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BIOCATALYSIS: Biochemical Fundamentals and Applications
Grunwald, Peter
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Últimas novedades
química general
química orgánica
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The book covers the fundamentals of the field of biocatalysis that are not treated in such detail (or even not at all) in existing biocatalysis books or biochemistry textbooks. It of course does not substitute existing biochemistry textbooks but will serve a suitable supplement as it discusses biochemical fundamentals in connection with the respective topics.
With focus on the interdisciplinary nature of biocatalysis, the book contains many aspects of fundamental organic chemistry and some of inorganic chemistry as well, which should make it interesting not only for biochemistry but also for chemistry students. An important theme being emphasized in the book is that applied biocatalysis is one of the main prerequisites for a sustainable development.
The topics covered ranges from basic enzyme chemistry (biosynthesis, structure, properties, interaction forces, kinetics) to a detailed description of catalytic mechanisms. It covers the fundamentals of the different enzyme classes together with their applications in native and in immobilized state or in the form of whole cells in aqueous as well as non-conventional media. Topics such as catalytic antibodies, nucleic acid catalysts, non-ribosomal peptide synthesis, evolutionary methods, and the design of cells are also included.
Contents:
Introduction
History of Biocatalysis
Classification of Enzymes
Non-protein Groups in Biocatalysis
Introduction into Kinetics
Enzyme Kinetics
Mechanisms in Enzymatic Catalysis and Enzyme Models
Synthesis of Peptide Antibiotics
Immobilization Biocatalysts
Structure, Function, and Application of Enzymes
Enzymes in Non-conventional Media
Methods to Improve Biocatalysts
Metabolic Pathway Engineering
Catalytic Antibodies
Nucleic Acids as Catalysts
Use of Enzymes in Industry
White Biotechnology
Readership: Advanced undergraduate and graduate students in biology, chemistry, biochemistry and medicine. Biochemists, biologists and chemists.
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ix
Contents
Preface v
1. Introduction 1
1.1 Advantages and Disadvantages of Biocatalysts 3
1.2 Biocatalysis – An Interdisciplinary Science 6
1.3 The Impact of Biocatalysis on Teaching Natural Science 8
2. History of Biocatalysis 11
3. Classification of Enzymes 15
4. Non-protein Groups in Biocatalysis 22
4.1 Thiamine 24
4.2 Niacin and Riboflavin 28
4.3 Vitamin B6 31
4.4 Folic Acid, Tetrahydrofolate and Dihydrobiopterin 38
4.5 Cofactors in Methanogenesis 45
4.6 Ascorbic Acid Exerts a Protective Function 50
5. Introduction into Kinetics 54
5.1 Rate of Reactions and Rate Equations 54
5.2 Reaction Mechanisms 56
5.3 Steady-state 58
5.4 Pre-equilibria 59
5.5 Temperature Dependence 60
5.5.1 Chemical equilibria and temperature 61
5.5.2 Arrhenius parameters 64
5.5.3 Transition state theory 65
5.6 Reactions in Solutions 68
5.6.1 Diffusion controlled reactions 70
Biocatalysis
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6. Enzyme Kinetics 74
