Oxidative folding of peptides and proteins:
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| Format: | Book |
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| Language: | English |
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Cambridge
RSC Publ.
2009
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| Series: | RSC biomolecular sciences
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| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXI, 429 S. Ill., graph. Darst. |
| ISBN: | 9780854041480 |
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| 245 | 1 | 0 | |a Oxidative folding of peptides and proteins |c ed. by Johannes Buchner ... |
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| adam_text | Contents
Chapter 1 Oxidative Folding of Proteins in vivo
Chapter 1.1 Thioredoxins and the Regulation of Redox Conditions
in Prokaryotes
Cars ten Berndt and Arne Holmgren
1.1.1 The Thioredoxin Family of Proteins 2
1.1.1.1 The Thioredoxin Fold 2
1.1.1.2 Thioredoxins and the Thioredoxin
System 3
1.1.1.3 Glutaredoxins and the Glutaredoxin
System 4
1.1.1.4 NrdH and Other Related Proteins 5
1.1.2 Functions of Thioredoxin and Glutaredoxin 6
1.1.2.1 Regulation of Redox Conditions 6
1.1.2.2 Regulation of Metabolic Enzymes 7
1.1.3 Thioredoxins, Glutaredoxins and Protein
Folding 8
1.1.3.1 Regulation of Protein Folding via
Electrons Provided by Thioredoxins
and Glutaredoxins 8
1.1.3.2 Thioredoxins and Glutaredoxins Acting
as Protein Disulfide Isomerases or
Molecular Chaperones 9
1.1.4 Concluding Remarks 11
Acknowledgments 12
References 12
RSC Biomolecular Sciences
Oxidative Folding of Peptides and Proteins
Edited by Johannes Buchner and Luis Moroder
© Royal Society of Chemistry 2009
Published by the Royal Society of Chemistry, www.rsc.org
xi
xii Contents
Chapter 1.2 Disulfide-bond Formation and Isomerization
in Prokaryotes
Goran Malojcic and Rudi Glockshuber
1.2.1 Introduction 19
1.2.2 Disulfide-bond Formation 20
1.2.2.1 The Periplasmic Dithiol Oxidase DsbA 20
1.2.2.2 DsbB 23
1.2.3 Disulfide-bond Isomerization 27
1.2.3.1 Disulfide-bond Isomerase DsbC 27
1.2.3.2 Reactivation of DsbC: The Inner
Membrane Electron Transporter DsbD 29
1.2.3.3 DsbG, a Structural Homolog of DsbC
with Unknown Function 33
1.2.3.4 The Cytochrome c Maturation Factor
CcmG is a DsbD Substrate 33
1.2.4 Coexistence of the Oxidative Disulfide-bond
Formation and the Reductive Disulfide
Isomerization Pathways 34
1.2.5 Concluding Remarks 36
Acknowledgements 36
References 36
Chapter 1.3 The Periplasm of E. coli - Oxidative Folding
of Recombinant Proteins
Katharina M. Gebendorfer and Jeannette Winter
1.3.1 Escherichia coli as Host for the Production of
Recombinant Proteins - Benefits and Drawbacks 41
1.3.2 Cytoplasm, Periplasm or Cultivation Media
Where to Direct the Target Protein? 42
1.3.3 Physiology and Properties of the Periplasm 44
1.3.4 The Periplasm - How to Get There? 45
1.3.4.1 Signal Sequences 45
1.3.4.2 Secretion of Unfolded Proteins via the Sec
Pathway 47
1.3.4.3 Secretion of Folded Proteins via the Tat
Pathway 48
1.3.5 Biotechnological Application - the Periplasm
as Production Compartment for
Recombinant Proteins 50
1.3.5.1 Production of Antibodies and Antibody
Fragments 51
1.3.5.2 Secretory Production of Human Proinsulin 54
1.3.5.3 Production of Other Therapeutic Proteins 57
Contents xiii
1.3.6 Conclusions and Future Directions 58
Acknowledgements 59
References 59
Chapter 1.4 Oxidative Protein Folding in Mitochondria
Kai Hell and Walter Neupert
1.4.1 Introduction 67
1.4.2 Disulfide Bonds in the IMS of Mitochondria 69
