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Book Details
Abstract
The synergy between synthetic biology and biocatalysis is emerging as an important trend for future sustainable processes. This book reviews all modern and novel techniques successfully implemented in biocatalysis, in an effort to provide better performing enzymatic systems and novel biosynthetic routes to (non-)natural products. This includes the use of molecular techniques in protein design and engineering, construction of artificial metabolic pathways, and application of computational methods for enzyme discovery and design. Stress is placed on current ‘hot’ topics in biocatalysis, where recent advances in research are defining new grounds in enzyme-catalyzed processes. With contributions from leading academics around the world, this book makes a ground-breaking contribution to this progressive field and is essential reading for graduates and researchers investigating (bio)catalysis, enzyme engineering, chemical biology, and synthetic biology.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| Preface | vii | ||
| Contents | ix | ||
| Section I: Accessing New Enzymes | 1 | ||
| Chapter 1 Genome Mining for Enzyme Discovery | 3 | ||
| 1.1 Introduction | 3 | ||
| 1.2 Text-based Searches Using Enzyme Name | 5 | ||
| 1.3 Sequence-driven Approaches | 7 | ||
| 1.3.1 Probe Technology Based on PCR Primer Design | 7 | ||
| 1.3.2 Pairwise Sequence Alignment-based Strategy | 8 | ||
| 1.3.3 Signature-/Key Motif-based Strategy | 15 | ||
| 1.4 3D Structure-guided Approach | 18 | ||
| 1.4.1 Exploring 3D Structures of Proteins | 19 | ||
| 1.4.2 Active Site Topology/Constellation-guided Strategy | 19 | ||
| 1.5 Conclusion | 22 | ||
| References | 23 | ||
| Chapter 2 Exploiting Natural Diversity for Industrial Enzymatic Applications | 28 | ||
| 2.1 Introduction | 28 | ||
| 2.2 Screening Enzymes from Soil Microbes, Plants, and Animals (Millipede) by Activity Measurement | 29 | ||
| 2.2.1 Hydrolases | 30 | ||
| 2.2.2 Oxidoreductases | 30 | ||
| 2.2.3 Lyases | 32 | ||
| 2.3 Genetic Approaches to Natural Enzyme Sources | 34 | ||
| 2.3.1 Isomerases | 36 | ||
| 2.3.2 Oxidoreductases | 37 | ||
| 2.4 Creation of Amine Oxidase by Directed Evolution of D-Amino Acid Oxidase | 40 | ||
| 2.5 From Discovery to Application – Aldoxime Dehydratases | 41 | ||
| 2.5.1 Isolation, Characterization and Comparison of Aldoxime Dehydratases | 41 | ||
| 2.5.2 Iron Heme Redox Catalysis and Mechanistic Studies | 42 | ||
| 2.5.3 Substrate Spectrum of Aldoxime Dehydratases | 43 | ||
| 2.5.4 Application of Oxds for Nitrile Synthesis | 43 | ||
| 2.5.5 Perspectives | 48 | ||
| 2.6 Conclusion | 48 | ||
| Acknowledgements | 49 | ||
| References | 49 | ||
| Chapter 3 Artificial Metalloenzymes | 53 | ||
| 3.1 Introduction | 53 | ||
| 3.2 Direct Insertion of Inorganic Metal Ions into Proteins | 55 | ||
| 3.2.1 Carbonic Anhydrase | 55 | ||
| 3.2.2 Ferritin | 57 | ||
| 3.2.3 Serum Albumins | 57 | ||
| 3.2.4 Phytase and Other Proteins | 57 | ||
| 3.3 Supramolecular Anchoring of Metal Cofactors | 59 | ||
| 3.3.1 The \"Trojan-Horse\" Strategy | 59 | ||
| 3.3.2 The \"Host–Guest\" Strategy | 64 | ||
| 3.4 Covalent Linking of Metallic Cofactors to a Protein | 71 | ||
| 3.5 Cascade Reactions | 75 | ||
| 3.6 Conclusion | 79 | ||
| References | 81 | ||
| Chapter 4 Computational Enzyme Design: Successes, Challenges, and Future Directions | 88 | ||