6.1 The Michaelis-Menten Equation 75
6.1.1 Determination of KM and rmax 79
6.1.2 Integrated Michaelis-Menten equation 82
6.1.3 Reversible equilibria 83
6.1.4 Inhibition 87
6.1.4.1 Non-competitive inhibition 91
6.1.4.2 Competitive inhibition 94
6.1.4.3 Uncompetitive inhibition 95
6.1.4.4 Substrate inhibition 97
6.1.5 Formation of intermediates 98
6.1.6 Bisubstrate reactions 100
6.1.7 Multi-substrate reactions 105
6.1.8 King and Altman method 110
6.1.9 Importance of KM and kcat 113
6.2 Parameters Affecting Enzymatic Activity 120
6.2.1 pH-dependence 121
6.2.2 Temperature-dependence 126
6.3 The Kinetic Isotope Effect and Hydrogen Tunneling 129
6.3.1 The kinetic isotope effect 129
6.3.1.1 Kinetic isotope effect and reaction mechanisms 131
6.3.2 Hydrogen tunnelling 134
7. Mechanisms in Enzymatic Catalysis and Enzyme Models 142
7.1 Enzyme-substrate Interactions 142
7.2 Enzymes and Other Catalysts – The Entropy Effect 150
7.3 Single Mechanisms with Examples 151
7.3.1 Acid-base catalysis 152
7.3.2 Covalent catalysis 153
7.3.3 Metal ion catalysis 156
7.3.3.1 Methylmalonyl-CoA mutase – a cobalamin
enzyme 165
7.4 Metalloenzyme of Biotechnological Relevance 170
7.4.1 Hydrogenases 170
7.4.2 Enzymes of the nitrogen cycle 178
7.4.3 Dinitrogenoxide reductase 185
7.4.4 Vanadium and vanadium-containing enzymes 186
7.4.4.1 Vanadium-nitrogenases 189
7.4.4.2 Fe-nitrogenases 192
7.4.4.3 VNase model compounds 193
7.4.4.4 Vanadium haloperoxidases 196
Contents xi
8. Synthesis of Peptide Antibiotics 201
8.1 Mechanism of Nonribosomal Peptide Synthesis 207
8.2 Other Multi-functional Enzymes 211
8.2.1 Fatty acid synthetases 211
8.2.2 Polyketide synthetases 213
8.3 Naturally Occurring Peptide/Polyketide Hybrids 219
8.4 Application of Nonribosomal Peptide Synthetases 220
8.5 The Case Mycosubtilin 224
8.6 Ribosomal Synthesis of Antibiotics 228
9. Immobilized Biocatalysts 231
9.1 Definition and Characterization 232
9.2 Reasons for Immobilizing Biocatalyst 234
9.3 Properties of Carriers for Immobilization 235
9.4 Different Types of Carrier Materials 237
9.5 Immobilization Methods 238
9.5.1 Immobilization by adsorption 239
9.5.2 Covalent immobilization 241
9.5.2.1 Optimizing experimental parameters 245
9.5.3 Immobilization by crosslinking 246
9.5.4 Entrapment of biocatalysts 249
9.5.4.1 Sol-gel processes – inorganic polymers 250
9.5.4.1.1 Silicon-based matrixes 251
9.5.5 Encapsulation 252
9.6 Kinetics of Immobilized Biocatalysts 253
9.6.1 Conformational changes 253
9.6.2 Partitioning effects 254
9.6.3 Diffusion limitation 255
9.7 Improving the Properties of Enzymes by Immobilization 257
9.8 Carrier-free Immobilizates 263
9.8.1 Crosslinked enzyme crystals 264
9.8.1.1 Application of CLECs 265
9.8.2 Crosslinked enzyme aggregates 277
10. Structure, Function, and Application of Enzymes 289
10.1 Hydrolases 292
10.1.1 Lipases – general aspects 293
10.1.1.1 Reaction behavior of lipases 293
10.1.1.2 Stereoselectivity of lipases 294
10.1.1.3 Different types of lipases and nomenclature 295
10.1.1.4 Kinetic resolution 297
10.1.1.5 The Kazlauskaz rules 301
Biocatalysis
xii
10.1.1.6 Dynamic kinetic resolution 304
10.1.1.7 Enantioselectivity 307
10.1.2 Esterases 312
10.1.2.1 Structural aspects and mechanism 313
10.1.2.2 Application of estereases 314