1.4.3 Protein Import into the IMS by Oxidative
Protein Folding 70
1.4.4 The Redox-dependent Import Receptor Mia40 70
1.4.5 The FAD-dependent Sulfhydryl Oxidase Ervl 72
1.4.6 The Mia40-Ervl Disulfide Relay System 73
1.4.7 Cytochrome c Links the Disulfide Relay System to
the Respiratory Chain of Mitochondria 75
1.4.8 Oxidative Protein Folding Drives Import of Sod I 76
1.4.9 Conclusion and Perspectives 77
Acknowledgements 77
References 77
Chapter 1.5 Oxidative Folding in the Endoplasmic Reticulum
Seema Chakravarthi, Catherine E. Jessop
and Neil J. Bulleid
1.5.1 Introduction 81
1.5.2 Biochemistry of Disulfide-bond Formation 82
1.5.3 Folding Environment of the ER 82
1.5.4 Thiol Disulfide Oxidoreductase Family 85
1.5.5 Disulfide-bond Oxidation Pathway 86
1.5.5.1 Protein Disulfide Isomerase (PDI) 86
1.5.5.2 Oxidation by Erol 89
1.5.5.3 Oxidation by QSOX 91
1.5.6 Disulfide-bond Reduction Pathway 92
1.5.6.1 The RoleofGlutathione in the ER 93
1.5.7 Maintaining the Redox Balance of the ER 95
1.5.8 Substrate Recognition by PDI and its Homologs 97
1.5.9 Conclusion 99
References 100
Chapter 1.6 The Erol Sulfhydryl Oxidase and the Oxidizing
Potential of the Endoplasmic Reticulum
Deborah Fass and Carolyn S. Sexier
1.6.1 Introduction 105
1.6.2 Mechanism for Generation and Transfer of
Disulfides by Erol 106
xiv Contents
1.6.2.1 A Route for Intramolecular Electron
Transfer Supported by the Erol
Structure 106
1.6.2.2 Oxidation of PDI by Erol 108
1.6.2.3 Comparison of Erol with the DsbB
Intramembrane Sulfhydryl Oxido-
reductase of Bacteria 110
1.6.2.4 Comparison of Erol to Erv Sulfhydryl
Oxidases 113
1.6.3 Destination of Reducing Equivalents Derived from
Cysteine Thiol Oxidation by Erol 113
1.6.4 Regulation of Ero 1 and the Maintenance of Redox
Homeostasis in the ER 114
1.6.5 Erol Orthologs 116
1.6.6 Summary 117
References 117
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!
Robert B. Freedman
1.7.1 Introduction 121
1.7.2 Evidence that PDI is Rate or Yield Limiting in the
Production of High-value Proteins 123
1.7.2.1 Oxidative Folding in vitro 123
1.7.2.2 Optimizing Production of Disulfide-
bonded Proteins in Escherichia coli 126
1.7.2.3 Optimizing Production of Disulfide-
bonded Proteins in Saccharomyces
cerevisiae 128
1.7.2.4 Optimizing Production of Disulfide-
bonded Proteins in Mammalian and
Insect Cells 129
1.7.3 What Limits our Ability to Enhance the Usefulness
of PDI in the Production of High-value
Proteins? 132
1.7.3.1 Functional Organization of Chaperones
and Folding Factors in the ER 132
1.7.3.2 Functional Significance of the Existence
of Multiple Members of the PDI Family 135
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? 140
Contents xv
1.7.3.4 Dynamic Description of the Action of
PDI on Protein Substrates 146
Acknowledgements 151
References 151
Chapter 1.8 Cellular Responses to Oxidative Stress
Marianne Ilbert, Caroline Kumsta and Ursula Jakob
1.8.1 Oxidative Stress: An Imbalance in Favor of
Pro-oxidants 158
1.8.1.1 Reactive Oxygen Species 158
1.8.1.2 The Deleterious Effects of Oxidative
Stress 159
1.8.1.3 Cellular Responses to Oxidative Stress 159
1.8.1.4 Cysteines: The Building Blocks of
ROS-sensing Nano-switches 160
1.8.2 OxyR: A Redox-regulated Transcription Factor 161
1.8.2.1 Discovery of an HiOi-response Regulator
in E. coli 161
1.8.2.2 The OxyR Regulon 162
1.8.2.3 Redox Regulation of OxyR s Function 162
1.8.2.4 Biotechnological Application of OxyR 166
1.8.3 Hsp33: A Chaperone Specialized for Oxidative
Stress Protection 167
1.8.3.1 The Redox-regulated Chaperone Holdase
Hsp33 167
