Enzymes (2003)

The article contains sections titled: 1. Introduction 1.1. History 1.2. Enzyme Nomenclature 1.2.1. General Principles of Nomenclature 1.2.2. Classification and Numbering of Enzymes 1.3. Structure of Enzymes 1.3.1. Primary Structure 1.3.2. Three-Dimensional Structure 1.3.3. Quaternary Structure, Folding, and Domains 1.3.4. The Ribozyme 1.4. Enzymes and Molecular Biology 1.4.1. Biosynthesis of Enzymes 1.4.2. Enzymes and DNA 2. Catalytic Activity of Enzymes 2.1. Factors Governing Catalytic Activity 2.1.1. Temperature 2.1.2. Value of pH 2.1.3. Activation 2.1.4. Inhibition 2.1.5. Allostery 2.1.6. Biogenic Regulation of Activity 2.2. Enzyme Assays 2.2.1. Reaction Rate as a Measure of Catalytic Activity 2.2.2. Definition of Units 2.2.3. Absorption Photometry 2.2.4. Fluorometry 2.2.5. Luminometry 2.2.6. Radiometry 2.2.7. Potentiometry 2.2.8. Conductometry 2.2.9. Calorimetry 2.2.10. Polarimetry 2.2.11. Manometry 2.2.12. Viscosimetry 2.2.13. Turbidimetry 2.2.14. Immobilized Enzymes 2.2.15. Electrophoresis 2.3. Quality Evaluation of Enzyme Preparations 2.3.1. Quality Criteria 2.3.2. Specific Activity 2.3.3. Protein Determination 2.3.4. Contaminating Activities 2.3.5. Electrophoretic Purity 2.3.6. High-Performance Liquid Chromatography 2.3.7. Performance Test 2.3.8. Amino Acid Analysis and Protein Sequence Analysis 2.3.9. Stability 2.3.10. Formulation of Enzyme Preparations 3. General Production Methods 3.1. Microbial Production 3.1.1. Organism and Enzyme Synthesis 3.1.2. Strain Improvement 3.1.3. Physiological Optimization 3.1.4. The Fermentor and its Limitations 3.1.5. Process Design 3.1.6. Modeling and Optimization 3.1.7. Instrumentation and Control 3.2. Isolation and Purification 3.2.1. Preparation of Biological Starting Materials 3.2.1.1. Cell Disruption by Mechanical Methods 3.2.1.2. Cell Disruption by Nonmechanical Methods 3.2.2. Separation of Solid Matter 3.2.2.1. Filtration 3.2.2.2. Centrifugation 3.2.2.3. Extraction 3.2.2.4. Flocculation and Flotation 3.2.3. Concentration 3.2.3.1. Thermal Methods 3.2.3.2. Precipitation 3.2.3.3. Ultrafiltration 3.2.4. Purification 3.2.4.1. Crystallization 3.2.4.2. Electrophoresis 3.2.4.3. Chromatography 3.2.5. Product Formulation 3.2.6. Waste Disposal 3.3. Immobilization 3.3.1. Definitions 3.3.2. History 3.3.3. Methods 3.3.3.1. Carrier Binding 3.3.3.2. Cross-linking 3.3.3.3. Entrapment 3.3.4. Characterization 3.3.5. Application 4. Discovery and Development of Enzymes 4.1. Enzyme Screening 4.1.1. Overview 4.1.2. Natural Isolate Screening 4.1.3. Molecular Screening 4.1.4. Environmental Gene Screening 4.1.5. Genomic Screening 4.1.6. Proteomic Screening 4.2. Protein Engineering 4.2.1. Introduction 4.2.2. Application of Protein Engineering in Academia and Industry 4.2.3. Outlook 5. Industrial Enzymes 5.1. Enzymes in Food Applications 5.1.1. Enzymes in Baking 5.1.1.1. Introduction 5.1.1.2. Amylases 5.1.1.3. Xylanases 5.1.1.4. Oxidoreductases 5.1.1.5. Lipases 5.1.1.6. Proteases 5.1.1.7. Transglutaminase 5.1.2. Enzymes in Fruit Juice Production and Fruit Processing 5.1.2.1. Introduction 