Protein engineering handbook 2

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Datensatz im Suchindex

DE-BY-TUM_call_number 0304 CHE 820b 2008 A 9640
1302 CHE 820b 2009 A 8843
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adam_text Contents XIII Volume 2 16 A Method for Rapid Directed Evolution 409 Manfred T. Reetz 16.1 Introduction 409 16.2 Focused Libraries Generated by Saturation Mutagenesis 414 16.3 Iterative Saturation Mutagenesis 416 16.3.1 General Concept 416 16.3.2 Combinatorial Active-Site Saturation Test (CAST) as a Means to Control Substrate Acceptance and/or Enantioselectivity 418 16.3.3 B-Factor Iterative Test (B-FIT) as a Means to Increase Thermostability 425 16.3.4 Practical Hints for Applying ISM 430 16.4 Conclusions 430 References 431 XIV Contents 17 Evolution of Enantioselective Bacillus subtilis Lipase 441 Thorsten Eggert, Susanne A. Funke, Jennifer N. Andexer, Manfred T. Reetz and Karl-Erich Jaeger 17.1 Introduction 441 Yl .2 Directed Evolution of Enantioselective Lipase from Badllus subtilis 444 17.3 Directed Evolution by Error-Prone PCR 445 17 A Complete Site-Saturation Mutagenesis 446 17.5 Conclusions 448 References 449 18 Circular Permutation of Proteins 453 Clenna E. Meister, Manu Kanwar, and Marc Ostermeier 18.1 Introduction 453 18.2 Evolution of Circular Permutations in Nature 454 18.2.1 Naturally Occurring Circular Permutations 454 18.2.2 Identification of Natural Circular Permutations 455 18.2.3 Mechanisms of Circular Permutation 457 18.3 Artificial Circular Permutations 459 18.3.1 Early Studies 459 18.3.2 Systematic and Random Circular Permutation 460 18.3.3 Protein Folding and Stability 462 18.4 Circular Permutation and Protein Engineering 463 18.4.1 Alteration of the Spatial Arrangement of Protein Fusions 463 18.4.2 Oligomeric State Modification 464 18.4.3 Improvement of Function 465 18.4.4 Creation of Protein Switches 466 18.4.5 Protein Crystallization 467 18.5 Perspective 468 Acknowledgments 468 References 468 19 Incorporating Synthetic Oligonucleotides via Cene Reassembly (ISOR): A Versatile Tool for Generating Targeted Libraries 473 Asael Herman ond Dan S. Tawfik 19.1 Introduction 473 19.1.1 Background 473 19.1.2 Overview of the Method 474 19.1.3 Applications 475 19.2 Materials 475 19.2.1 DNasel Digestion 475 19.2.2 Assembly 476 19.2.3 Magnetic Separation and Product Amplification 476 19.3 Methods 476 19.3.1 DNasel Digestion 476 Contents IXV 19.3.2 Assembly 477 19.3.3 Magnetic Separation and Product Amplification 477 19.4 Notes 478 Acknowledgments 479 References 479 20 Protein Engineering by Structure-Guided SCHEMA Recombination 481 Cloria Saab-Rincon, Yougen Li, Michelle Meyer, Martina Carbone, Marco Landwehr, and Frances H. Arnold 20.1 Introduction 481 20.1.1 SCHEMA Recombination of Proteins: Theoretical Framework 481 20.1.2 Comparison of SCHEMA with Other Guided-Recombination Methods 483 20.1.3 Practical Guidelines for SCHEMA Recombination 485 20.2 Examples of Chimeric Libraries Designed Using the SCHEMA Algorithm 485 20.2.1 SCHEMA Recombination of ß-Lactamases 485 20.2.2 SCHEMA-Guided Recombination of Cytochrome P450 Heme Domains 486 20.3 Conclusions 490 References 493 21 Chimeragenesis in Protein Engineering 493 Manuela