Biocatalysis: [fundamentals and applications]
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| Main Authors: | , |
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| Format: | Book |
| Language: | German |
| Published: |
Weinheim
Wiley-VCH
2004
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Physical Description: | XXIII, 611 S. graph. Darst. |
| ISBN: | 3527303448 |
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| 100 | 1 | |a Bommarius, Andreas Sebastian |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Biocatalysis |b [fundamentals and applications] |c A. S. Bommarius ; B. R. Riebel |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2004 | |
| 300 | |a XXIII, 611 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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Record in the Search Index
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| adam_text | Contents
Preface
V
Acknowledgments
VII
1
Introduction to
Biocatalysis
1
1.1
Overview:The Status of Biocatalysis at the Turn of the 21st Century
1.1.1
State of Acceptance of Biocatalysis
2
1.1.2
Current Advantages and Drawbacks of Biocatalysis
4
1.1.2.1
Advantages of Biocatalysts
4
1.1.2.2
Drawbacks of Current Biocatalysts
5
1.2
Characteristics of Biocatalysis as a Technology
6
1.2.1
Contributing Disciplines and Areas of Application
6
1.2.2
Characteristics of Biocatalytic Transformations
7
1.2.2.1
Comparison of Biocatalysis with other Kinds of Catalysis
8
1.2.3
Applications of Biocatalysis in Industry
9
1.2.3.1
Chemical Industry of the Future: Environmentally Benign
Manufacturing, Green Chemistry, Sustainable Development in the
Future
9
1.2.3.2
Enantiomerically Pure Drugs or Advanced Pharmaceutical
Intermediates (APIs)
10
1.3
Current Penetration of Biocatalysis
11
1.3.1
The Past: Historical Digest of Enzyme Catalysis
11
1.3.2
The Present: Status of Biocatalytic Processes
11
1.4
The Breadth of Biocatalysis
14
1.4.1
Nomenclature of Enzymes
14
1.4.2
Biocatalysis and Organic Chemistry, or
Do we Need to Forget our Organic Chemistry?
14
2
Characterization of a (Bio-Jcatalyst
19
2.1
Characterization of Enzyme Catalysis
20
2.1.1
Basis of the Activity of Enzymes: What is Enzyme Catalysis?
20
2.1.1.1
Enzyme Reaction in a Reaction Coordinate Diagram
21
2.1.2
Development of Enzyme Kinetics from Binding and Catalysis
21
ΧΙ
Contents
2.2
Sources and Reasons for the Activity of Enzymes as Catalysts
23
2.2.1
Chronology of the Most Important Theories of Enzyme Activity
23
2.2.2
Origin of Enzymatic Activity: Derivation of the
Kurz
Equation
24
2.2.3
Consequences of the
Kurz
Equation
25
2.2.4
Efficiency of Enzyme Catalysis: Beyond Pauling s Postulate
28
2.3
Performance Criteria for Catalysts, Processes, and Process Routes
30
2.3.1
Basic Performance Criteria for a Catalyst: Activity, Selectivity and
Stability of Enzymes
30
2.3.1.1
Activity
30
2.3.1.2
Selectivity
31
2.3.1.3
Stability
32
2.3.2
Performance Criteria for the Process
33
2.3.2.1
Product Yield
33
2.3.2.2
(Bio)catalyst Productivity
34
2.3.2.3
(Bio)catalyst Stability
34
2.3.2.4
Reactor Productivity
35
2.3.3
