Peptide, protein and enzyme design:
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Elektronisch E-Book |
| Sprache: | English |
| Veröffentlicht: |
Cambridge, MA, United States
Academic Press
2016
|
| Ausgabe: | First edition |
| Schriftenreihe: | Methods in enzymology
volume 580 |
| Schlagworte: | |
| Online-Zugang: | TUM01 UBM01 UBR01 UBT01 UBW01 UER01 URL des Erstveröffentlichers Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource (xxii, 653 Seiten) |
| ISBN: | 9780128053805 9780128054345 |
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Datensatz im Suchindex
| _version_ | 1804176546769928192 |
|---|---|
| adam_text | Titel: Peptide, protein and enzyme design
Autor: Pecoraro, Vincent L
Jahr: 2016
CONTENTS
Contributors
Preface
1. Chemical Posttranslational Modification with Designed
Rhodium(ll) Catalysts
S.C. Martin, M.B. Minus, and Z.T. Bail
1. Introduction
2. Synthesis of Rhodium(ll) Conjugates as Protein Modification Catalysts
3. Modification of an SH3 Domain and Gel-Based Visualization Thereof
References
2. Cell-Binding Assays for Determining the Affinity of Protein-Protein
Interactions: Technologies and Considerations
S.A. Hunter and J.R. Cochran
1. Introduction
2. General Binding Theory and Relevance of Kd
3. General Pitfalls in Cell-Based Binding Assays
4. Measuring Binding on the Surface of Yeast
5. Measuring Binding on the Surface of Mammalian Cells
6. Other Methods of Measuring Binding: Kinetic Exclusion Assay and
Surface Plasmon Resonance
7. Summary
Acknowledgments
References
3. Protein and Antibody Engineering by Phage Display
J.C. Frei and J.R. Lai
1. Introduction
2. Equipment
3. Materials
4. Phage Display and Library Design
5. Library Production
6. Library Selections and Screening
References
xiii
XV/ /
1
2
4
11
18
21
22
23
25
30
35
37
42
42
42
45
46
48
50
57
66
73
85
»I
vi
Contents
4. Incorporation of Unnatural Amino Acids into Proteins
Expressed in Mammalian Cells 89
R. Serfling and I. Coin
1. Introduction 90
2. Fluorescence Assay for Straightforward Evaluation of
Uaa-lncorporating Systems 92
3. Incorporation of Uaas into Membrane Proteins 99
4. Conclusion 104
References 104
5. Method for Enzyme Design with Genetically Encoded Unnatural
Amino Acids 109
C. Hu and J. Wang
1. Introduction 110
2. The General Procedure for Enzyme Design with Unnatural Amino Acids 112
3. Unnatural Amino Acid Design 112
4. Synthetic Chemistry-Guided Unnatural Amino Acid Design 116
5. Synthetic Methods for Unnatural Amino Acids 117
6. Aminoacyl-tRNA Synthetase Screening 125
7. Protein Design 127
8. Protein Expression 128
9. Conclusion and Perspective 129
References 130
6. Methods for Solving Highly Symmetric De Novo Designed
Metalloproteins: Crystallographic Examination of a Novel
Three-Stranded Coiled-Coil Structure Containing D-Amino Acids 135
L. Ruckthong, J.A. Stuckey, and V.L. Pecoraro
1. Introduction 136
2. Materials 140
3. Methods 141
Acknowledgments 146
References 146
7. SpyRings Declassified: A Blueprint for Using Isopeptide-Mediated
Cyclization to Enhance Enzyme Thermal Resilience 149
C. Schoene, S.P. Bennett, and M. Howarth
1. Introduction 150
2. Isopeptide-Mediated Enzyme Cyclization 151
3. Characterization of Enzyme Resilience After SpyRing Cyclization 159
Contents vii
4. Concluding Remarks 164
Acknowledgments 164
References 164
8. Engineering and Application of LOV2-Based Photoswitches 169
5.P. Zimmerman, B. Kuhlman, and H. Yumerefendi
1. Introduction 170
2. Engineering LOV2-Based Photoswitches 171
3. Using LOV2-Based Photoswitches 181
4. Summary and Perspectives 188
References 188
9. Minimalist Design of Allosterically Regulated
Protein Catalysts 191
0.V. Makhlynets and I.V. Korendovych
1. Introduction 192
2. Methods 193
Acknowledgments 201
References 201
10. Combining Design and Selection to Create Novel
Protein-Peptide Interactions 203
E.B. Speltz, N. Sawyer, and L. Regan
1. Introduction 204
2. Structure-Guided Rational Design 206
3. Split Fluorescent Protein Assays for Identifying PPIs 207
4. Validation 216
5. Future Perspective: Modular Design of PPI 218
6. Conclusion 218
References 219
11. Metal-Directed Design of Supramolecular Protein Assemblies
J.B. Bailey, R.H. Subramanian, L.A. Churchfield, and F.A. Tezcan
1. Introduction
2. Metal-Directed Protein Self-Assembly
3. Metal-Templated Interface Redesign
4. Methods
5. Conclusion
Acknowledgments
References
223
224
227
231
237
247
247
247
vjjj _ Contents
12. Designing Fluorinated Proteins
E.N.G. Marsh
1. Introduction
2. Methods
Acknowledgments
References
13. Solid Phase Synthesis of Helically Folded Aromatic Oligoamides 279
SJ. Dawson, X. Hu, S. Claerhout, and I. Hue
1. Introduction 280
2. Materials 285
3. Synthetic Protocols 286
4. Characterization of Foidamers 297
References 299