Irani and Stefan Lutz 21.1 Introduction 493 21.1.1 Homology-Independent in vitro Recombination (Chimeragenesis) 494 21.1.1.1 Homology-Independent Random Gene Fusion 494 21.1.1.2 Homology-Independent Recombination with Multiple Crossovers 496 21.1.2 Predictive Algorithms in Chimeragenesis 498 21.2 Experimental Aspects of the SCRATCHY Protocol 499 21.2.1 Creation of ITCHY Libraries 499 21.2.2 Size and Reading Frame Selection 502 21.2.3 Enhanced SCRATCHY via Forced Crossovers 503 21.3 Future Trends in Chimeragenesis 506 21.3.1 Combining SCRATCHY and SCHEMA 508 21.3.2 The Future of Chimeragenesis 508 21 A Conclusions 511 Acknowledgments 511 References 511 XVIII Contents 25.2 Glycosynthases 607 25.3 Glycosyltransferases 608 25.4 Protocol and Practicai Considerations for Using HTS Methodology in the Directed Evolution of STs 610 25.4.1 Cloning of the Target ST and CMP-NeuSAc-Synthetase 610 25.4.2 Synthesis of Fluorescently Labeled Acceptor Sugar 611 25.4.3 Cell-Based Assay in JM107 Nan A Strain 611 25.4.4 Transformation, Growth and Expression of Plasmids Containing ST and CMP-syn Genes in JM107 Nan A Strain 612 25.4.5 Cell-Based Assay 613 25.4.6 Validation, Sensitivity and Dynamic Range of the Cell-Based Assay 613 25.4.7 Model Selection 614 25.4.8 Generation of Genetic Diversity in the Target ST Gene: Strategies for Constructing Large Mutant Libraries 614 25.4.9 Library Sorting, Rounds of Enrichment and the Stringency of Selection 615 25.4.10 Identification and Isolation of Improved Mutants 635 25.4.11 Characterization of Improved ST Mutants 616 25.5 Challenges and Prospects of GT Engineering 617 References 617 26 Yeast Surface Display in Protein Engineering and Analysis 621 Benjamin J. Hackel and K. Dane Wittrup 26.1 Review 621 26.1.1 Introduction 621 26.1.2 Protein Engineering 622 26.1.2.1 Affinity Engineering 623 26.1.2.2 Stability and Expression Engineering 623 26.1.2.3 Enzyme Engineering 624 26.1.3 Protein Analysis 624 26.1.3.1 Clone Characterization 624 26.1.3.2 Paratope: Epitope Study 625 26.1.3.3 YSD in Bioassays 626 26.2 Protocols and Practical Considerations 626 26.2.1 Materials 627 26.2.1.1 Cells and Plasmids 627 26.2.1.2 Media and Buffers 627 26.2.1.3 Buffers 627 26.2.1.4 Flow Cytometry Reagents 627 26.2.2 Nucleic Acid and Yeast Preparation 628 26.2.2.1 DNA Preparation 628 26.2.2.2 Yeast Transformation 630 26.2.2.3 Yeast Culture 632 26.2.3 Combinatorial Library Selection 632 Contents XIX 26.2.4 FACS 633 26.2.4.1 Other Selection Techniques 635 26.2.4.2 Stability 636 26.2.4.3 Clone Identification 637 26.2.5 Analysis 637 26.2.5.1 Binding Measurements 637 26.2.5.2 Stability Measurement 641 26.3 The Future of Yeast Surface Display 642 Abbreviations 644 Acknowledgments 644 References 644 27 In Vitro Compartmentalization (IVC) and Other High-Throughput Screens of Enzyme Libraries 649 Amir Aharoni and Dan S. Таифк 27.1 Introduction 649 27.2 The Fundamentals of High-Throughput Screens and Selections 650 27.3 Enzyme Selections by Phage-Display 651 27 A HTS of Enzymes Using Cell-Display and FACS 652 27.5 Other FACS-Based Enzyme Screens 653 27.6 In vivo Genetic Screens and Selections 653 27.7 In vitro Compartmentalization (IVC) 654 27.8 IVC in Double Emulsions 657 27.9 What s Next? 