Links between Enzyme Reaction Performance Parameters
36
2.3.3.1
Rate Acceleration
36
2.3.3.2
Ratio between Catalytic Constant kax and Deactivation Rate Constant kd
38
2.3.3.3
Relationship between Deactivation Rate Constant kd and
Total Turnover Number TTN
38
2.3.4
Performance Criteria for Process Schemes, Atom Economy, and
Environmental Quotient
39
3
Isolation and Preparation of Microorganisms
43
3.1
Introduction
44
3.2
Screening of New Enzyme Activities
46
3.2.1
Growth Rates in Nature
47
3.2.2
Methods in Microbial Ecology
47
3.3
Strain Development
48
3.3.1
Range of Industrial Products from Microorganisms
48
3.3.2
Strain Improvement
50
3.4
Extremophiles
52
3.4.1
Extremophiles in Industry
54
3.5
Rapid Screening of Biocatalysts
56
4
Molecular Biology Tools for Biocatalysis
61
4.1
Molecular Biology Basics:
DNA
versus Protein Level
62
4.2 DNA
Isolation and Purification
65
4.2.1
Quantification of
DNA/RNA
66
4.3
Gene Isolation, Detection, and Verification
67
4.3.1
Polymerase Chain Reaction
67
4.3.2
Optimization of a PC
R
Reaction
69
4.3.3
Special PCR Techniques
71
Contents
4.3.3.1
Nested PCR
71
4.3.3.2
Inverse PCR
71
4.3.3.3
RACE:
Rapid
Amplification of cDNA Ends
71
4.3.4
Southern Blotting
74
4.3.4.1
Probe Design and Labeling
76
4.3.4.2
Hybridization
76
4.3.4.3
Detection
76
4.3.5 DNA-
Sequencing
77
4.4
Cloning Techniques
77
4.4.1
Restriction Mapping
78
4.4.2
Vectors
78
4.4.3
Ligation
80
4.4.3.1
Propagation of Plasmids and Transformation in Hosts
81
4.5
(Over)expression of an Enzyme Function in a Host
81
4.5.1
Choice of an Expression System
81
4.5.2
Translation and Codon Usage in
E. coli
82
4.5.3
Choice of Vector
84
4.5.3.1
Generation of Inclusion Bodies
85
4.5.3.2
Expression of Fusion Proteins
85
4.5.3.3
Surface Expression
87
4.5.4
Expression of Eukaryotic Genes in Yeasts
87
5
Enzyme Reaction Engineering
91
5.1
Kinetic Modeling: Rationale and Purpose
92
5.2
The Ideal World: Ideal Kinetics and Ideal Reactors
94
5.2.1
The Classic Case: Michaelis-Menten Equation
94
5.2.2
Design of Ideal Reactors
96
5.2.3
Integrated Michaelis-Menten Equation in Ideal Reactors
96
5.2.3.1
Case
1:
No Inhibition
97
5.3
Enzymes with Unfavorable Binding: Inhibition
97
5.3.1
Types of Inhibitors
97
5.3.2
Integrated Michaelis-Menten Equation for Substrate and Product
Inhibition
99
5.3.2.1
Case
2:
Integrated Michaelis-Menten Equation in the Presence of
Substrate Inhibitor
99
5.3.2.2
Case
3:
Integrated Michaelis-Menten Equation in the Presence of
Inhibitor
99
5.3.3
The KI
—
[I]50 Relationship: Another Useful Application of Mechanism
Elucidation
103
5.4
Reactor Engineering
105
5.4.1
Configuration of Enzyme Reactors
105
5.4.1.1
Characteristic Dimensionless Numbers for Reactor Design
107
5.4.2
Immobilized Enzyme Reactor (Fixed-Bed Reactor with Plug-Flow)
108
5.4.2.1
Reactor Design Equations
108
5.4.2.2
Immobilization
109
XII Contents
5.4.2.3
Optimal
Conditions for an Immobilized Enzyme
Reactor
110
5.4.3 Enzyme
Membrane Reactor
(Continuous Stirred Tank Reactor, CSTR)
110
5.4.3.1
Design Equation: Reactor Equation and Retention
110
5.4.3.2
Classification of Enzyme Membrane Reactors 111
5.4.4