5.1.2.2. Biochemistry of Fruit Cell Walls 5.1.2.3. Cell-Wall-Degrading Enzymes 5.1.2.4. Apple Processing 5.1.2.4.1. Apple Pulp Maceration 5.1.2.4.2. Apple Juice Depectinization 5.1.2.5. Red-Berry Processing 5.1.2.6. Tropical Fruit and Citrus Processing 5.1.2.7. Conclusion 5.1.3. Enzymes in Brewing 5.1.3.1. Introduction 5.1.3.2. Enzymes in Malting and Mashing 5.1.3.3. Enzymes for Problem Prevention or Solving 5.1.3.3.1. Bacterial α-Amylase in Mashing 5.1.3.3.2. Fungal α-Amylase in Fermentation 5.1.3.3.3. β-Glucanase in Mashing 5.1.3.3.4. Cysteine Endopeptidases (Postfermentation) 5.1.3.3.5. Glucoamylase in Mashing 5.1.3.4. Enzymes for Process Improvement 5.1.3.4.1. Adjunct Brewing 5.1.3.4.2. Improved Mashing Processes 5.1.3.4.3. Shelf-Life Improvement 5.1.3.4.4. Accelerated Maturation 5.1.3.4.5. Starch-Haze Removal 5.1.3.5. Special Brewing Processes 5.1.4. Enzymes in Dairy Applications 5.1.4.1. Introduction 5.1.4.2. Cheesemaking 5.1.4.2.1. Cheesemaking Process 5.1.4.2.2. Mechanism of Renneting 5.1.4.2.3. Types of Coagulants 5.1.4.2.4. Properties of Coagulating Enzymes 5.1.4.2.5. Cheese Ripening 5.1.4.2.6. Cheese Flavors and Ripening Acceleration 5.1.4.2.7. Lipase 5.1.4.2.8. Lysozyme 5.1.4.2.9. Milk Protein Hydrolysates 5.1.4.2.10. Transglutaminase 5.1.4.3. Milk Processing 5.1.4.3.1. β-Galactosidase 5.1.4.3.2. Other Enzymes 5.1.5. Other Food Applications 5.1.5.1. Introduction 5.1.5.2. Meat and Fish 5.1.5.2.1. Meat Processing 5.1.5.2.2. Fish Processing 5.1.5.3. Protein Cross-linking 5.1.5.4. Flavor Development 5.1.5.4.1. Protein Hydrolysis 5.1.5.4.2. Lipid Hydrolysis 5.1.5.5. Egg powder 5.1.5.6. Oils and Fats 5.1.5.6.1. Fat Splitting 5.1.5.6.2. Interesterification 5.1.5.6.3. Esterification 5.1.5.6.4. Oil Degumming 5.2. Enzymes in Nonfood Applications 5.2.1. Enzymes in Household Detergents 5.2.1.1. Historical Development 5.2.1.2. Laundry Soils 5.2.1.3. Detergent Composition and Washing Process 5.2.1.3.1. Washing Process 5.2.1.3.2. Detergent Compositions 5.2.1.4. Enzyme-Aided Detergency and Soil Removal 5.2.1.5. Detergent Enzyme Performance Evaluation and Screening 5.2.1.6. Enzyme Types 5.2.1.6.1. Proteases 5.2.1.6.2. Amylases 5.2.1.6.3. Lipases 5.2.1.6.4. Cellulases 5.2.1.6.5. Mannanase 5.2.1.7. Future Trends 5.2.2. Enzymes in Automatic Dishwashing 5.2.2.1. Introduction 5.2.2.2. Characteristics of Enzymes for ADDs 5.2.2.3. Proteases 5.2.2.3.1. Proteins: The Substrate of Proteases 5.2.2.3.2. Proteases for ADDs 5.2.2.4. Amylases 5.2.2.4.1. Starch: The Substrate of Amylases 5.2.2.4.2. Amylases for ADDs 5.2.2.5. Other Enzymes 5.2.2.6. Automatic Dishwashing Detergents 5.2.2.6.1. Composition of Automatic Dishwashing Detergents 5.2.2.6.2. Application of Enzymes in ADD 5.2.2.6.3. Stability and Compatibility 5.2.3. Enzymes in Grain Wet-Milling 5.2.3.1. Introduction 5.2.3.2. Overview of the Conversion of Corn to HFCS 5.2.3.2.1. Corn Steeping 5.2.3.2.2. Coarse Grinding and Germ Removal by Cyclone Separation 5.2.3.2.3. Fine Grinding and Fiber Removal by Screening 5.2.3.2.4. Centrifugation and Washing to Separate Starch from Protein 