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An authoritative and up-to-date discussion of enzyme engineering and its applications In Enzyme Engineering: Selective Catalysts for Applications in Biotechnology, Organic Chemistry, and Life Science, a team of distinguished researchers deliver a robust treatment of enzyme engineering and its applications in various fields such as biotechnology, life science, and synthesis. The book begins with an introduction to different protein engineering techniques, covers topics like gene mutagenesis methods for directed evolution and rational enzyme design. It includes industrial case studies of enzyme engineering with a focus on selectivity and activity. The authors also discuss new and innovative areas in the field, involving machine learning and artificial intelligence. It offers several insightful perspectives on the future of this work. Readers will also find: A thorough introduction to directed evolution and rational design as protein engineering techniques Comprehensive explorations of screening and selection techniques, gene mutagenesis methods in directed evolution, and guidelines for applying gene mutagenesis in organic chemistry, pharmaceutical applications, and biotechnology Practical discussions of protein engineering of enzyme robustness relevant to organic and pharmaceutical chemistry Treatments of artificial enzymes as promiscuous catalysts Various lessons learned from semi-rational and rational directed evolution A transdisciplinary treatise, Enzyme Engineering: Selective Catalysts for Applications in Biotechnology, Organic Chemistry, and Life Science is perfect for protein engineers, theoreticians, organic, and pharmaceutical chemists as well as transition metal researchers in catalysis and biotechnologists.