10.1.2.3 Screening assays 318
10.1.2.4 Pig liver esterase 320
10.1.2.4.1 Pig liver esterase model 325
10.1.2.5 Acetylcholinesterase 327
10.1.2.5.1 AChE/CdS-nanoparticle hybrids 332
10.1.2.6 Cholesterol esterase and carbohydrate esterases 334
10.1.2.7 The salicylic acid-binding protein 336
10.1.3 Epoxide hydrolases and epoxides 337
10.1.3.1 Chemical synthesis of epoxides 338
10.1.3.2 Biological synthesis of epoxides 341
10.1.3.2.1 Bacterial monooxygenases 342
10.1.3.3 Structural aspects of epoxide hydrolases 345
10.1.3.4 Application of epoxide hydrolases in synthesis 354
10.1.3.5 Epoxid hydrolases from yeasts 367
10.1.4 Nitrile-converting enzymes 371
10.1.4.1 Nitrile hydratases; Fe- and Co-NHases 373
10.1.4.1.1 Mechanism of NHases 378
10.1.4.1.2 Co-nitrile hydratase 382
10.1.4.1.3 Application of NHases and
amidases in organic synthesis 384
10.1.4.1.4 Desymmetrization 391
10.1.4.1.5 Nitrile hydratase active site models 393
10.1.4.2 Nitrilases 395
10.1.4.2.1 Reaction mechanism of nitrilases 397
10.1.4.2.2 Application of nitrilases 399
10.1.5 Hydantoinases 402
10.1.5.1 Application of hydantoinases 404
10.1.5.2 Structural and functional aspects of
hydantoinases 407
10.1.5.3 Engineering of hydantoinases and
related enzymes 412
10.2 Carbohydrate-modifying Enzymes 424
10.2.1 The glycosidic linkage 427
10.2.2 Glycosidases 428
10.2.2.1 Application of glycosidases 434
10.2.2.2 Synthesis of glycoconjugates 437
10.2.2.3 Stable glycosidic bonds 441
Contents xiii
10.2.2.4 Examples of unusual glycosidases 449
10.2.3 Glycosyltransferases 455
10.2.3.1 Structural and mechanistic aspects 467
10.2.3.2 Synthesis of glycoconjugates catalyzed by GTs 474
10.2.3.3 High-throughput screening for GTs 480
10.2.3.4 Bidirectional glycosyltransferases 482
10.2.4 Applications of glycoconjugates 492
10.3 Catalysts for Redox Reactions 509
10.3.1 Oxidoreductases – general aspects 509
10.3.1.1 Stereochemical aspects 511
10.3.1.2 Co-factor regeneration 512
10.3.1.2.1 Electrochemical methods of
cofactor regeneration or bypassing 514
10.3.1.3 Examples of oxidoreductases 522
10.3.2 Dehydrogenases 525
10.3.2.1 NAD(P)+-dependent dehydrogenases 525
10.3.2.2 Flavin-dependent dehydrogenases 527
10.3.2.3 Application of dehydrogenases 528
10.3.3 Oxygenases 532
10.3.3.1 Monooxygenases 532
10.3.3.1.1 Cytochrom P-450 oxygenases 533
10.3.3.1.2 Aromatic hydroxylases 536
10.3.3.1.3 Baeyer-Villiger monooxygenases 538
10.3.3.2 Dioxygenases 559
10.3.3.2.1 Application of dioxygenases 562
10.3.3.2.2 Dioxygenases in environmental
biotechnology 567
10.3.3.2.3 Catechol dioxygenases 572
10.3.3.2.4 Lipoxygenases 577
10.4 Lyases 610
10.4.1 Aldolases 610
10.4.1.1 The aldol reaction 610
10.4.1.2 Aldolases – mechanisms and mimics 612
10.4.1.3 Aldolases in organic synthesis 622
10.4.1.3.1 DHAP dependent aldolases 622
10.4.1.3.2 DHAP – problems and solutions 641
10.4.1.3.3 Aldolases accepting DHA 645
10.4.1.3.4 Pyruvate and phosphoenolpyruvate
dependent aldolases 647
10.4.1.3.5 DER aldolases 659
10.4.1.3.6 Glycine-dependent aldolases 666
10.4.1.4 Aldolases – environmental aspects 669
Biocatalysis
xiv
10.4.2 Hydroxynitril lyases 675
10.4.2.1 Mechanism of hydroxynitrile lyases and
structural aspects 677
10.4.2.2 Application of hydroxynitrile lyases 680