| 4.1 Introduction | 88 | ||
| 4.2 Examples of Computational Enzyme Design | 91 | ||
| 4.2.1 Phase I: Initial Application of CPD Towards Enzyme Design | 91 | ||
| 4.2.2 Phase II: Incorporation of TransitionStates and Theozymes into Computational Enzyme Design | 96 | ||
| 4.3 Challenges in Computational Enzyme Design | 106 | ||
| 4.4 Future Directions | 107 | ||
| 4.5 Conclusions | 110 | ||
| Acknowledgements | 111 | ||
| References | 111 | ||
| Section II: Understanding and Engineering Enzymes | 117 | ||
| Chapter 5 Computational Techniques for Efficient Biocatalysis | 119 | ||
| 5.1 Introduction to Computational Biocatalysis | 119 | ||
| 5.1.1 Bioinformatic Tools | 122 | ||
| 5.1.2 Ancestral Gene Resurrection | 126 | ||
| 5.1.3 Structure-based Computational Tools | 128 | ||
| 5.1.4 QM Computational Tools | 129 | ||
| 5.1.5 Molecular Mechanics and Molecular Dynamics Computational Tools | 131 | ||
| 5.1.6 QM/MM | 132 | ||
| 5.2 Implementation of Computational Tools in Biocatalysis | 133 | ||
| 5.2.1 Identification of Novel Biocatalysts from Sequence Space | 133 | ||
| 5.2.2 Ancestral Enzyme Reconstruction for theStudy and Engineering of Binding and Catalysis | 135 | ||
| 5.3 Structural-based In Silico Modelling for Efficient Biocatalysis | 140 | ||
| 5.3.1 QM Is a Powerful Tool for the Elucidationof Reaction Mechanisms and Associated Energies in \"Frozen\" Models of the Active Site | 140 | ||
| 5.3.2 Molecular Dynamics Simulation Allowsfor the Study of Dynamical Aspects of Biocatalysis | 141 | ||
| 5.3.3 A Combination of QM and MM Allows for an Enhanced Understanding of Enzymes | 144 | ||
| 5.4 Conclusion | 146 | ||
| Disclosure | 146 | ||
| Acknowledgements | 146 | ||
| References | 146 | ||
| Chapter 6 Modulating Enzyme Activity via Incorporation of Non-canonical Amino Acids | 153 | ||
| 6.1 Introduction | 153 | ||
| 6.2 Residue-specific vs. Site-specific UAA Incorporation | 155 | ||
| 6.2.1 Residue-specific UAA Incorporation | 155 | ||
| 6.2.2 Site-specific UAA Incorporation | 156 | ||
| 6.2.3 In Vitro and In Vivo UAA Incorporation | 158 | ||
| 6.3 Engineering tRNA Synthetases for UAA Incorporation | 158 | ||
| 6.4 Enzyme Engineering with UAAs | 159 | ||
| 6.4.1 UAAs for Increased Protein Thermostability | 159 | ||
| 6.4.2 UAAs for Increased Catalytic Efficiency | 161 | ||
| 6.4.3 UAAs to Alter Specificity and Selectivity | 164 | ||
| 6.4.4 UAAs to Probe Enzyme Function and Mechanism | 166 | ||
| 6.4.5 UAAS to Control Enzyme Activity and Interactions | 168 | ||
| 6.4.6 UAAs for Chemical Modification of Enzymes | 169 | ||
| 6.4.7 Engineering Enzymes for UAA Biosynthesis | 171 | ||
| 6.5 Future Perspectives | 171 | ||
| 6.6 Conclusion | 172 | ||
| Acknowledgements | 172 | ||
| References | 173 | ||
| Chapter 7 Enhancing Enzymatic Performance via Restricted Sequence Space Approaches | 178 | ||
| 7.1 Background and Scope | 178 | ||
| 7.2 Variant Generation via Restriction of Sequence Space | 180 | ||
| 7.2.1 Restricted Sequence Space via Restricted Codon Libraries | 180 | ||
| 7.2.2 Restricted Sequence Space via Selection of Mutation Sites: Focused Libraries | 184 | ||
| 7.3 Variant Generation via Molecular Biology Protocols | 188 | ||
| 7.3.1 Gene Splicing by Overlap Extension | 188 | ||
| 7.3.2 In Vivo Overlap Extension | 189 | ||
| 7.3.3 Omnichange | 189 | ||
| 7.3.4 Circular Permutation | 191 | ||
| 7.4 Some Computational Design Tools | 191 | ||
