Evolutionary Approaches to Protein Design
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Table of contents
- CONTENTSv
- PREFACEix
- Chapter 1. New Functions from Old Scaffolds: How Nature Reengineers Enzymes for New Functions1
- I. Introduction1
- II. Defining Protein Superfamilies3
- III. The Enolase Superfamily: A Paradigm for Understanding How Nature Evolved Enzymes for New Functi6
- IV. Studies of Other Superfamilies and Fold Classes21
- V. Conclusions26
- VI. References26
- Chapter 2. Evolution of Protein Functon by Domain Swapping29
- I. Introduction29
- II. Terminology30
- III. Evolution of Proteins in Nature by Domain Swapping31
- IV. Domain Swapping for Protein Engineering43
- V. Methodologies59
- VI. Perspective67
- References68
- Chapter 3. Rational Evolutionary Design: The Theory of In Vitro Protein Evolution79
- I. Introduction79
- II. Sequence Space and Fitness Landscapes81
- III. Modeling Directed Evolution97
- IV. Rational Evolutionary Design138
- V. Summary and Conclusions152
- References154
- Chapter 4. Temperature Adaptation of Enzymes: Lessons from Laboratory Evolution161
- I. Introduction161
- II. Influence of Temperature on Enzymes164
- III. Studies of Natural Extremophilic Enzymes167
- IV. Directed Evolution173
- V. Stability, Flexibility, and Catalytic Activity208
- VI. Why Are Proteins Marginally Stable?216
- VII. Why Are Thermophilic Enzymes Poorly Active at Low Temperature?218
- VIII. Conclusions219
- References221
- Chapter 5. Structural Analysis of Affinity Matured Antibodies and Laboratory-Evolved Enzymes227
- I. Introduction227
- II. Structural Studies of Antibody Affnity Maturation228
- III. Structural Studies of Enzyme Directed Evolution244
- IV. Conclusions254
- References257
- Chapter 6. Molecular Breeding: The Natural Approach to Protein Design261
- I. Introduction261
- II. The Need for Better Proteins263
- III. Strategies for Optimizing Proteins264
- IV. Screening Is Key277
- V. Beyond Proteins281
- VI. Concluding Remarks285
- References286
- Chapter 7. Analysis of Large Libraries of Protein Mutants Using Flow Cytometry293
- I. Introduction293
- II. Library Screening Technologies294
- III. Cell Surface Display Technologies301
- IV. Library Screening by Flow Cytometry303
- V. Concluding Remarks311
- References311
- Chapter 8. From Catalytic Asymmetric Synthesis to the Transcriptional Regulation of Genes: In Vivo a317
- I. Introduction and Scope of Review317
- II. Selecting and Evolving Therapeutic Human Antibodies318
- III. Directing Evolution at the Level of Chemical Mechanism: Aldolase Antibodies and Asymmetric Cata331
- IV. Multiple Hapten Selection: Refining the Active Site of a Catalytic Antibody by In Vitro Selectio349
- V. Selection and Evolution of Novel DNA-Binding Proteins: From Principles to Applications350
- References363
- Chapter 9. In Vitro Selection and Evolution of Proteins367
- I. Introduction367
- II. The Key to In Vitro Protein Evolution: Cell-Free Translation372
- III. In Vitro Selection Strategies374
- IV. Applications of Ribosome Display388
- V. Perspectives of Directed In Vitro Evolution398
- References399
- AUTHOR INDEX405
- SUBJECT INDEX429
This is the first high-quality, comprehensive overview of the field of evolutionary protein design. Topics include new protein design strategies, the structures of laboratory-evolved proteins, the evolution of non-natural enzyme functions, and the theory of laboratory evolution.