5.2.3.2.5. Hydrolysis with α-Amylase (Liquefaction) 5.2.3.2.6. Hydrolysis with Glucoamylase (Saccharification) 5.2.3.2.7. Isomerization with Glucose Isomerase 5.2.3.2.8. Fructose Enrichment and Blending 5.2.3.3. α-Amylase 5.2.3.3.1. Origin and Enzymatic Properties 5.2.3.3.2. Structure 5.2.3.3.3. Industrial Use 5.2.3.4. Glucoamylase 5.2.3.4.1. Origin and Enzymatic Properties 5.2.3.4.2. Structure 5.2.3.4.3. Industrial Use 5.2.3.5. Pullulanase 5.2.3.5.1. Origin and Enzymatic Properties 5.2.3.5.2. Structure 5.2.3.5.3. Industrial Use 5.2.3.6. Glucose Isomerase 5.2.3.6.1. Origin and Enzymatic Properties 5.2.3.6.2. Structure 5.2.3.6.3. Industrial Use of Glucose Isomerase 5.2.3.7. Use of Wheat Starch 5.2.4. Enzymes in Animal Feeds 5.2.4.1. Introduction 5.2.4.2. Enzymes Used in Animal Feed 5.2.4.2.1. Fiber-Degrading Enzymes 5.2.4.2.2. Phytic Acid Degrading Enzymes (Phytases) 5.2.4.2.3. Protein-Degrading Enzymes (Proteases) 5.2.4.2.4. Starch-Degrading Enzymes (Amylases) 5.2.4.3. Future Developments 5.2.5. Enzymes in Textile Production 5.2.5.1. Introduction 5.2.5.2. Cellulose Fibers 5.2.5.2.1. Desizing of Cotton Cellulose Fibers 5.2.5.2.2. Scouring of Cotton 5.2.5.2.3. Bleaching of Cotton 5.2.5.2.4. Removal of Hydrogen Peroxide 5.2.5.2.5. Cotton Finishing 5.2.5.2.6. Ageing of Denim 5.2.5.2.7. Processing of Man-Made Cellulose Fibers 5.2.5.2.8. Processing of Bast Fibers 5.2.5.3. Proteinous Fibers 5.2.5.3.1. Wool Processing 5.2.5.3.2. Degumming of Silk 5.2.5.4. Textile Effluent Treatment and Recycling 5.2.5.5. Outlook 5.2.6. Enzymes in Pulp and Paper Processing 5.2.6.1. Introduction 5.2.6.2. Enzymes 5.2.6.2.1. Cellulases 5.2.6.2.2. Hemicellulases 5.2.6.2.3. Lignin-Modifying, Oxidative Enzymes 5.2.6.3. Enzymes in Pulp and Paper Processing 5.2.6.3.1. Mechanical Pulping 5.2.6.3.2. Chemical Pulping 5.2.6.3.3. Bleaching 5.2.6.3.4. Papermaking 5.2.6.3.5. Deinking 5.3. Development of New Industrial Enzyme Applications 5.3.1. Introduction 5.3.2. Enzymes in Cosmetics 5.3.2.1. Hair Dyeing 5.3.2.1.1. Oxidases 5.3.2.1.2. Peroxidases 5.3.2.1.3. Polyphenol Oxidases 5.3.2.2. Hair Waving 5.3.2.3. Skin Care 5.3.2.4. Toothpastes and Mouthwashes 5.3.2.5. Enzymes in Cleaning of Artificial Dentures 5.3.3. Enzymes for Preservation 5.3.4. Enzymes in Hard-Surface Cleaning 5.3.4.1. Enzymes in Membrane Cleaning 5.3.4.1.1. Proteases 5.3.4.1.2. Hemicellulases 5.3.5. Enzymes Generating a pH Shift 5.3.6. Enzymes in Cork Treatment 5.3.7. Enzymes in Oil-Field Applications 5.3.8. Enzymes in Wastewater Treatment 5.3.9. Enzymes for Polymerisation: Wood Fiberboard Production 5.4. Overview of Industrial Enzyme Applications 6. Nonindustrial Enzyme Usage 6.1. Enzymes in Organic Synthesis 6.1.1. Introduction 6.1.2. Examples of Enzymatic Conversions 6.1.2.1. Syntheses by Means of Hydrolases 6.1.2.2. Reduction of CO and CC Bonds 6.1.2.3. Oxidation of Alcohols and Oxygenation of CH and CC Bonds 6.1.2.4. CC Coupling 6.1.2.5. Formation of Glycosidic Bonds 6.1.2.6. Enzymatic Protecting Proup Techniques 6.1.3. Enzyme-Analogous Catalysts 6.1.4. Commercial Applications 6.1.4.1. General 