| 7.4.1 Statistical Coupling Analysis (SCA) | 191 | ||
| 7.4.2 ProSAR | 191 | ||
| 7.4.3 Structure-guided Recombination (SCHEMA) | 192 | ||
| 7.4.4 Strong Neutral Drift | 194 | ||
| 7.5 Examples of Developed Biocatalysts in Industrial Setting | 194 | ||
| 7.5.1 Sitagliptin (Combination of ProSAR and CAPS) | 194 | ||
| 7.5.2 Montelukast (Singulairs) Using ProSAR | 195 | ||
| 7.6 Conclusions | 198 | ||
| Acknowledgements | 198 | ||
| References | 198 | ||
| Section III: Enzymes from Secondary Metabolism | 203 | ||
| Chapter 8 Customizing Transcription-factor Biosensors for Modern Biotechnology | 205 | ||
| 8.1 Introduction | 205 | ||
| 8.2 Introduction to Transcription Factor Engineering | 208 | ||
| 8.2.1 Diversity of Transcription Factor Structure, Function, and Ligand Repertoire | 208 | ||
| 8.2.2 Reporter Systems, Range of Throughput, and Scope of Biosensor Hosts | 209 | ||
| 8.2.3 Overview of Biosensor-driven Applications | 211 | ||
| 8.2.4 Quantitative Description of the Activity and Properties of Transcriptional Factors | 212 | ||
| 8.3 Allostery in Transcriptional Regulators | 213 | ||
| 8.4 Engineering the Sensitivity and Dynamic Range of Transcription Factors | 214 | ||
| 8.5 Engineering the Ligand Specificity of Transcription Factors | 216 | ||
| 8.5.1 Expanding Specificity Towards Non-native Ligands | 217 | ||
| 8.5.2 Engineering the Ligand Selectivity of Transcription Factors | 223 | ||
| 8.6 Conclusions and Future Outlook | 226 | ||
| Acknowledgements | 227 | ||
| References | 227 | ||
| Chapter 9 Exploiting Biosynthetic Pathways in Fungi: Opportunities for Enhanced or Novel Production | 234 | ||
| 9.1 Introduction | 234 | ||
| 9.2 Impacts of the Genetic and Then Genomic Era on Pathway Discovery | 237 | ||
| 9.3 Reshaping Regulatory Networks | 238 | ||
| 9.3.1 Exploiting Pathway-specific Regulators | 240 | ||
| 9.3.2 Exploiting Genome-wide Regulators | 241 | ||
| 9.3.3 Spatial Regulation | 243 | ||
| 9.4 Heterologous Production of Compounds | 244 | ||
| 9.4.1 S. cerevisiae as a Host | 244 | ||
| 9.4.2 Filamentous Fungi as Hosts | 246 | ||
| 9.5 Developing Novel Products | 250 | ||
| 9.5.1 Manipulation of the Core Megasynthases for New Core Molecules | 250 | ||
| 9.5.2 Novelty via Feeding or Semi-synthesis | 254 | ||
| 9.6 Conclusion | 254 | ||
| Acknowledgements | 255 | ||
| References | 255 | ||
| Chapter 10 Engineering Enzymes for Natural Product Biosynthesis and Diversification | 261 | ||
| 10.1 Introduction | 261 | ||
| 10.2 In Vivo Engineering of NRP and PK Biosynthetic Pathways | 263 | ||
| 10.2.1 Building Monomer Alteration | 263 | ||
| 10.2.2 Chimeric Domains and Domain Swapping | 267 | ||
| 10.2.3 Conclusion on In Vivo Engineering | 269 | ||
| 10.3 In Vitro Reconstitution and Engineering of NRP and PK Biosynthetic Pathways | 270 | ||
| 10.3.1 Nonnative Building MonomerIncorporation through In Vitro Biosynthesis | 271 | ||
| 10.3.2 In Vitro Biosynthesis Using Promiscuous Off-loading Enzymes for Macrocyclization | 272 | ||
| 10.3.3 Domain Swapping In Vitro | 273 | ||
| 10.3.4 Conclusion on In Vitro Reconstitution and Engineering | 273 | ||
| 10.4 Directed Evolution of NRPSs and PKSs | 274 | ||
| 10.4.1 Mutagenesis Strategies for Constructing NRPS and PKS Mutant Libraries | 274 | ||
| 10.4.2 Screening of NRPS and PKSMutant Libraries | 276 | ||
| 10.4.3 Conclusions on Directed Evolution of NRPSs and PKSs | 280 | ||
| References | 280 | ||