Rules for Choice of Reaction Parameters and Reactors
113
5.5
Enzyme Reactions with Incomplete Mass Transfer. Influence of
Immobilization
113
5.5.1
External Diffusion (Film Diffusion)
114
5.5.2
Internal Diffusion (Pore Diffusion)
114
5.5.3
Methods of Testing for Mass Transfer Limitations
116
5.5.4
Influence of Mass Transfer on the Reaction Parameters
118
5.6
Enzymes with Incomplete Stability: Deactivation Kinetics
119
5.6.1
Resting Stability
119
5.6.2
Operational Stability
120
5.6.3
Comparison of Resting and Operational Stability
122
5.6.4
Strategy for the Addition of Fresh Enzyme to Deactiving Enzyme in
Continuous Reactors
124
5.7
Enzymes with Incomplete Selectivity:
Е
-Value and its Optimization
126
5.7.1
Derivation of the E-Value
126
5.7.2
Optimization of Separation of Racemates by Choice of Degree of
Conversion
128
5.7.2.1
Optimization of an Irreversible Reaction
128
5.7.2.2
Enantioselectivity of an Equilibrium Reaction
129
5.7.2.3
Determination of Enantiomeric Purity from a Conversion-Time Plot
130
5.7.3
Optimization of Enantiomeric Ratio
E
by Choice of Temperature
130
5.7.3.1
Derivation of the
Isoinversion
Temperature
130
5.7.3.2
Example of Optimization of Enantioselectivity by Choice of
Temperature
131
б
Applications of Enzymes as Bulk Actives:
Detergents, Textiles, Pulp and Paper, Animal Feed
135
6.1
Application of Enzymes in Laundry Detergents
136
6.1.1
Overview
136
6.1.2
Proteases against Blood and Egg Stains
138
6.1.3
Upases against Grease Stains
139
6.1.4
Amylases against Grass and Starch Dirt
139
6.1.5
Cellulases
139
6.1.6
Bleach Enzymes
140
6.2
Enzymes in the Textile Industry: Stone-washed Denims, Shiny Cotton
Surfaces
140
6.2.1
Build-up and Mode of Action of Enzymes for the Textile Industry
140
6.2.2
Cellulases: the Shinier Look
141
Contents
6.2.3
Stonewashing: Biostoning of Denim: the Worn Look
143
6.2.4
Peroxidases
144
6.3
Enzymes in the Pulp and Paper Industry: Bleaching of Pulp with
Xylanases or
Laceases
145
6.3.1
Introduction
145
6.3.2
Wood
146
6.3.2.1
Cellulose
146
6.3.2.2
Hemicellulose
147
6.3.2.3
Lignin
147
6.3.3
Papermaking: Kraft Pulping Process
149
6.3.4
Research on Enzymes in the Pulp and Paper Industry
150
6.3.4.1
Laceases
150
6.3.4.2
Xylanases
151
6.3.4.3
Cellulases in the Papermaking Process
152
6.4
Phytase for Animal Feed: Utilization of Phosphorus
152
6.4.1
The Farm Animal Business and the Environment
152
6.4.2
Phytase
153
6.4.3
Efficacy of Phytase: Reduction of Phosphorus
154
6.4.4
Efficacy of Phytase: Effect on Other Nutrients
155
7
Application of Enzymes as Catalysts: Basic Chemicals, Fine Chemicals, Food,
Crop Protection, Bulk Pharmaceuticals
159
7.1
Enzymes as Catalysts in Processes towards Basic Chemicals
160
7.1.1
Nitrile Hydratase: Acrylamide from Acrylonitrile, Nicotinamide from
3-Cyanopyridme, and
5-Cyanovaleramide
from Adiponitrile
160
7.1.1.1
Acrylamide from Acrylonitrile
160
7.1.1.2
Nicotinamide from 3-Cyanopyridine
162
7.1.1.3
5-Cyanovaleramide from Adiponitrile
162
7.1.2
Nitrilase:
l,5-Dimethyl-2-piperidone
from 2-Methylglutaronitrile
163
7.1.3
Toluene Dioxygenase: Indigo or Prostaglandins from Substituted
