Protein engineering : tools and applications / edited by Huimin Zhao. -- Weinheim, Germany : Wiley-VCH, 2021. --- (82.95/P967)

Contents

Part I  Directed Evolution  1
1      Continuous Evolution of Proteins In Vivo  3
1.1    Introduction 3
1.2    Challenges in Achieving In Vivo Continuous Evolution  5
1.3    Phage-Assisted Continuous Evolution (PACE)  10
1.4    Systems That Allow In Vivo Continuous Directed Evolution  13
1.5    Conclusion 22
        References  22
2      In Vivo Biosensors for Directed Protein Evolution  29
2.1    Introduction 29
2.2    Nucleic Acid-Based In Vivo Biosensors for Directed Protein Evolution  32
2.3    Protein-Based In Vivo Biosensors for Directed Protein Evolution  37
2.4    Characteristics of Biosensors for In Vivo Directed Protein Evolution  44
2.5    Conclusions and Future Perspectives  45
        Acknowledgments  46
        References  46
3      High-Throughput Mass Spectrometry Complements Protein Engineering 57
3.1    Introduction  57
3.2    Procedures and Instrumentation for MS-Based Protein Assays  59
3.3    Technology Advances Focusing on Throughput Improvement 62
3.4    Applications of MS-Based Protein Assays: Summary 63
3.5    Conclusions and Perspectives  68
       Acknowledgments  68
       References  69
4      Recent Advances in Cell Surface Display Technologies for Directed Protein Evolution  81
4.1    Cell Display Methods  81
4.2    Selection Methods and Strategies  86
4.3    Modifications of Cell Surface Display Systems  89
4.4    Recent Advances to Expand Cell-Display Directed Evolution Techniques  93
4.5    Conclusion and Outlook 96
       References 97
5      Iterative Saturation Mutagenesis for Semi-rational Enzyme Design 105
5.1    Introduction  105
5.2    Recent Methodology Developments in ISM-Based Directed Evolution  108
5.3    B-FIT as an ISM Method for Enhancing Protein Thermostability 120
5.4    Learning from CAST/ISM-Based Directed Evolution  121
5.5    Conclusions and Perspectives. 121
       Acknowledgment  124
       References  124
Part II  Rational and Semi-Rational Design  133
6      Data-driven Protein Engineering  135
6.1    Introduction  135
6.2    The Data Revolution in Biology  136
6.3    Statistical Representations of Protein Sequence, Structure, and Function  138
6.4    Learning the Sequence-Function Mapping from Data  141
6.5    Applying Statistical Models to Engineer Proteins  145
6.6    Conclusions and Future Outlook 147
       References  148
7      Protein Engineering by Efficient Sequence Space Exploration Through Combination of Directed Evolution and Computational Design Methodologies 153
7.1    Introduction  153
7.2    Protein Engineering Strategies  154
7.3    Conclusions and Future Perspectives  171
       Acknowledgments  171
       References  171
8      Engineering Artificial Metalloenzymes 177
8.1    Introduction  177
8.2    Rational Design  177
8.3    Engineering Artificial Metalloenzyme by Directed Evolution in Combination with Rational Design  188
8.4    Summary and Outlook 200
       Acknowledgment  201
       References  201
9      Engineered Cytochromes P450 for Biocatalysis 207
9.1    Cytochrome P450 Monooxygenases  207
9.2    Engineered Bacterial P450s for Biocatalytic Applications 210
9.3    High-throughput Methods for Screening Engineered P450s 227
9.4    Engineering of Hybrid P450 Systems 229
9.5    Engineered P450s with Improved Thermostability and Solubility  230
9.6    Conclusions  231
       Acknowledgments 232
       References  232
Part III Applications in Industrial Biotechnology 243
10     Protein Engineering Using Unnatural Amino Acids 245
10.1   Introduction 245
10.2   Methods for Unnatural Amino Acid Incorporation 246
10.3   Applications of Unnatural Amino Acids in Protein Engineering 247
10.4   Outlook 256
10.5   Conclusions  258
       References  258
11     Application of Engineered Biocatalysts for the Synthesis of Active Pharmaceutical Ingredients (APIs) 265
11.1   Introduction 265
11.2   Conclusions  282
       References 287
12     Directing Evolution of the Fungal Ligninolytic Secretome 295
12.1   The Fungal Ligninolytic Secretome 295
12.2   Functional Expression in Yeast  297
12.3   Yeast as a Tool-Box in the Generation of DNA Diversity 302
12.4   Bringing Together Evolutionary Strategies and Computational Tools 305
12.5   High-Throughput Screening (HTS) Assays for Ligninase Evolution  306
12.6   Conclusions and Outlook  309
       Acknowledgments  309
       References 310
13     Engineering Antibody-Based Therapeutics: Progress and Opportunities 317
13.1   Introduction  317
13.2   Antibody Formats 318
13.3   Antibody Discovery 322
13.4   Therapeutic Optimization of Antibodies 328
13.5   Manufacturability of Antibodies  336
13.6   Conclusions  339
       Acknowledgments  339
       References 339
14     Programming Novel Cancer Therapeutics: Design Principles for Chimeric Antigen Receptors 353
14.1   Introduction 353
14.2   Metrics to Evaluate CART Cell Function  354
14.3   Antigen-Recognition Domain  356
14.4   Extracellular Spacer  360
14.5   Transmembrane Domain 362
14.6   Signaling Domain  362
14.7   High-Throughput CAR Engineering 366
14.8   Novel Receptor Modalities  367
       References  369
Part IV Applications in Medical Biotechnology 377
15     Development of Novel Cellular Imaging Toots Using Protein Engineering  379
15.1   Introduction  379
15.2   Cellular Imaging Tools Developed by Protein Engineering 380
15.3   Application in Cellular Imaging 386
15.4   Conclusion and Perspectives  393
       References 394
Index 403