| Chapter 11 Impact of Synthetic Biology on Secondary Metabolite Biosynthesis | 287 | ||
| 11.1 Introduction | 287 | ||
| 11.2 Host and Heterologous Strain Improvement | 290 | ||
| 11.2.1 Genome Reduction | 290 | ||
| 11.2.2 Regulatory Network Engineering | 291 | ||
| 11.3 Genetic Refactoring | 293 | ||
| 11.4 DNA Manipulation Technologies | 296 | ||
| 11.5 Natural Product Discovery in the Post-genomic Era | 298 | ||
| 11.6 Precursor Supplementation | 300 | ||
| 11.7 Compartmentalization | 304 | ||
| 11.8 Combinatorial Biosynthesis | 306 | ||
| 11.9 Concluding Remarks | 309 | ||
| References | 309 | ||
| Section IV: Biocatalysis for Modern Synthesis | 321 | ||
| Chapter 12 Self-contained Biocatalysts | 205 | ||
| 12.1 Introduction | 323 | ||
| 12.1.1 The \"One-enzyme\" Solution | 323 | ||
| 12.1.2 The \"Two-enzyme Solution | 325 | ||
| 12.1.3 Whole Microbial Cells | 326 | ||
| 12.1.4 Self-contained Biocatalysis | 327 | ||
| 12.2 Chimeric Enzymes | 328 | ||
| 12.2.1 Cytochrome P450's | 328 | ||
| 12.2.2 Baeyer–Villiger Monooxygenases | 330 | ||
| 12.2.3 Amino Acid Dehydrogenases | 332 | ||
| 12.2.4 3-Ketoacyl-carrier-protein Reductase | 333 | ||
| 12.3 Engineered Whole Cells | 333 | ||
| 12.3.1 Cytochrome P450's | 335 | ||
| 12.3.2 Ketoreductases | 338 | ||
| 12.3.3 Amino Acid Dehydrogenase | 342 | ||
| 12.3.4 NAD1 Regeneration | 342 | ||
| 12.3.5 Non-E. coli Systems | 345 | ||
| 12.4 Conclusions | 348 | ||
| References | 348 | ||
| Chapter 13 Designing Multi-enzymatic Systems for the Preparation of Optically Active Molecules | 351 | ||
| 13.1 Introduction | 351 | ||
| 13.2 Multi-enzymatic Linear Cascades | 354 | ||
| 13.2.1 Synthesis of Chiral Hydroxy-functionalised Compounds | 354 | ||
| 13.2.2 Synthesis of Chiral Amino-functionalised Compounds | 362 | ||
| 13.2.3 Synthesis of Chiral Cyclic Carboxylic Acid Derivatives | 369 | ||
| 13.2.4 Synthesis of Natural Product Derivatives | 372 | ||
| 13.3 Multi-enzymatic Orthogonal Cascades | 373 | ||
| 13.4 Multi-enzymatic Parallel Cascades | 373 | ||
| 13.5 Multi-enzymatic Cyclic Cascades | 374 | ||
| 13.6 Other Multi-enzymatic Systems | 377 | ||
| 13.6.1 Enantioconvergent Processes | 377 | ||
| 13.6.2 Dynamic Kinetic Resolutions (DKRs) | 378 | ||
| 13.7 Summary and Outlook | 380 | ||
| Acknowledgements | 381 | ||
| References | 381 | ||
| Chapter 14 Artificial Biocatalytic Cascades to Alcohols and Amines | 387 | ||
| 14.1 Introduction | 387 | ||
| 14.2 Alcohols | 389 | ||
| 14.2.1 Alcohol Dehydrogenases | 389 | ||
| 14.2.2 Phosphatases and Epoxide Hydrolases | 395 | ||
| 14.3 Amines | 399 | ||
| 14.3.1 Transaminases | 399 | ||
| 14.3.2 Amine Dehydrogenases and Imine Reductases | 419 | ||
| 14.3.3 C–C Bond-forming Enzymes Leading to Chiral Amines | 428 | ||
| 14.4 Conclusion | 432 | ||
| Acknowledgements | 432 | ||
| References | 432 | ||
| Chapter 15 Emerging Fields in One-pot Multi-step Synthesis with Combined Chemo- and Bio-catalysts: Sequential- and Domino-type Process Concepts as well as Compartmentation Strategies | 439 | ||
| 15.1 Introduction and Current Status Overview | 439 | ||
| 15.2 Overview of Selected Current Emerging Fields | 440 | ||
| 15.3 New Sequential-type Chemoenzymatic One-pot Syntheses | 442 | ||
| 15.3.1 Introduction and Overview | 442 | ||
| 15.3.2 Emerging Fields and Selected RecentExamples of Sequential-type Chemoenzymatic One-pot Syntheses | 442 | ||
| 15.4 New Tandem-type (Domino-type) Chemoenzymatic One-pot Syntheses | 444 | ||