Benzenes via cis-Dihydrodiols
163
7.1.4
Oxynitrilase (Hydroxy Nitrile Lyase, HNL): Cyanohydrins from
Aldehydes
167
7.2
Enzymes as Catalysts in the Fine Chemicals Industry
170
7.2.1
Chirality, and the Cahn-Ingold-Prelog and
Pfeiffer
Rules
170
7.2.2
Enantiomerically Pure
Amino
Acids
172
7.2.2.1
The Aminoacylase Process
172
7.2.2.2
The Amidase Process
174
7.2.2.3
The Hydantoinase/Carbamoylase Process
174
7.2.2.4
Reductive Animation of Keto Acids (L-tert-Leucine as Example)
177
7.2.2.5
Aspartase
180
7.2.2.6 L-Aspartate-ß-decarboxylase 180
7.2.2.7
L^-Aminobutyric acid
181
7.2.3
Enantiomerically Pure Hydroxy Acids, Alcohols, and Amines
182
7.2.3.1
Fumarase
182
IV
Contents
7.2.3.2
Enantiomerically Pure Amines with
Lipase
182
7.2.3.3
Synthesis of Enantiomerically Pure Amines through
Transamination
183
7.2.3.4
Hydroxy esters with carbonyl reductases
185
7.2.3.5
Alcohols with ADH
186
7.3
Enzymes as Catalysts in the Food Industry
187
7.3.1
HFCS with Glucose Isomerase (GI)
187
7.3.2
AspartameO, Artificial Sweetener through Enzymatic
Peptide
Synthesis
188
7.3.3
Lactose Hydrolysis
191
7.3.4
Nutraceuticals : t-Carnitine as a Nutrient for Athletes and
Convalescents
(Lonza)
191
7.3.5
Decarboxylases for Improving the Taste of Beer
194
7.4
Enzymes as Catalysts towards Crop Protection Chemicals
195
7.4.1
Intermediate for Herbicides: (R)-2-(4-Hydroxyphenoxypropionic acid
(BASF, Germany)
195
7.4.2
Applications of Transaminases towards Crop Protection Agents:
L-Phosphinothricin and (S)-MOIPA
196
7.5
Enzymes for Large-Scale Pharma Intermediates
197
7.5.1
Penicillin
G
(or V) Amidase (PGA, PVA):
ß-Lactam
Precursors, Semi-synthetic
ß-Lactams 197
7.5.2
Ephedrine
200
8
Biotechnological Processing Steps for Enzyme Manufacture
209
8.1
Introduction to Protein Isolation and Purification
210
8.2
Basics of Fermentation
212
8.2.1
Medium Requirements
213
8.2.2
Sterilization
214
8.2.3
Phases of a Fermentation
214
8.2.4
Modeling of a Fermentation
215
8.2.5
Growth Models
216
8.2.6
Fed-Batch Culture
216
8.3
Fermentation and its Main Challenge: Transfer of Oxygen
218
8.3.1
Determination of Required Oxygen Demand of the Cells
218
8.3.2
Calculation of Oxygen Transport in the
Fermenter
Solution
219
8.3.3
Determination of feL, a, and kya
220
8.3.2.1
Methods of Measurement of the Product kLa
221
8.4
Downstream Processing: Crude Purification of Proteins
223
8.4.1
Separation (Centrifugation)
223
8.4.2
Homogenization
225
8.4.3
Precipitation
226
8.4.3.1
Precipitation in Water-Miscible Organic Solvents
228
8.4.3.2
Building Quantitative Models for the
Hofmeister
Series and Cohn-
Edsall and Setschenow Equations
228
8.4.4
Aqueous Two-Phase Extraction
229
Contents
8.5
Downstream
Processing:
Concentration and Purification of Proteins
231
8.5.1
Dialysis
(Ultrafiltration)
(adapted in part from Blanch,
1997) 231
8.5.2
Chromatography
233
8.5.2.1
Theory of Chromatography
233
8.5.2.2
Different Types of Chromatography
235
8.5.3
Drying: Spray Drying, Lyophilization, Stabilization for Storage
236
8.6
Examples of Biocatalyst Purification
237
8.6.1
Example
1:
Alcohol Dehydrogenase [(R)-ADH from L.