1.8.3.2 Mechanism of Hsp33 s Redox
Regulation 168
1.8.3.3 Hsp33: Central Member of a Multi-
chaperone Network 172
1.8.4 Oxidative Stress and Redox Regulation:
Turning Lemons into Lemonade 173
References 174
Chapter 2 Oxidative Folding of Proteins in vitro
Chapter 2.1 The Role of Disulfide Bonds in Protein Folding
and Stability
Matthias Johannes Feige and Johannes Buchner
2.1.1 Introduction 179
2.1.2 Stabilization of Proteins by Disulfide Bonds 180
2.1.3 Disulfide Bonds in Protein Folding Reactions 185
2.1.4 Conclusions 188
References 188
xvi Contents
Chapter 2.2 Strategies for the Oxidative in vitro Refolding
of Disulfide-bridge-containing Proteins
Rainer Rudolph and Christian Lange
2.2 A Introduction 192
2.2.2 Chemical Systems for the in vitro Formation
of Disulfide Bridges 195
2.2.2.1 Transition Metal-catalyzed Air Oxidation 196
2.2.2.2 Thiol-Disulfide Exchange Systems 197
2.2.2.3 Mixed Disulfides 200
2.2.2.4 Enzymatic Catalysis of Disulfide-bond
Formation in vitro 202
2.2.3 Alternative Approaches to Oxidative
in vitro Folding 205
2.2.3.1 Dithiols 205
2.2.3.2 Aromatic Thiols 206
2.2.3.3 Matrix-assisted Oxidative Refolding 207
2.2.3.4 Other Oxidizing Compounds 209
2.2.3.5 Electrochemical Oxidation 210
2.2.4 Chemical Modification of Cysteine Residues
in vitro 211
2.2.5 Cell-free Expression Systems 212
2.2.6 Conclusions 213
References 213
Chapter 3 Redox Potentials of Cysteine Residues in Peptides
and Proteins: Methods for their Determination
Dallas L. Rabenstein
3.1 Introduction 220
3.2 Formation of Disulfide Bonds by
Thiol-disulfide Exchange 220
3.3 Redox Potentials of Mixed Disulfide Bonds 222
3.4 Redox Potentials of Intramolecular Disulfide
Bonds 223
3.5 Measurement of Equilibrium Constants
for Thiol-disulfide Exchange 224
3.6 Reference Redox Couples 227
3.7 The GSH/GSSG Reference Redox Couple 229
3.8 Determination of Redox Potentials
with GSH/GSSG 1 Redox Buffers: an Example 230
3.9 Determination of Redox Potentials by the Direct
Protein-Protein Equilibration Method:
an Example 232
References 233
Contents xvii
Chapter 4 Engineered Disulfide Bonds for Protein Design
Luis Moroder, Hans-Jiirgen Musiol and Christian Renner
4.1 Introduction 236
4.2 Helices 238
4.2.1 Disulfide-stabilized Helices 238
4.2.2 Helical Bundles 239
4.3 P-Turns 242
4.4 P-Sheets 243
4.4.1 P-Hairpins 243
4.4.2 Multi-stranded P-Sheets 247
4.5 Conclusions 247
Acknowledgements 248
References 248
Chapter 5 Selenocysteine as a Probe of Oxidative Protein Folding
Joris Beld, Kenneth J. Woycechowsky and Donald Hilvert
5.1 Introduction 253
5.2 Incorporation of Selenocysteine into Proteins 256
5.2.1 Codon Suppression 256
5.2.2 Codon Reassignment 257
5.2.3 Post-translational Modification 258
5.2.4 Peptide Synthesis 259
5.3 Oxidative Protein Folding 260
5.3.1 Selenium as a Folding Probe 260
5.3.2 Selenium as a Folding Catalyst 264
5.4 Perspectives 267
References 268
Chapter 6 Oxidative Folding of Peptides in vitro
Chapter 6.1 Oxidative Folding of Single-stranded Disulnde-rich
Peptides
Grzegorz Bulaj and Aleksandra Walewska
6.1.1 Introduction 274
6.1.1.1 Molecular Diversity of Disulnde-rich
Peptides 274
6.1.1.2 Oxidative Folding Problem 275
6.1.1.3 Scope of the Chapter 279
6.1.2 Mechanisms of in vitro Oxidative Folding 279
6.1.2.1 Thiol/Disulfide Exchange Reactions in
Peptides 280
6.1.2.2 Cysteine Patterns and Loop
Sizes 280
xviii Contents
6.1.2.3 Amino Acid Sequences and Non-covalent
Interactions 282
6.1.2.4 A Case Study - Folding of oo-Conotoxin
MVIIA 284
6.1.2.5 Role of Post-translational Modifications 284
6.1.2.6 Oxidative Folding Conditions - Practical
