Protein engineering handbook. (2009)

PREFACE DIRIGENT EFFECTS IN BIOCATALYSIS Introduction Dirigent Proteins Solvents and Unconventional Reaction Media Structure and Folding Structured and Unstructured Domains Isozymes, Moonlighting Proteins, and Promiscuity: Supertalented Enzymes Conclusions PROTEIN ENGINEERING GUIDED BY NATURAL DIVERSITY Approaches Protocols Future Directions Conclusions PROTEIN ENGINEERING USING EUKARYOTIC EXPRESSION SYSTEMS Introduction Eukaryotic Expression Systems Conclusions PROTEIN ENGINEERING IN MICRODROPLETS Introduction Droplet Formats Perspectives FOLDING AND DYNAMICS OF ENGINEERED PROTEINS Introduction Proof-of-Principle Protein Designs Proteins Designed for Function Conclusions and Outlook ENGINEERING PROTEIN STABILITY Introduction Power and Scope of Protein Engineering to Enhance Stability Measurement of a Protein's Kinetic Stability Developments in Protein Stabilization ENZYMES FROM THERMOPHILIC ORGANISMS Introduction Hyperthermophiles Enzymes from Thermophiles and Their Reactions Production of Proteins from (Hyper)Thermophiles Protein Engineering of Thermophilic Proteins Cell Engineering in Hyperthermophiles Future Perspectives ENZYME ENGINEERING BY COFACTOR REDESIGN Introduction Natural Cofactors: Types, Occurrence, and Chemistry Inorganic Cofactors Organic Cofactors Redox Cofactors Concluding Remarks BIOCATALYST IDENTIFICATION BY ANAEROBIC HIGH-THROUGHPUT SCREENING OF ENZYME LIBRARIES AND ANAEROBIC MICROORGANISMS Introduction Oxygen-Sensitive Biocatalysts Biocatalytic Potential of Oxygen-Sensitive Enzymes and Microorganisms Anaerobic High-Throughput Screening Conclusions and Outlook ORGANOMETALLIC CHEMISTRY IN PROTEIN SCAFFOLDS Introduction Protocol/Practical Considerations Goals Summary ENGINEERING PROTEASE SPECIFICITY Introduction Protocol and Practical Considerations Concepts, Challenges, and Visions on Future Developments POLYMERASE ENGINEERING: FROM PCR AND SEQUENCING TO SYNTHETIC BIOLOGY Introduction PCR Sequencing Polymerase Engineering Strategies Synthetic Informational Polymers ENGINEERING GLYCOSYLTRANSFERASES Introduction to Glycosyltransferases Glycosyltransferase Sequence, Structure, and Mechanism Examples of Glycosyltransferase Engineering Practical Considerations for Screening Glycosyltransferases Future Directions and Outlook PROTEIN ENGINEERING OF CYTOCHROME P450 MONOOXYGENASES Cytochrome P450 Monooxygenases Engineering of P450 Monooxygenases Conclusions PROGRESS AND CHALLENGES IN COMPUTATIONAL PROTEIN DESIGN Introduction The Technique of Computational Protein Design Protein Core Redesign, Structural Alterations, and Thermostabilization Computational Enzyme Design Computational Protein - Protein Interface Design Computational Redesign of DNA Binding and Specificity Conclusions SIMULATION OF ENZYMES IN ORGANIC SOLVENTS Enzymes in Organic Solvents Molecular Dynamics Simulations of Proteins and Solvents The Role of the Solvent Simulation of Protein Structure and Flexibility Simulation of Catalytic Activity and Enantioselectivity Simulation of Solvent-Induced Conformational Transitions Challenges The Future of Biocatalyst Design ENGINEERING OF PROTEIN TUNNELS: THE KEYHOLE - LOCK - KEY MODEL FOR CATALYSIS BY ENZYMES WITH BURIED ACTIVE SITES Traditional Models of Enzymatic Catalysis Definition of the Keyhole - Lock - Key Model Robustness and Applicability of the Keyhole - Lock - Key Model Evolutionary and Functional Implications of the Keyhole - Lock - Key Model Engineering Implications of the Keyhole - Lock - Key Model Software Tools for the Rational Engineering of Keyholes Case Studies with Haloalkane Dehalogenases Conclusions INDEX