brevis (Riebel,
1997)] 237
8.6.2
Example
2:
L-Amino Acid
Oxidase
from Rhodococcus opacus (Geueke
2002a,b)
238
8.6.3
Example
3:
Xylose Isomerase from Thermoanaerobium Strain JW/SL-
YS
489 240
9
Methods for the Investigation of Proteins
243
9.1
Relevance of Enzyme Mechanism
244
9.2
Experimental Methods for the Investigation of an Enzyme Mechanism
245
9.2.1
Distribution of Products (Curtin-Hammett Principle)
245
9.2.2
Stationary Methods of Enzyme Kinetics
246
9.2.3
Linear Free Enthalpy Relationships (LFERs): Brensted and Hammett
Effects
248
9.2.4
Kinetic Isotope Effects
249
9.2.5
Non-stationary Methods of Enzyme Kinetics:
Titration
of Active Sites
249
9.2.5.1
Determination of Concentration of Active Sites
249
9.2.6
Utility of the Elucidation of Mechanism: Transition-
S
tate
Analog
Inhibitors
251
9.3
Methods of Enzyme Determination
253
9.3.1
Quantification of Protein
253
9.3.2
Isoelectric Point Determination
254
9.3.3
Molecular Mass Determination of Protein Monomer: SDS-PAGE
254
9.3.4
Mass of an Oligomeric Protein: Size Exclusion Chromatography (SEC)
256
9.3.5
Mass Determination: Mass Spectrometry (MS) (after
Kellner,
Lottspeich, Meyer)
257
9.3.6
Determination of
Amino
Acid Sequence by Tryptic Degradation, or
Acid, Chemical or Enzymatic Digestion
258
9.4
Enzymatic Mechanisms: General Acid-Base Catalysis
258
9.4.1
Carbonic Anhydrase II
258
9.4.2
Vanadium Haloperoxidase
260
9.5
Nucleophilic Catalysis
261
9.5.1
Serine
Proteases
261
9.5.2
Cysteine
in Nucleophilic Attack
265
XVI Contents
9.5.3
Lipase,
Another Catalytic Triad Mechanism
266
9.5.4
Metalloproteases
268
9.6
Electr
ophilic catalysis
269
9.6.1
Utilization of Metal Ions: ADH, a Different Catalytic Triad
269
9.6.1.1
Catalytic Mechanism of Horse Liver Alcohol Dehydrogenase,
a Medium-Chain Dehydrogenase
269
9.6.1.2
Catalytic Reaction Mechanism of
Drosophila ADH,
a Short-Chain Dehydrogenase
271
9.6.2
Formation of
a
Schiff
Base, Part I: Acetoacetate Decarboxylase, Aldolase
274
9.6.3
Formation of
a
Schiff
Base with Pyridoxal Phosphate (PLP):
Alaninę Racemase,
Amino
Acid
Transferase
275
9.6.4
Utilization of Thiamine
Pyrophosphate (TPP):
Transketolase
277
10
Protein Engineering
281
10.1
Introduction: Elements of Protein Engineering
282
10.2
Methods of Protein Engineering
283
10.2.1
Fusion PCR
284
10.2.2 Kunkel
Method
285
10.2.3
Site-Specific Mutagenesis Using the QuikChange Kit from Stratagene
287
10.2.4
Combined Chain Reaction (CCR)
288
10.3
Glucose (Xylose) Isomerase (GI) and Glycoamylase: Enhancement of
Thermostability
289
10.3.1
Enhancement of Thermostability in Glucose Isomerase (GI)
289
10.3.2
Resolving the Reaction Mechanism of Glucose Isomerase (GI):
Diffusion-Limited Glucose Isomerase?