659 27.10 Experimental Details 660 Acknowledgments 662 References 662 28 Colorimetrie and Fluorescence-Based Screening 669 Jean-Louis Reymond 28.1 Introduction 669 28.2 Enzyme-Coupled Assays 670 28.2.1 Alcohol Dehydrogenase (ADHJ-Coupled Assays 671 28.2.2 Peroxidase-Coupled Assays 673 28.2.3 Hydrolase-Coupled Assays 674 28.2.4 Luciferase-Coupled Assays 676 28.3 Fluorogenic and Chromogenic Substrates 678 28.3.1 Release of Aromatic Alcohols 678 28.3.2 Aniline Release 681 28.3.3 FRET 682 28.3.4 Reactions that Modify the Chromophore Directly 685 28.3.5 Separation of Labeled Substrates 685 28.3.6 Precipitation 687 28.4 Chemosensors and Biosensors 688 28.4.1 Quick -Е with pH-Indicators 688 XX Contents 28.4.2 Functional Group-Selective Reagents 689 28.4.3 Antibodies, Aptamers and Lectins 690 28.4.4 Gold Nanopartides 691 28.5 Enzyme Fingerprinting with Multiple Substrates 693 28.5.1 APIZYM 693 28.5.2 Protease Profiling 695 28.5.3 Cocktail Fingerprinting 695 28.5.4 Substrate Microarrays 697 28.6 Conclusions 698 Acknowledgments 699 References 699 29 Confocal and Conventional Fluorescence-Based High Throughput Screening in Protein Engineering 713 Ulrich Haupts, Oliver Hesse, Michael Strerath, Peter J. Walla, and Wayne M. Coco 29.1 General Aspects 713 29.1.1 HTS and Combinatorial DNA Library Strategies in Protein Engineering 713 29.1.2 HTS in Protein Engineering: Coupling Genotype and Phenotype and the Advantages of Clonal Assays 715 29.1.3 Well-Based HTS Formats 716 29.2 Fluorescence 718 29.2.1 Overview of Theory and Principles of Fluorescence 719 29.2.1.1 Choice of Fluorophores in HTS 721 29.2.1.2 Concentration Requirements for Fluorescent Analytes 722 29.2.1.3 Fluorescence Intensity Measurements with a Precautionary Note on Fluorescent Labeling of Substrates and Binding Partners 722 29.2.1.4 Confocal Versus Bulk Detection Methods 723 29.2.1.5 Advantages of the Confocal Fluorescence Detection Format 724 29.2.1.6 Anisotropy 724 29.2.1.7 FRET/TR-FRET/Iifetime 725 29.2.1.8 Fluorescence Correlation Spectroscopy 726 29.2.1.9 FIDA 726 29.3 Hardware and Instrumentation 727 29.3.1 Confocal and Bulk Concepts 727 29.3.1.1 Light Sources 727 29.3.1.2 Wavelength Selection/Filtering 729 29.3.1.3 Detectors 729 29.3.1.4 Reader Systems 730 29.4 Practical Considerations and Screening Protocol 730 29.4.1 Introduction 730 29.4.2 Fluorescence-Based Assay Design: Practical Considerations 731 29.4.2.1 Choice of Assay Design 731 29.4.2.2 Labeling 731 Contents XXI 29.4.2.3 Choice of Fluorophore 732 29.4.3 Assay Quality 733 29.4.3.1 What Needs to Be Discriminated? 733 29.4.3.2 Mathematical Description 733 29.4.4 A Specific HTS Protein Engineering Program Using a Fluorescence- Based Screen 735 29.4.5 The Assay 735 29.4.5.1 Expression Host 736 29.4.6 Multiwell Format and Unit Operations in the HTS Protocol 738 29.4.6.1 Liquid Handling 738 29.4.6.2 Incubation 738 29.4.6.3 Centrifugation 739 29.4.6.4 Scheduling 739 29.4.6.5 Screening Protocol 739 29.5 Challenges and Future Directions 742 Abbreviations 748 Acknowledgments 748 References 748 30 Alteration of Substrate Specificity and Stereoselectivity of Lipases and Esterases 753 Dominique Böttcher, Marlen Schmidt, and Uwe T. Bornscheuer 30.1 Introduction 753 30.2 