Directed Molecular Evolution of Proteins

Автор(ы):Brakmann Susanne
06.10.2007
Год изд.:2002
Описание: "Не уж то современные белки появились сразу в том сложнейшем видовом и внутреннем разнообразии, что и сейчас? Обладали ли "первобелки" какими-то свойствами современных или полностью отличались? Как эволюционировали белки? Остановилась ли эволюция белков? Обо всем этом рассказывает настоящая книга."
Оглавление:
Directed Molecular Evolution of Proteins — обложка книги.
1 Introduction [1]
2 Evolutionary Biotechnology - From Ideas and Concepts to Experiments and Computer Simulations [5]
  2.1 Evolution in vivo - From Natural Selection to Population Genetics [5]
  2.2 Evolution in vitro - From Kinetic Equations to Magic Molecules [8]
  2.3 Evolution in silico - From Neutral Networks to Multi-stable Molecules [16]
  2.4 Sequence Structure Mappings of Proteins [25]
  2.5 Concluding Remarks [26]
3 Using Evolutionary Strategies to Investigate the Structure and Function of Chorismate Mutases [29]
  3.1 Introduction [29]
  3.2 Selection versus Screening [30]
    3.2.1 Classical solutions to the sorting problem [31]
    3.2.2 Advantages and limitations of selection [32]
  3.3 Genetic Selection of Novel Chorismate Mutases [33]
    3.3.1 The selection system [35]
    3.3.2 Mechanistic studies [37]
      3.3.2.1 Active site residues [37]
      3.3.2.2 Random protein truncation [42]
    3.3.3 Structural studies [44]
      3.3.3.1 Constraints on interhelical loops [44]
    3.3.4 Altering protein topology [46]
      3.3.4.1 New quaternary structures [47]
      3.3.4.2 Stable monomeric mutases [49]
    3.3.5 Augmenting weak enzyme activity [51]
    3.3.6 Protein design [53]
  3.4 Summary and General Perspectives [57]
4 Construction of Environmental Libraries for Functional Screening of Enzyme Activity [63]
  4.1 Sample Collection and DNA Isolation from Environmental Samples [65]
  4.2 Construction of Environmental Libraries [68]
  4.3 Screening of Environmental Libraries [71]
  4.4 Conclusions [76]
5 Investigation of Phage Display for the Directed Evolution of Enzymes [79]
  5.1 Introduction [79]
  5.2 The Phage Display [79]
  5.3 Phage Display of Enzymes [81]
    5.3.1 The expression vectors [81]
      5.3.1.1 Filamentous bacteriophages [81]
      5.3.1.2 Other phages [83]
    5.3.2 Phage-enzymes [84]
  5.4 Creating Libraries of Mutants [87]
  5.5 Selection of Phage-enzymes [89]
    5.5.1 Selection for binding [89]
    5.5.2 Selection for catalytic activity [90]
      5.5.2.1 Selection with substrate or product analogues [90]
      5.5.2.2 Selection with transition-state analogues [92]
      5.5.2.3 Selection of reactive active site residues by affinity labeling [96]
      5.5.2.4 Selection with suicide substrates [98]
      5.5.2.5 Selections based directly on substrate transformations [102]
  5.6 Conclusions [108]
6 Directed Evolution of Binding Proteins by Cell Surface Display: Analysis of the Screening Process [111]
  6.1 Introduction [111]
  6.2 Library Construction [113]
    6.2.1 Mutagenesis [113]
    6.2.2 Expression [114]
  6.3 Mutant Isolation [115]
    6.3.1 Differential labeling [115]
    6.3.2 Screening [119]
  6.4 Summary [124]
        Acknowledgments [124]
7 Yeast n-Hybrid Systems for Molecular Evolution [127]
  7.1 Introduction [127]
  7.2 Technical Considerations [130]
    7.2.1 Yeast two-hybrid assay [130]
    7.2.2 Alternative assays [141]
  7.3 Applications [147]
    7.3.1 Protein-protein interactions [147]
    7.3.2 Protein-DNA interactions [149]
    7.3.3 Protein-RNA interactions [150]
    7.3.4 Protein-small molecule interactions [153]
  7.4 Conclusion [155]
8 Advanced Screening Strategies for Biocatalyst Discovery [159]
  8.1 Introduction [159]
  8.2 Semi-quantitative Screening in Agar-plate Formats [161]
  8.3 Solution-based Screening in Microplate Formats [164]
  8.4 Robotics and Automation [169]
9 Engineering Protein Evolution [177]
  9.1 Introduction [177]
  9.2 Mechanisms of Protein Evolution in Nature [178]
    9.2.1 Gene duplication [179]
    9.2.2 Tandem duplication [180]
        (?)-barrels [181]
    9.2.3 Circular permutation [182]
    9.2.4 Oligomerization [183]
    9.2.5 Gene fusion [184]
    9.2.6 Domain recruitment [184]
    9.2.7 Exon shuffling [186]
  9.3 Engineering Genes and Gene Fragments [187]
    9.3.1 Protein fragmentation [188]
    9.3.2 Rational swapping of secondary structure elements and domains [189]
    9.3.3 Combinatorial gene fragment shuffling [190]
    9.3.4 Modular recombination and protein folding [194]
    9.3.5 Rational domain assembly - engineering zinc fingers [199]