292
10.4
Enhancement of Stability of Proteases against Oxidation and Thermal
Deactivation
293
10.4.1
Enhancement of Oxidation Stability of Subtilisin
293
10.4.2
Thermostability of Subtilisin
295
10.5
Creating New Enzymes with Protein Engineering
295
10.5.1
Redesign of
a Lactate
Dehydrogenase
295
10.5.2
Synthetic Peroxidases
297
10.6
Dehydrogenases, Changing Cofactor Specificity
298
10.7
Oxygenases
300
10.8
Change of Enantioselectivity with Site-Specific Mutagenesis
302
10.9
Techniques Bridging Different Protein Engineering Techniques
303
10.9.1
Chemically Modified Mutants, a Marriage of Chemical Modification
and Protein Engineering
303
10.9.2
Expansion of Substrate Specificity with Protein Engineering and
Directed Evolution
304
11
Applications of
Recombinant
DNA
Technology: Directed Evolution
309
11.1
Background of Evolvability of Proteins
310
Contents
1.1.1.1
Purpose of Directed
Evolution 310
11.1.2
Evolution and Probability
311
11.1.3
Evolution: Conservation of Essential Components of Structure
313
11.2
Process steps in Directed Evolution: Creating Diversity and Checking
for Hits
314
11.2.1
Creation of Diversity in
a
DNA
Library
315
11.2.2
Testing for Positive Hits: Screening or Selection
318
11.3
Experimental Protocols for Directed Evolution
319
11.3.1
Creating Diversity: Mutagenesis Methods
319
11.3.2
Creating Diversity: Recombination Methods
319
11.3.2.1 DNA
Shuffling
320
11.3.2.2
Staggered Extension Process (StEP)
321
11.3.2.3
RACHITT (Random Chimeragenesis on Transient Templates)
322
11.3.3
Checking for Hits: Screening Assays
323
11.3.4
Checking for Hits: Selection Procedures
324
11.3.5
Additional Techniques of Directed Evolution
325
11.4
Successful Examples of the Application of Directed Evolution
325
11.4.1
Application of Error-prone PCR: Activation of Subtilisin in DMF
325
11.4.2
Application of
DNA
Shuffling: Recombination of p-Nitrobenzyl
Esterase
Genes
326
11.4.3
Enhancement of Thermostability: p-Nitrophenyl
Esterase
328
11.4.4
Selection instead of Screening: Creation of
a
Monomeric Chorismate
Mutase
329
11.4.5
Improvement of Enantioselectivity: Pseudomonas aeruginosa
Lipase
329
11.4.6
Inversion of Enantioselectivity: Hydantoinase
330
1.1.4.7
Redesign of an Enzyme s Active Site: KDPG Aldolase
331
11.5
Comparison of Directed Evolution Techniques
331
11.5.1
Comparison of Error-Prone PCR and
DNA
Shuffling:
Increased Resistance against Antibiotics
331
11.5.2
Protein Engineering in Comparison with Directed Evolution:
Aminotransferases
332
11.5.2.1
Directed Evolution of Aminotransferases
332
11.5.3
Directed Evolution of a Pathway:
Caro
tenoids
333
12
Biocatalysis in Non-conventional Media
339
12.1
Enzymes in Organic Solvents
340
12.2
Evidence for the Perceived Advantages of Biocatalysts in Organic Media
341
12.2.1
Advantage
1:
Enhancement of Solubility of Reactants
341
12.2.2
Advantage
2:
Shift of Equilibria in Organic Media
342
12.2.2.1
Biphasic Reactors
342
12.2.3
Advantage
3:
Easier Separation
343
12.2.4
Advantage
4:
Enhanced Stability of Enzymes in Organic Solvents
344
12.2.5
Advantage
5:
Altered Selectivity of Enzymes in Organic Solvents
344
XVIII Contents
12.3
State
of Knowledge of Functioning of Enzymes in Solvents
344
12.3.1
Range of Enzymes, Reactions, and Solvents
344
12.3.2
The Importance of Water in Enzyme Reactions in Organic Solvents
345
12.3.2.1
Exchange of Water Molecules between Enzyme Surface and
Bulk Organic Solvent
345
12.3.2.2
Relevance of Water Activity
346
12.3.3