| 15.4.1 Introduction and Overview | 444 | ||
| 15.4.2 Novel Dynamic Kinetic Resolutions:Expanded Substrate Scope and Process Concepts | 446 | ||
| 15.4.3 Domino-type Cascade Processes withConcurrently Running Chemo-and Biocatalytic Steps | 451 | ||
| 15.4.4 Related One-pot Processes withSimultaneously Interacting Chemo-and Biocatalysts | 455 | ||
| 15.5 The Concept of Compartmentation forCombination of Chemo-and Biocatalytic Steps Towards One-pot Syntheses | 458 | ||
| 15.5.1 Introduction and Overview:Compartmentation Strategies inChemoenzymatic One-pot Syntheses and Size Scale of Compartments | 458 | ||
| 15.5.2 Nanoscale Reactor Compartmentation | 458 | ||
| 15.5.3 Process Engineering Strategies inChemoenzymatic One-pot Syntheses:Use of One Liquid Medium andCompartmentation in Different Reactor Segments in a Flow Process | 461 | ||
| 15.5.4 Microscopic Compartmentation of Catalysts in Polymer Beads/Particles | 463 | ||
| 15.5.5 Macroscopic Compartmentation of Reaction Media | 464 | ||
| 15.6 Summary | 468 | ||
| References | 469 | ||
| Section V: Applied Biocatalysis | 473 | ||
| Chapter 16 Technical Biocatalysis | 475 | ||
| 16.1 Enzyme Catalysis: The Route from Degradation to Synthesis | 475 | ||
| 16.2 Organic Synthesis: Chemical or Enzymatic? | 478 | ||
| 16.3 Enzyme Catalysis in Organic Synthesis. SWOT Analysis | 481 | ||
| 16.4 Enzyme Catalysis in Non-conventional Media | 485 | ||
| 16.4.1 Enzyme Catalysis in Organic Solvents | 485 | ||
| 16.4.2 Enzyme Catalysis in Other Non-conventional Media | 488 | ||
| 16.4.3 Strategies for Building-up Enzyme Biocatalysts for Organic Synthesis | 492 | ||
| 16.4.4 Industrial Perspective of EnzymeCatalysis: Reality, Challenges and Opportunities | 500 | ||
| References | 503 | ||
| Chapter 17 Biocatalytic Process Engineering | 516 | ||
| 17.1 Introduction | 516 | ||
| 17.2 Types of Biocatalytic Process | 518 | ||
| 17.3 Requirements for Implementing a Scalable Industrial Process | 519 | ||
| 17.3.1 Reaction Yield and Process Yield | 521 | ||
| 17.3.2 Biocatalyst Yield | 522 | ||
| 17.3.3 Productivity | 523 | ||
| 17.3.4 Product Concentration | 524 | ||
| 17.4 Biocatalytic Process Technology | 525 | ||
| 17.4.1 Biocatalytic Reactor Options | 525 | ||
| 17.4.2 Downstream Processing | 526 | ||
| 17.4.3 Special Cases Deserving of Particular Attention | 527 | ||
| 17.5 Technology Toolbox for the Development of Biocatalytic Processes | 528 | ||
| 17.5.1 Biocatalyst Engineering | 528 | ||
| 17.5.2 Biocatalyst Immobilization | 528 | ||
| 17.5.3 Reaction Engineering | 530 | ||
| 17.5.4 Process Engineering | 531 | ||
| 17.6 Systematic and Accelerated Process Development | 533 | ||
| 17.7 Future Perspectives | 535 | ||
| References | 535 | ||
| Chapter 18 Enzymes for Detection and Decontamination of Chemical Warfare Agents | 539 | ||
| 18.1 Introduction | 539 | ||
| 18.2 Chemical Warfare Agents | 541 | ||
| 18.2.1 Nerve Agents | 542 | ||
| 18.2.2 Blister Agents | 542 | ||
| 18.2.3 Other Agents | 545 | ||
| 18.2.4 Decontamination of Chemical Warfare Agents | 545 | ||
| 18.3 Enzymes in Decontamination of Warfare Chemicals | 547 | ||
| 18.3.1 Enzymes Converting Nerve Agents | 547 | ||
| 18.3.2 Enzymes Converting Blister Agents | 554 | ||
| 18.4 Practical Applications of Enzymes Converting Warfare Chemicals | 555 | ||
| 18.5 Conclusions and Perspectives | 558 | ||
| Acknowledgements | 560 | ||
| References | 560 | ||
| Subject Index | 566 |