Background of Protein Engineering Methods 754 30.2.1 Directed Evolution 754 30.2.2 Rational Design 756 30.3 Assay Systems 757 30.3.1 Selection 757 30.3.1.1 Display Techniques 757 30.3.1.2 In vivo Selection 758 30.3.2 Screening 759 30.4 Examples 764 30.5 Conclusions 770 References 770 31 Altering Enzyme Substrate and Cofactor Specificity via Protein Engineering 777 Matthew DeSieno, Jing Du, and Huimin Zhao 31.1 Introduction 777 31.1.1 Overview 777 31.1.2 Approaches 779 31.1.2.1 Rational Design 779 31.1.2.2 Directed Evolution 781 31.1.2.3 Semi-Rational Design 781 31.2 Specific Examples 782 XXII Contents 31.2.1 Cofactor Specificity 782 31.2.1.1 NAD(P)(H) 783 31.2.1.2 ATP 783 31.2.1.3 Summary and Comments for Cofactor Specificity 784 31.2.2 Substrate Specificity 784 31.2.2.1 P450s 785 31.2.2.2 Aldolases 785 31.2.2.3 Transfer-RNA Synthetases 786 31.2.2.4 Restriction Endonudeases 786 31.2.2.5 Homing Endonudeases 788 31.2.2.6 Polymerases 789 31.2.2.7 Summary and Comments for Substrate Specificity 789 31.3 Challenges and Future Prospects 790 31.3.1 New Strategies for Engineering Cofactor/Substrate Specificity 790 31.3.2 Cofactor/Substrate Specificity Engineering for Combinatorial Biosynthesis 79І 31.3.3 Cofactor/Substrate Specificity Engineering for Metabolic Engineering 792 31.3.4 Cofactor/Substrate Specificity Engineering for Gene Therapy 793 Acknowledgments 793 References 793 32 Protein Engineering of Modular Polyketide Synthases 797 Alice Y. Chen and Chaitan Khosla 32.1 Introduction 797 32.2 Polyketide Biosynthesis and Engineering 798 32.2.1 Active Sites and Domain Boundaries in Multimodular PKSs 799 32.2.2 Past Achievements in Genetic Reprogramming of Polyketide Biosynthesis 802 32.2.2.1 Starter Unit Incorporation 802 32.2.2.2 Extender Unit Incorporation 804 32.2.2.3 ß-Carbon Processing 805 32.2.2.4 Chain Length Control 807 32.2.2.5 Additional Modifications 807 32.2.2.6 Other PKS Engineering Opportunities 807 32.2.3 Pre^Post-PRS Pathway Engineering 809 32.2.3.1 Precursor Production 809 32.2.3.2 Post-PKS Modification 810 32.3 Engineering and Characterization Techniques 810 32.3.1 Common Genetic Techniques for PKS Engineering 810 32.3.1.1 Restriction Site Engineering 811 32.3.1.2 Gene SOEing 811 32.3.1.3 Red/ET Homology Recombination 811 32.3.1.4 Gene Synthesis 812 32.3.1.5 Gene Shuffling 813 Contents XXIII 32.3.2 In vitro Characterization 814 32.3.2.1 Protein Expression 814 32.3.2.2 Protein Purification 814 32.3.2.3 Protein Characterization 815 32.3.3 In vivo Characterization 816 32.3.3.1 Host Engineering 816 32.3.3.2 High-Throughput Screening Assay 817 32.4 The Path Forward 818 Abbreviations 819 References 819 33 Cyanophycin Synthetases 829 Anna Steinte and Alexander Steinbiichel 33.1 Introduction 829 33.2 Occurrence of Cyanophycin Synthetases 830 33.3 General Features 830 33.4 Reaction Mechanism 831 33.5 Substrate Specificity 832 33.6 Primary Structure Analysis 836 33.7 Enzyme Engineering 838 33.8 Biotechnical Applications 843 Acknowledgments 843 References 843 34 Biosynthetic Pathway Engineering Strategies 849 Claudia Schmidt-Dannert and Alexander Pisarchik 34.1 Introduction 849 34.2 Initial Pathway Design 850 34.2.1 Functional Pathway Assembly 850 34.2.2 Selection of the Heterologous