of Disulfide-bond Formation in vitro -- 2.2.3 Alternative Approaches to Oxidative in vitro Folding -- 2.2.3.1 Dithiols -- 2.2.3.2 Aromatic Thiols -- 2.2.3.3 Matrix-assisted Oxidative Refolding -- 2.2.3.4 Other Oxidizing Compounds -- 2.2.3.5 Electrochemical Oxidation -- 2.2.4 Chemical Modification of Cysteine Residues in vitro -- 2.2.5 Cell-free Expression Systems -- 2.2.6 Conclusions -- References. , Chapter 3 Redox Potentials of Cysteine Residues in Peptides and Proteins: Methods for their Determination -- 3.1 Introduction -- 3.2 Formation of Disulfide Bonds by Thiol-disulfide Exchange -- 3.3 Redox Potentials of Mixed Disulfide Bonds -- 3.4 Redox Potentials of Intramolecular Disulfide Bonds -- 3.5 Measurement of Equilibrium Constants for Thiol-disulfide Exchange -- 3.6 Reference Redox Couples -- 3.7 The GSH/GSSG Reference Redox Couple -- 3.8 Determination of Redox Potentials with GSH/GSSG1 Redox Buffers: an Example -- 3.9 Determination of Redox Potentials by the Direct Protein-Protein Equilibration Method: an Example -- References -- Chapter 4 Engineered Disulfide Bonds for Protein Design -- 4.1 Introduction -- 4.2 Helices -- 4.2.1 Disulfide-stabilized Helices -- 4.2.2 Helical Bundles -- 4.3 β-Turns -- 4.4 β-Sheets -- 4.4.1 β-Hairpins -- 4.4.2 Multi-stranded β-Sheets -- 4.5 Conclusions -- Acknowledgements -- References -- Chapter 5 Selenocysteine as a Probe of Oxidative Protein Folding -- 5.1 Introduction -- 5.2 Incorporation of Selenocysteine into Proteins -- 5.2.1 Codon Suppression -- 5.2.2 Codon Reassignment -- 5.2.3 Post-translational Modification -- 5.2.4 Peptide Synthesis -- 5.3 Oxidative Protein Folding -- 5.3.1 Selenium as a Folding Probe -- 5.3.2 Selenium as a Folding Catalyst -- 5.4 Perspectives -- References -- Chapter 6 Oxidative Folding of Peptides in vitro -- Chapter 6.1 Oxidative Folding of Single-stranded Disulfide-rich Peptides -- 6.1.1 Introduction -- 6.1.1.1 Molecular Diversity of Disulfide-rich Peptides -- 6.1.1.2 Oxidative Folding Problem -- 6.1.1.3 Scope of the Chapter -- 6.1.2 Mechanisms of in vitro Oxidative Folding -- 6.1.2.1 Thiol/Disulfide Exchange Reactions in Peptides -- 6.1.2.2 Cysteine Patterns and Loop Sizes -- 6.1.2.3 Amino Acid Sequences and Non-covalent Interactions. , 6.1.2.4 A Case Study - Folding of ω-Conotoxin MVIIA.