Physical Organic Chemistry of Enzymes in Organic Solvents
347
12.3.3.1
Active Site and Mechanism
347
12.3.3.2
Flexibility of Enzymes in Organic Solvents
347
12.3.3.3
Polarity and Hydrophobicity of Transition State and Binding Site
348
123.4
Correlation of Enzyme Performance with Solvent Parameters
349
12.3.4.1
Control through Variation of Hydrophobocity: log
Ρ
Concept
350
12.3.4.2
Correlation of Enantioselectivity with Solvent Polarity and
Hydrophobicity
350
12.4
Optimal Handling of Enzymes in Organic Solvents
351
12.4.1
Enzyme Memory in Organic Solvents
352
12.4.2
Low Activity in Organic Solvents Compared to Water
353
12.4.3
Enhancement of Selectivity of Enzymes in Organic Solvents
354
12.5
Novel Reaction Media for Biocatalytic Transformations
355
12.5.1
Substrate as Solvent (Neat Substrates):
Acrylamide from Acrylonitrile with Nitrile Hydratase
355
12.5.2
Supercritical Solvents
356
12.5.3
Ionic Liquids
356
12.5.4
Emulsions [Manufacture of Phosphatidylglycerol (PG)]
357
12.5.5
Microemulsions
358
12.5.6
Liquid Crystals
358
12.5.7
Ice-Water Mixtures
359
12.5.8
High-Density Eutectic Suspensions
361
12.5.9
High-Density Salt Suspensions
362
12.5.10
Solid-to-Solid Syntheses
363
12.6
Solvent as a Parameter for Reaction Optimization ( Medium
Engineering )
366
12.6.1
Change of Substrate Specificity with Change of ReactionM:
Specificity of
Serine
Proteases
366
12.6.2
Change of Regioselectivity by Organic Solvent Medium
367
12.6.3
Solvent Control of Enantiospecificity of Nifedipines
367
13
Pharmaceutical Applications of Biocatalysis
373
13.1
Enzyme Inhibition for the Fight against Disease
374
13.1.1
Introduction
374
13.1.2
Procedure for the Development of Pharmacologically Active
Compounds
376
13.1.3
Process for the Registration of New Drugs
377
13.1.4
Chiral versus Non-chiral Drugs
379
Contents
XIX
13.2 Enzyme
Cascades
and Biology of Diseases
380
13.2.1
β-
Lactam
Antibiotics
380
13.2.2
Inhibition of Cholesterol Biosynthesis (in part after Suckling,
1990)
382
13.2.3
Pulmonary Emphysema, Osteoarthritis: Human Leucocyte Elastase
(HLE)
385
13.2.4
AIDS: Reverse Transcriptase and
HIV
Protease Inhibitors
389
13.3
Pharmaceutical Applications of Biocatalysis
393
13.3.1
Antiinfectives (see also Chapter
7,
Section
7.5.1) 393
13.3.1.1
Cilastatin
393
13.3.2
Anticholesterol Drugs
393
13.3.2.1
Cholesterol Absorption Inhibitors
395
13.3.3
Anti-AIDS Drugs
396
13.3.3.1
Abacavir Intermediate
396
13.3.3.2
Lobucavir Intermediate
397
13.3.3.3
cis-Aminoindanol: Building Block for Indinavir (Crixivan®)
397
13.3.4
High Blood Pressure Treatment
398
13.3.4.1
Biotransformations
towards Omaparrilat
398
13.3.4.2
Lipase
Reactions to Intermediates for Cardiovascular Therapy
400
13.4
Applications of Specific Biocatalytic Reactions in Pharma
402
13.4.1
Reduction of Keto Compounds with Whole Cells
402
13.4.1.1
Trimegestone
402
13.4.1.2
Reduction of Precursor to Carbonic Anhydrase Inhibitor L-685393
404
13.4.1.3
Montelukast
404
13.4.1.4
LY300164
404
13.4.2
Applications of Pen
G
Acylase in Pharma
406
13.4.2.1
Loracarbef®
406
13.4.2.2
Xemilofibran
406
13.4.3
Applications of Lipases and
Esterases
in Pharma
407
13.4.3.1
ITD4 Antagonist MK-0571
407
13.4.3.2
Tetrahydrolipstatin
407
14
Bioinformatics
413
14.1
Starting Point: from Consequence (Function) to Sequence
414
14.1.1
Conventional Path: from Function to Sequence
414
14.1.2
Novel Path: from Sequence to Consequence (Function)
414
14.2
Bioinformatics: What is it, Why do we Need it, and Why Now? (NCBI
Homepage)
415
14.2.1
What is Bioinformatics?