10.4.2.3 Engineering of HNLs 688
10.4.2.4 Further modifications of cyanohydrins 695
10.4.2.5 Immobilized (R)-oxynitrilases 700
10.5 Epimerases and Racemases 706
10.5.1 Racemases 708
10.5.2 Conversion of a racemase into an aldolase 713
10.5.3 Industrial application of racemases 715
10.5.4 Isomerases 718
10.6 Transaminases – Catalysts for Amino Acid Synthesis 722
11. Enzymes in Non-conventional Media 731
11.1 Enzymes in Organic Solvents 731
11.1.1 Thermal stability of enzymes in organic solvents 735
11.1.2 The role of water 738
11.1.3 The role of solvent properties 741
11.1.4 pH-memory in organic solvents 746
11.1.5 (Low) enzymatic activity in organic solvents 746
11.1.6 Structure of enzymes in organic solvents 750
11.1.7 Improving enzymatic activity in organic solvents 751
11.2 Other Non-conventional Media 752
11.2.1 Supercritical fluids 752
11.2.2 Ionic liquids 759
11.2.2.1 Ionic liquids in enzyme catalysis 763
11.2.3 Combination of ILs and scCO2 771
12. Methods to Improve Biocatalysts 777
12.1 Protein Design and Related Aspects 777
12.2 Fundamentals of Genetic Engineering 780
12.2.1 Transcription 780
12.2.2 Translation 783
12.2.3 Transformation and expression 788
12.2.4 Recombinant techniques 789
12.2.4.1 The PCR reaction 791
12.2.4.2 Restriction enzymes and DNA ligases 793
12.3 Engineering of New Proteins 799
12.4 Evolutionary Methods in Biocatalysis 802
12.4.1 Generating diversity 805
12.4.1.1 Saturation mutagenesis 805
Contents xv
12.4.1.2 Error-prone PCR 808
12.4.1.3 Gen-shuffling, recombining methods 811
12.4.2 Recent developments 817
12.4.2.1 Substrate acceptance 817
12.4.2.2 Improvement of enantioselectivity 819
12.4.2.3 Thermal stability 824
13. Metabolic Pathway Engineering 830
13.1 Metabolic Engineering in Oligosaccharide Synthesis 838
13.2 Further Applications of Pathway Engineering 843
13.3 Novel Carotenoids 850
13.4 Combining Transketolase and Transaminase Activity 854
14. Catalytic Antibodies 857
14.1 Antibodies 860
14.2 Some Historical Aspects 863
14.3 Cleavage of C–O and C–N Bonds 866
14.4 Further Examples 870
14.5 Catalysis of Unfavored Reactions 887
14.6 Catalytic Antibodies in Medicine 889
14.6.1 Catalytic antibodies and detoxification 889
14.6.2 Activation of prodrugs by antibodies 893
14.7 Evolution of Binding Energy and Catalysis 897
15. Nucleic Acids as Catalysts 908
15.1 Nucleic Acid Catalysts and Protein Enzymes 914
15.2 Examples of the Mechanism of RNA Catalysis 920
15.3 Characterization of a Ribozyme 930
15.4 Selection of Catalytic Nucleic Acids 940
15.5 Expanding the Scope of Catalysis by Nucleic Acids 945
15.6 Examples of Catalytic RNA and DNA 948
15.6.1 RNA-based catalysts – ribozymes 948
15.6.2 DNA-based catalysts 960
16. Use of Enzymes in Industry 968
16.1 Industrial Biotechnology in Numbers 968
16.2 Enzymes for Starch Conversion 972
16.3 Milk Processing 977
16.4 Cheesemaking 978
16.5 Enzymes and Beer 980
16.6 Bread Processing 982
16.7 Application in Fruit Juice Production 986
Biocatalysis
xvi
16.8 The Detergent Industry 987
16.9 Textile Applications 988
16.10 Pulp and Paper Processing 990
17. White Biotechnology 993
Outlook 1008
List of Abbreviations 1011
Index 1015 |
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