Host 854 34.3 Optimization of the Precursor Supply 855 34.3.1 Identification and Overexpression of Rate-limiting Enzymes 856 34.4 Engineering of Control Loops 858 34.5 Engineering of Alternative Precursor Routes 858 34.6 Balancing Gene Expression Levels and Activities of Metabolic Enzymes 859 34.7 Metabolic Network Integration and Optimization 861 34.8 Engineering Pathways for the Production of Diverse Compounds 863 34.9 Future Perspectives 866 Abbreviations 867 References 868 XXIV I Contents 35 Natural Polyester-Related Proteins: Structure, Function, Evolution and Engineering 877 Seiichi Taguchi and Takeharu Tsuge 35.1 Introduction 877 35.2 Enzymes Related to the Synthesis and Degradation of PHA 878 35.3 Structure-Based Engineering of PHA Synthase and Monomer- Supplying Enzymes 879 35.3.1 PHA Synthase (PhaC, PhaEC, PhaRC) 880 35.3.2 S-Ketoacyl-CoA Thiolase (PhaA) 882 35.3.3 Acetoacetyl-CoA Reducíase (PhaB) 887 35.3.4 (R)-Specific Enoyl-CoA Hydratase (PhaJ) 890 35.3.5 (R^-Hydroxyacyl-ACP-CoA Transferase (PhaG) 891 35.3.6 3-Ketoacyl-ACP Synthase III (FabH) 891 35.4 Directed Evolution of PHA Synthases 892 35.4.1 Engineering of the Type I Synthases 893 35.4.2 Engineering of the Type II Pseudomonas Species PHA Synthases 897 35.5 Structure-Function Relationship of PHA Depolymerases 899 35.5.1 Domain Structure of Extracellular PHA Depolymerases 899 35.5.2 Intracellular PHA Depolymerase 903 35.5.3 Amino Acid Residues Related to Binding Affinity 904 35.6 Application of PHA-Protein Binding Affinity 905 35.7 Perspectives 906 References 907 36 Bioengineering of Sequence-Repetitive Polypeptides: Synthetic Routes to Protein-Based Materials of Novel Structure and Function 915 Sonha С. Payne, Melissa Patterson, and Vincent P. Conticello 36.1 Introduction 915 36.2 Block Copolymers as Targets for Materials Design 918 36.2.1 Amphiphilic Block Copolymers 919 36.2.2 Elastin-Mimetic Block Copolymers 920 36.3 Strategies for the Construction of Synthetic Genes Encoding Sequence-Repetitive Polypeptides 923 36.3.1 DNA Cassette Concatemerization 924 36.3.2 Recursive Directional ligation 925 36.3.3 Genetic Assembly of Synthetic Genes Encoding Block Architectures 926 36.4 A Hybrid Approach to the Controlled Assembly of Complex Architectures of Sequence-Repetitive Polypeptides 928 36.5 Future Outlook 935 Acknowledgments 936 References 936 Contents XXV 37 Silk Proteins-Biomaterials and Bioengineering 939 Xiaoqin Wang, Peggy Cebe, and David. L Kaplan 37.1 Silk Protein Polymers-An Overview 939 37.2 Silk Protein Polymers-Methods of Preparation 947 37.2.1 Preparation of Spider Silks 947 37.2.2 Preparation of Scaffolds 949 37.3 Silk Protein Polymers-Future Perspectives and Challenges 951 Acknowledgments 954 References 954 Index 961
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title_auth Protein engineering handbook
title_exact_search Protein engineering handbook
title_full Protein engineering handbook 2 ed. by Stefan Lutz ...
title_fullStr Protein engineering handbook 2 ed. by Stefan Lutz ...
title_full_unstemmed Protein engineering handbook 2 ed. by Stefan Lutz ...
title_short Protein engineering handbook
title_sort protein engineering handbook
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