Considerations 285
6.1.3 Biosynthetic Aspects of the Oxidative Folding 287
6.1.3.1 Precursor Sequences 287
6.1.3.2 Protein Disulfide Isomerase 289
6.1.3.3 Macromolecular Crowding 289
6.1.3.4 Oxidative Folding in the Endoplasmic
Reticulum 291
6.1.4 Conclusions and Outlook 292
Acknowledgements 292
References 292
Chapter 6.2 Regioselective Disulfide Formation
Knut Adermann and Kleomenis Barlos
6.2.1 Introduction 297
6.2.2 Thiol-protecting Groups 298
6.2.3 Regioselective Disulfide Formation in Solution 300
6.2.3.1 Peptides with Two Disulfides 301
6.2.3.2 Peptides with Three Disulfides 305
6.2.3.3 Peptides with Multiple Disulfides 308
6.2.4 Disulfide Formation on the Solid Support 310
6.2.5 Semi-selective Formation of Disulfide Bonds 312
6.2.6 Concluding Remarks 313
References 314
Chapter 6.3 Folding Motifs of Cystine-rich Peptides
Norelle L. Daly and David J. Craik
6.3.1 Overview of Folding Motifs
in Disulfide-rich Peptides 318
6.3.1.1 Sources, Activities and Structures
of Disulfide-rich Peptides 318
6.3.1.2 Scope of Review 320
6.3.2 Classes of Disulfide-rich Motifs 320
6.3.2.1 Geometry of the Disulfide Bond 321
6.3.2.2 Disulfide-bond Frameworks 322
6.3.2.3 Fold Classifications 328
6.3.3 Examples and Applications of Peptide Classes with
Disulfide-rich Motifs 330
Contents xix
6.3.3.1 Cyclotides 330
6.3.3.2 Conotoxin Frameworks 333
6.3.3.3 Defensin Frameworks 334
6.3.4 Disulfide-rich Frameworks as Bioengineering
Scaffolds 335
6.3.5 Outlook 337
Acknowledgements 337
References 337
Chapter 6.4 Double-stranded Cystine Peptides
John D. Wade
6.4.1 Introduction 345
6.4.2 Insulin and Insulin-like Peptides 346
6.4.2.1 Human Insulin 346
6.4.2.2 Insulin-like Peptides from Other Species 348
6.4.3 Other Double-stranded Cystine Peptides 349
6.4.3.1 From Natural Origin 349
6.4.3.2 Synthetic Constructs 350
6.4.4 Oxidative Folding 350
6.4.4.1 Combination of Two Chains into
Double-stranded Peptides 350
6.4.4.2 Insulin and Insulin-like Peptides 351
6.4.5 Regioselective Disulfide Formation 353
6.4.6 Oxidative Folding of Single Chain Precursors 357
6.4.6.1 Head-to-tail Constructs 358
6.4.6.2 Precursors with Mini-connecting
Peptides 358
6.4.7 Folding Pathways of Insulin 359
6.4.8 Concluding Remarks 361
Acknowledgements 361
References 361
Chapter 6.5 Multiple-strand Cystine Peptides
Marion G. Gotz, Hans-Jiirgen Musiol and Luis Moroder
6.5.1 Introduction 367
6.5.2 Synthesis of Disulfide Cross-linked Homotrimeric
Collagenous Peptides 369
6.5.2.1 Oxidative Assembly of Collagenous
Homotrimers with the C-Terminal
Cystine Knot of Collagen Type III 369
6.5.2.2 Oxidative Assembly of Collagenous
Homotrimers with the Cystine Knot of
FACIT COL 1-NCI Junctions 371
xx Contents
6.5.2.3 Assembly of Homotrimeric Collagen
Peptides by Regioselective Disulfide
Formation 372
6.5.3 Synthesis of Disulfide Cross-linked Heterotrimeric
Collagenous Peptides 374
6.5.3.1 Oxidative Assembly of Collagenous
Heterotrimers with the Cystine Knot
of Collagen Type IX 375
6.5.3.2 Assembly of Heterotrimeric Collagen
Molecules by Regioselective Disulfide
Formation 375
6.5.4 Concluding Remarks 377
References 377
Chapter 7 Cystine-based Scaffolds for Functional Miniature
Proteins
Rudolf K Allemann
7.1 Introduction 381
7.2 Pre-organization of Amino Acid Side-chains 382
7.3 Natural Linear Cystine-stabilized Peptides and
Cyclotides 383
7.4 Cystine-stabilized Miniature Proteins 385
7.4.1 A Metal Ion Induced Helical Foldamer 385
7.4.2 ApaMyoD: A Miniature DNA-binding
Protein 386
7.4.3 Apoxaldie-1: A Miniature Oxaloacetate
Decarboxylase 389
7.5 Conclusion 392
