Grunwald P. Biocatalysis: biochemical fundamentals and applications (London; Singapore; Hackensack, 2009). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаGrunwald P. Biocatalysis: biochemical fundamentals and applications. - London: Imperial College Press; Singapore; Hackensack: Distributed by World Scientific Pub. Co., 2009. - xvi, 1035 p.: ill. (some col.). - Incl. bibl. ref. - Ind.: p.1015-1033. - ISBN-10 1-86094-744-1; ISBN-13 978-186094-744-5
 

Оглавление / 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

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  Вisubstrate 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  Temperatute-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 Вiotechnological 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

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
               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
               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
        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
               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
   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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