    9.3.6 Combinatorial domain recombination - exon shuffling [200]
  9.4 Gene Fusion - From Bi- to Multifunctional Enzymes [203]
    9.4.1 End-to-end gene fusions [203]
    9.4.2 Gene insertions [203]
    9.4.3 Modular design in multifunctional enzymes [204]
  9.5 Perspectives [208]
10 Exploring the Diversity of Heme Enzymes through Directed Evolution [215]
  10.1 Introduction [215]
  10.2 Heme Proteins [216]
  10.3 Cytochromes P450 [218]
    10.3.1 Introduction [218]
    10.3.1 Mechanism [220]
      10.3.2.1 The catalytic cycle [220]
      10.3.2.2 Uncoupling [222]
      10.3.2.3 Peroxide shunt pathway [222]
  10.4 Peroxidases [223]
    10.4.1 Introduction [223]
    10.4.2 Mechanism [223]
      10.4.2.1 Compound I formation [223]
      10.4.2.2 Oxidative dehydrogenation [226]
      10.4.2.3 Oxidative halogenation [226]
      10.4.2.4 Peroxide disproportionation [226]
      10.4.2.5 Oxygen transfer [227]
  10.5 Comparison of P450s and Peroxidases [227]
  10.6 Chloroperoxidase [228]
  10.7 Mutagenesis Studies [229]
    10.7.1 P450s [230]
      10.7.1.1 P450cam [230]
      10.7.1.2 Eukaryotic P450s [230]
    10.7.2 HRP [231]
    10.7.3 CPO [231]
    10.7.4 Myoglobin (Mb) [232]
  10.8 Directed Evolution of Heme Enzymes [233]
    10.8.1 P450s [233]
    10.8.2 Peroxidases [234]
    10.8.3 CPO [236]
    10.8.4 Catalase I [236]
    10.8.5 Myoglobin [237]
    10.8.6 Methods for recombination of P450s [237]
  10.9 Conclusions [238]
11 Directed Evolution as a Means to Create Enantioselective Enzymes for Use in Organic Chemistry [245]
  11.1 Introduction [245]
  11.2 Mutagenesis Methods [247]
  11.3 Overexpression of Genes and Secretion of Enzymes [248]
  11.4 High-Throughput Screening Systems for Enantioselectivity [250]
  11.5 Examples of Directed Evolution of Enantioselective Enzymes [257]
    11.5.1 Kinetic resolution of a chiral ester catalyzed by mutant Upases [257]
    11.5.2 Evolution of a lipase for the stereoselective hydrolysis of a meso-compound [268]
    11.5.3 Kinetic resolution of a chiral ester catalyzed by a mutant esterase [269]
    11.5.4 Improving the enantioselectivity of a transaminase [270]
    11.5.5 Inversion of the enantioselectivity of a hydantoinase [270]
    11.5.6 Evolving aldolases which accept both D- and L-glyceraldehydes [271]
  11.6 Conclusions [273]
12 Applied Molecular Evolution of Enzymes Involved in Synthesis and Repair of DMA [281]
  12.1 Introduction [281]
  12.2 Directed Evolution of Enzymes [282]
    12.2.1 Site-directed mutagenesis [283]
    12.2.2 Directed evolution [284]
    12.2.3 Genetic damage [285]
    12.2.4 PCR mutagenesis [286]
    12.2.5 DNA shuffling [287]
    12.2.6 Substitution by oligonucleotides containing random mutations (random mutagenesis) [288]
  12.3 Directed Evolution of DNA polymerases [289]
    12.3.1 Random mutagenesis of Thermus aquaticus DNA Pol I [291]
      12.3.1.1 Determination of structural components for Taq DNA polymerase fidelity [292]
      12.3.1.2 Directed evolution of a RNA polymerase from Taq DNA polymerase [293]
      12.3.1.3 Mutability of the Taq polymerase active site [294]
    12.3.2 Random oligonucleotide mutagenesis of Escherichia coli Pol I [294]
  12.4 Directed Evolution of Thymidine Kinase [295]
  12.5 Directed Evolution of Thymidylate Synthase [297]
  12.6 O6-Alkylguanine-DNA Alkyltransferase [300]
  12.7 Discussion [302]
13 Evolutionary Generation versus Rational Design of Restriction Endonucleases with Novel Specificity [309]
  13.1 Introduction [309]
    13.1.1 Biology of restriction/modification systems [309]
    13.1.2 Biochemical properties of type II restriction endonucleases [310]
    13.1.3 Applications for type II restriction endonucleases [311]
    13.1.4 Setting the stage for protein engineering of type II restriction endonucleases [313]
  13.2 Design of Restriction Endonucleases with New Specificities [313]
    13.2.1 Rational design [313]
      13.2.1.1 Attempts to employ rational design to change the specificity of restriction enzymes [313]
      13.2.1.2 Changing the substrate specificity of type Us restriction enzymes by domain fusion [316]
      13.2.1.3 Rational design to extend specificities of type II restriction enzymes [316]
    13.2.2 Evolutionary design of extended specificities [318]
  13.3 Summary and Outlook [324]
14 Evolutionary Generation of Enzymes with Novel Substrate Specificities [329]
  14.1 Introduction [329]
  14.2 General Considerations [331]
  14.3 Examples [333]
    14.3.1 Group 1 [333]
    14.3.2 Group 2 [337]
    14.3.3 Group 3 [338]
  14.4 Conclusions [339]
Index [343]
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