Acknowledgements 392
References 392
Chapter 8 Selenocystine Peptides - Synthesis, Folding and
Applications
Markus Muttenthaler and Paul F. Alewood
8.1 Introduction 396
8.2 Selenium - Isosteric Replacement for Sulfur 397
8.2.1 Selenium 397
8.2.2 Selenocysteine - the 21st Proteinogenic
Amino Acid 398
8.2.3 Selenocysteine as an Isosteric Replacement
for Cysteine 399
8.2.4 Selenocysteine and its Role as a
Mechanistic Probe 399
Contents xxi
8.2.5 pKa, Nucleophilicity and Reactivity 400
8.2.6 The Redox Potential of Selenocysteine 402
8.2.7 Selenocystine in Reducing Environments 402
8.3 Incorporation of Selenocysteine into Peptides
and Proteins 403
8.3.1 Peptide Synthesis 403
8.3.2 Deprotection, Cleavage 405
8.4 Synthesis of Selenocysteine Building Blocks 406
8.4.1 Overview 406
8.4.2 Selenol Protection 407
8.4.3 Building Blocks for Fmoc/tBu Chemistry 407
8.4.4 Building Blocks for Boc/Bzl Chemistry 407
8.5 Reactions with Selenocysteine 408
8.5.1 Selenocysteine-mediated Native Chemical
Ligation 408
8.5.2 Dehydroamino Acids Versatile Precursors 409
8.6 Concluding Remarks and Perspectives 412
8.6.1 Scaffold Design 412
8.6.2 Folding Pathways 412
8.6.3 Tailoring of Enzymatic Reactions 413
References 413
Subject Index 419
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| discipline | Biologie Chemie |
| format | Book |
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| id | DE-604.BV035458666 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T21:35:44Z |
| institution | BVB |
| isbn | 9780854041480 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017378551 |
| oclc_num | 244653596 |
| open_access_boolean | |
| owner | DE-19 DE-BY-UBM DE-91G DE-BY-TUM |
| owner_facet | DE-19 DE-BY-UBM DE-91G DE-BY-TUM |
| physical | XXI, 429 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | RSC Publ. |
| record_format | marc |
| series2 | RSC biomolecular sciences |
| spelling | Oxidative folding of peptides and proteins ed. by Johannes Buchner ... Cambridge RSC Publ. 2009 XXI, 429 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier RSC biomolecular sciences Protein folding Biologische Oxidation (DE-588)4126898-2 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 s Biologische Oxidation (DE-588)4126898-2 s DE-604 Buchner, Johannes 1960- Sonstige (DE-588)111549970X oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017378551&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Oxidative folding of peptides and proteins Protein folding Biologische Oxidation (DE-588)4126898-2 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| subject_GND | (DE-588)4126898-2 (DE-588)4324567-5 |
| title | Oxidative folding of peptides and proteins |
| title_auth | Oxidative folding of peptides and proteins |
| title_exact_search | Oxidative folding of peptides and proteins |
| title_full | Oxidative folding of peptides and proteins ed. by Johannes Buchner ... |
| title_fullStr | Oxidative folding of peptides and proteins ed. by Johannes Buchner ... |
| title_full_unstemmed | Oxidative folding of peptides and proteins ed. by Johannes Buchner ... |
| title_short | Oxidative folding of peptides and proteins |
| title_sort | oxidative folding of peptides and proteins |
| topic | Protein folding Biologische Oxidation (DE-588)4126898-2 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| topic_facet | Protein folding Biologische Oxidation Proteinfaltung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017378551&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT buchnerjohannes oxidativefoldingofpeptidesandproteins |