Contents Preface IX About the Authors XI 1 Introduction to Directed Evolution and Rational Design as Protein Engineering Techniques 1 1.1 Methods and Aims of Directed Enzyme Evolution 1 1.2 History of Directed Enzyme Evolution 4 1.3 Methods and Aims of Rational Design of Enzymes 19 References 21 2 Screening and Selection Techniques 29 2.1 Introductory Remarks 29 2.2 Screening Methods 29 2.3 Selection Methods 38 2.4 Conclusions and Perspectives 52 References 53 3 Gene Mutagenesis Methods in Directed Evolution and Rational Enzyme Design 59 3.1 Introductory Remarks 59 3.2 Directed Evolution Approaches 59 3.2.1 Mutator Strains 59 3.2.2 Error-Prone Polymerase Chain Reaction (epPCR) 60 3.2.3 Whole Gene Insertion/Deletion Mutagenesis 66 3.2.4 Saturation Mutagenesis as a Privileged Method: Away from Blind Directed Evolution 73 3.2.5 DNA Shuffling and Related Recombinant Gene Mutagenesis Methods 89 3.2.6 Circular Mutation and Other Domain Swapping Techniques 94 3.2.7 Solid-Phase Combinatorial Gene Synthesis as a PCR-Independent Mutagenesis Method for Mutant Library Creation 96 3.2.8 Computational Tools and the Role of Machine Learning (ML) in Directed Evolution and Rational Enzyme Design 102 3.3 Diverse Approaches to Rational Enzyme Design 112 3.3.1 Introductory Remarks 112 3.4 Merging Semi-rational Directed Evolution and Rational Enzyme Design by Focused Rational Iterative Site-Specific Mutagenesis (FRISM) 114 3.5 Conclusions and Perspectives 120 References 120 4 Guidelines for Applying Gene Mutagenesis Methods in Organic Chemistry, Pharmaceutical Applications, and Biotechnology 141 4.1 Some General Tips 141 4.1.1 Rational Design 141 4.1.2 Directed Evolution 149 4.2 Rare Cases of Comparative Directed Evolution Studies 152 4.2.1 Converting a Galactosidase into a Fucosidase 152 4.2.2 Enhancing and Inverting the Enantioselectivity of the Lipase from Pseudomonas aeruginosa (PAL) 156 4.3 Choosing the Best StrategyWhen Applying Saturation Mutagenesis 163 4.3.1 General Guidelines 163 4.3.2 Choosing Optimal Pathways in Iterative Saturation Mutagenesis (ISM) and Escaping from Local Minima in Fitness Landscapes 168 4.3.3 Systematization of Saturation Mutagenesis with Further Practical Tips 174 4.3.4 Single Code Saturation Mutagenesis (SCSM): Use of a Single Amino Acid as Building Block 183 4.3.5 Triple Code Saturation Mutagenesis (TCSM): A Viable Compromise When Choosing Optimal Reduced Amino Acid Alphabets in CAST/ISM 185 4.4 Techno-economical Analysis of Saturation Mutagenesis Strategies 187 4.5 Generating Mutant Libraries by Combinatorial Solid-Phase Gene Synthesis: The Future of Directed Evolution? 190 4.6 Fusing Directed Evolution and Rational Design: New Examples of Focused Rational Iterative Site-Specific Mutagenesis (FRISM) 192 References 194 5 Tables of Selected Examples of Directed Evolution and Rational Design of Enzymes with Emphasis on Stereo- and Regio-selectivity, Substrate Scope and/or Activity 203 5.1 Introductory Explanations 203 References 220 6 Protein Engineering of Enzyme Robustness Relevant to Organic and Pharmaceutical Chemistry and Applications in Biotechnology 233 6.1 Introductory Remarks 233 6.2 Rational Design of Enzyme Thermostability and Resistance to Hostile Organic Solvents 234 6.3 Ancestral and Consensus Approaches and Their Structure-Guided Extensions 241 6.4 Further Computationally Guided Methods for Protein Thermostabilization 242 6.4.1 SCHEMA Approach 243 6.4.2 FRESCO Approach 245 6.4.3 FireProt Approach 247 6.4.4 Constrained Network Analysis (CNA) Approach 249 6.4.5 Alternative Approaches 251 6.5 Directed Evolution of Enzyme Thermostability and Resistance to Hostile Organic Solvents 253 6.6 Application of epPCR and DNA Shuffling 255 6.7 Saturation Mutagenesis in the B-FIT Approach 258 6.8 Iterative Saturation Mutagenesis (ISM) at Protein–Protein Interfacial Sites for Multimeric Enzymes 263 6.9 Conclusions and Perspectives 265 References 265 7 Artificial Enzymes as Promiscuous Catalysts in Organic and Pharmaceutical Chemistry 279 7.1 Introductory Background Information 279 7.2 Applying Protein Engineering for Tuning the Catalytic Profile of Promiscuous Enzymes 285 7.3 Applying Protein Engineering to P450 Monooxygenases for Manipulating Activity and Stereoselectivity of Promiscuous Transformations 299 7.4 Conclusions and Perspectives 307 References 308 8 Learning Lessons from Protein Engineering 317 8.1 Introductory Remarks 317 8.2 Additive Versus Nonadditive Mutational Effects in Fitness Landscapes Revealed by Partial or Complete Deconvolution 318 8.3 Unexplored Chiral Fleeting Intermediates and Their Role in Protein Engineering 327 8.4 Case Studies Featuring Mechanistic, Structural, and/or Computational Analyses of the Source of Evolved Stereo- and/or Regioselectivity 329 8.4.1 Esterase 329 8.4.2 Epoxide Hydrolase 331 8.4.3 Ene-reductase of the Old Yellow Enzyme (OYE) 335 8.4.4 Cytochrome P450 Monooxygenase 343 8.4.5 Analysis of Baeyer–Villiger Monooxygenase with Consideration of Fleeting Chiral Intermediates 350 8.5 Conclusions and Suggestions for Further TheoreticalWork 358 References 360 9 Perspectives for Future Work 367 9.1 Introductory Remarks 367 9.2 Extending Applications in Organic and Pharmaceutical Chemistry 367 9.3 Extending Applications in Biotechnology 372 9.4 Patent Issues 376 9.5 Final Comments 376 References 377 Index 381

Manfred T. Reetz is Emeritus Professor at the Max-Planck-Institut für Kohlenforschung in Mülheim/Germany. He is a synthetic organic chemist who pioneered the concept of directed evolution of stereo- and regioselective enzymes as a prolific source of catalysts in organic chemistry and biotechnology. Zhoutong Sun, PhD, is Full Professor at Tianjin Institute of Industrial Biotechnology at the Chinese Academy of Sciences. His research interests include enzyme engineering,metabolic engineering and synthetic biology. Ge Qu, PhD, is Associated Professor at the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences/China and member of the Sun group. He specializes in computational enzyme design and biocatalysis.

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