6.1.4.2. Nonstereoselective Biocatalytic Reactions 6.1.4.3. Biocatalytic Resolution Processes 6.1.4.3.1. Enzymatic Acylation of Amino Groups 6.1.4.3.2. Enzymatic Hydrolysis of Hydantoins 6.1.4.3.3. Enzymatic Hydrolysis of Lactams 6.1.4.3.4. Enzymatic Hydrolysis of CO Bonds 6.1.4.3.5. Enzymatic Hydrolysis of Nitriles 6.1.4.3.6. Enzymatic Cleavage of threo Aldol Products 6.1.4.4. Biocatalytic Asymmetric Synthesis 6.1.4.4.1. Biocatalytic Reductive Amination of CO Bonds 6.1.4.4.2. Biocatalytic Hydrocyanation of CO Bonds 6.1.4.4.3. Biocatalytic Addition of Water to CO Bonds 6.1.4.4.4. Biocatalytic Amination of CC Bonds 6.1.5. Outlook 6.2. Therapeutic Enzymes 6.2.1. Requirements for the Use of Enzymes in Therapy 6.2.2. Coping with Peculiar Protein Properties 6.2.3. Sources of Enzymes and Production Systems 6.2.4. Overview of Therapeutic Enzymes 6.2.4.1. Oxidoreductases 6.2.4.2. Transferases 6.2.4.3. Esterases 6.2.4.4. Nucleases 6.2.4.5. Glycosidases 6.2.4.6. Proteases 6.2.4.6.1. Pancreatic and Gastric Proteases 6.2.4.6.2. Plasma Proteases 6.2.4.6.3. Coagulation Factors 6.2.4.6.4. Plasminogen Activators 6.2.4.6.5. Proteases from Snake Venoms 6.2.4.6.6. Plant and Microbial Proteases 6.2.4.7. Amidases 6.2.4.8. Lyases 6.3. Enzymes in Diagnosis 6.3.1. Determination of Substrate Concentration 6.3.2. Determination of Enzyme Activity 6.3.3. Immunoassays 6.4. Enzymes for Food Analysis 6.4.1. Carbohydrates 6.4.2. Organic Acids 6.4.3. Alcohols 6.4.4. Other Food Ingredients 6.5. Enzymes in Genetic Engineering 6.5.1. Restriction Endonucleases and Methylases 6.5.1.1. Classification 6.5.1.2. Activity of Class II Restriction Endonucleases 6.5.1.2.1. Reaction Parameters 6.5.1.2.2. Additional Structural Requirements Influencing Activity 6.5.1.3. Specificity of Class II Restriction Endonucleases 6.5.1.3.1. Palindromic Recognition Sequences 6.5.1.3.2. Nonpalindromic Recognition Sequences 6.5.1.3.3. Isoschizomers 6.5.1.4. Changes in Sequence Specificity 6.5.1.5. Novel Class II Restriction Endonucleases 6.5.2. DNA Polymerases 6.5.2.1. Escherichia coli DNA Polymerase I 6.5.2.2. Klenow Enzyme 6.5.2.3. T4 DNA Polymerase 6.5.2.4. Reverse Transcriptase 6.5.2.5. Terminal Transferase 6.5.3. RNA Polymerases 6.5.3.1. SP6 RNA Polymerase 6.5.3.2. T7 RNA Polymerase 6.5.4. DNA Nucleases 6.5.4.1. DNase I 6.5.4.2. Exonuclease III 6.5.4.3. Nuclease S1 6.5.4.4. Nuclease Bal 31 6.5.5. RNA Nucleases 6.5.5.1. RNase H 6.5.5.2. Site-Specific RNases 6.5.5.2.1. RNase A 6.5.5.2.2. RNase CL3 6.5.5.2.3. RNase T1 6.5.5.2.4. RNase U2 6.5.5.2.5. Nuclease S7 6.5.5.2.6. Site-Specific RNases in RNA Sequence Analysis 6.5.6. Modifying Enzymes 6.5.6.1. Alkaline Phosphatase 6.5.6.2. T4 DNA Ligase 6.5.6.3. Escherichia coli DNA Ligase 6.5.6.4. T4 Polynucleotide Kinase 6.5.6.5. T4 Polynucleotide Kinase, 3′-Phosphatase-Free 6.5.6.6. Methylase HpaII 7. Enzyme Safety and Regulatory Considerations 7.1. Safe Handling of Enzymes 7.1.1. Possible Health Effects 7.1.2. Control Technology 7.2. Product Regulatory Considerations 7.2.1. Food-Use Enzymes 7.2.2. Feed-Use Enzymes 7.2.3. Industrial-Use Enzymes