14. Conformational Restriction of Peptides Using Dithiol
Bis-Alkylation 303
L. Peraro, T.R. Siegert, and J.A. Kritzer
1. Introduction 304
2. Using Thiol Alkylation to Constrain Peptides 309
3. Protocols for Peptide Synthesis and Cross-Linking 312
4. Applications, Tips, and Troubleshooting 316
5. Future Directions 327
References 327
15. Engineering Short Preorganized Peptide Sequences for Metal
Ion Coordination: Copper(ll) a Case Study 333
L.M.P. Lima and O. Iranzo
1. Introduction 334
2. Design of Preorganized Peptidic Scaffolds for Metal Ion Coordination 340
3. Synthesis and Characterization of the Peptidic Scaffolds 341
4. Preparation of Analytical Stock Solutions 345
5. Study of the Metal Ion Coordination Properties 349
6. Concluding Remarks 360
Acknowledgments 360
References 361
251
252
265
272
272
Contents ix
16. De Novo Construction of Redox Active Proteins 365
C.C. Moser, M.M. Sheehan, N.M. Ennist, G. Kodali, C. Bialas, M.T. Englander,
B.M. Discher, and P.L. Dutton
1. Introduction 366
2. Sequence Selection: Binary Patterning 367
3. Sequence Selection: Cofactor Self-Assembly 370
4. Binding Heme Redox Cofactors 371
5. Electron-Transfer Reactions of Heme Maquettes 374
6. Binding Light-Activated Zn Tetrapyrrole Cofactors 377
7. Iron-Sulfur Cluster Cofactors 378
8. Redox Metal Binding Sites 379
9. Flavin Cofactor Binding and Electron Transfer 380
10. Translating Aqueous Redox Maquette Designs into Membranes 382
References 384
17. Design Strategies for Redox Active Metalloenzymes:
Applications in Hydrogen Production
R. Alcala-Torano, DJ. Sommer, Z. Bahrami Dizicheh, and G. Ghirlanda
1. Introduction
2. Design of FeS Clusters
3. Design of [FeFe]-Hydrogenase Mimics
4. Design of Porphyrin Redox Sites
5. Conclusion and Future Outlook
References
18. Equilibrium Studies of Designed Metalloproteins
B.R. Gibney
1. Introduction
2. Metalloprotein Thermodynamics
3. Essential Equilibrium Measurements
4. Thermodynamic Analysis of a Heme Binding Four Helix Bundle, [A7-His]2
5. Experimental Procedures
6. Summary
Acknowledgment
References
389
390
392
399
404
409
411
417
418
419
426
430
435
436
437
437
X
Contents
19. Reconstitution of Herne Enzymes with Artificial
Metalloporphyrinoids 439
K. Oohora and T. Hayashi
1. Introduction 440
2. Design and Synthesis of Artificial Metalloporphyrinoids 442
3. Reconstitution of Hemoproteins 446
4. Representative Characteristics of Reconstituted Hemoproteins 451
Acknowledgments 453
References 453
20. Creation of a Thermally Tolerant Peroxidase 455
Y. Watanabe and H. Nakajima
1. Introduction 456
2. Molecular Design for Cyt c552 to Acquire Peroxidase Activity 458
3. Gene Constructs of Recombinant Wild Type and Mutant Cyt c5S2 459
4. Expression and Purification of the Recombinant Proteins 460
5. Thermal Stability of the Cyt c552 Mutants 461
6. Analysis of a Key Intermediate in the Peroxidase Reaction of Cyt c552
V49D/M69A Mutant 462
7. Effect of Trp45 on the Active Intermediate of Mutants 465
References 468
21. Designing Covalently Linked Heterodimeric Four-Helix Bundles 471
M. Chino, L. Leone, O. Maglio, and A. Lombardi
1. Introduction 472
2. Selection of the Best Docking Hotspot Given a Predefined Anchor Bolt 477
3. Broadening the Hotspot and Linker Selections 486
4. Concluding Remarks 493
Acknowledgments 494
References 495
22. Design of Heteronudear Metalloenzymes 501
A. Bhagi-Damodaran, P. Hosseinzadeh, E. Mirts, J. Reed, I.D. Petrik, and Y. Lu
1. Step 1: Computational Design of Heteronudear Metal-Binding Sites
in Mb or CcP 505
2. Step 2: Purification and Structural Characterization of Rationally
Designed Proteins 513
3. Step 3: Functional Characterization of Designed Heterobinuclear
Metalloenzymes 518
Contents xi
4. Step 4: Further Improvement of Designed Heteronuclear Metalloenzymes:
Case Studies 527
5. Conclusions 529
Acknowledgments 529
References 529
23. Periplasmic Screening for Artificial Metalloenzymes 539
M. Jeschek, S. Panke, and T.R. Ward
1. Introduction 540
2. Anchoring Strategies 541
3. Increasing the Throughput 543
4. Advantages of Periplasmic Screening 544
5. Periplasmic Screening for ArMs 546
6. Summary 553
References 554
24. De Novo Designed Imaging Agents Based on Lanthanide
Peptides Complexes 557
A.F.A. Peacock
1. Introduction 558
2. Lanthanide Coordination Chemistry 558
3. Lanthanide Imaging Agents 558
4. Lanthanide Peptides and Proteins 560
5. Strategies for Designing CCs for Lanthanide Coordination 562
6. Conclusions and Perspectives 576
Acknowledgments 576
References 577
25. Peptide Binding for Bio-Based Nanomaterials 581
N.M. Bedford, C.J. Munro, and M.R. Knecht
1. Introduction 582
2. Materials 585
3. Methods 587
4. Conclusions 596
Acknowledgments 596
References 596
Author Index
Subject Index
599
639
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