415
14.2.2
Why do we Need Bioinformatics?
416
14.2.3
Why Bioinformatics Now?
416
14.3
Tools of Bioinformatics: Databases, Alignments, Structural Mapping
418
14.3.1
Available Databases
418
14.3.2
Protein Data Bank (PDB)
418
XX
Contents
14.3.3 Protein Explorer 419
14.3.4 ExPASy Server:
Roche
Applied Science Biochemical
Pathways
419
14.3.5 GenBank 419
14.3.6 SwissProt 420
14.3.7 Information
on an
Enzyme:
the Example of dehydrogenases
420
14.3.7.1
Sequence
Information 421
14.3.7.2
Structural
Information 422
14.4 Applied Bioinformatics Tools,
with Examples
422
14.4.1 BLAST 422
14.4.2
Aligning Several
Protein
Sequences using ClustalW
425
14.4.3
Task: Whole Genome Analysis
427
14.4.4
Phylogenetic Tree
427
14.5 Bioinformatics
for Structural Information on Enzymes
429
14.5.1
The Status of Predicting Protein Three-Dimensional Structure
430
14.6
Conclusion and Outlook
431
15
Systems Biology for Biocatalysis
433
15.1
Introduction to Systems Biology
434
15.1.1
Systems Approach versus Reductionism
434
15.1.2
Completion of Genomes: Man, Earthworm, and Others
435
15.2
Genomics, Proteomics, and other -omics
435
15.2.1
Genomics
435
15.2.2
Proteomics
436
15.3
Technologies for Systems Biology
438
15.3.1
Two-Dimensional Gel Electrophoresis (2D PAGE)
438
15.3.1.1
Separation by Chroma tography or Capillary Electrophoresis
439
15.3.1.2
Separation by Chemical Tagging
440
15.3.2
Mass Spectroscopy
441
15.3.2.1
MALDI-TOF-MS
(Matrix-Assisted Laser Desorption/Ionization Time-of-Flight MS)
444
15.3.2.2
ESI-triple-quadrupole MS
444
15.3.2.3
ESI-MS Using an Ion Trap Analyzer
445
15.3.3 DNA
Microarrays
446
15.3.4
Protein Microarrays
447
15.3.5
Applications of Genomics and Proteomics in Biocatalysis
448
15.3.5.1
Lactic Acid Bacteria and Proteomics
448
15.4
Metabolic Engineering
449
15.4.1
Concepts of Metabolic Engineering
449
15.4.2
Examples of Metabolic Engineering
451
16
Evolution of Biocatalytic Function
457
16.1
Introduction
458
16.1.2
Congruence of Sequence, Function, Structure, and Mechanism
460
16.2
Search Characteristics for Relatedness in Proteins
461
16.2.1
Classification of Relatedness of Proteins: the -log Family
461
Contents
XX
16.2.2
Classification into
Protein
Families
464
16.2.3
Dominance of Different Mechanisms
465
16.3
Evolution of New Function in Nature
466
16.3.1
Dual-Functionality Proteins
469
16.3.1.1
Moonlighting Proteins
469
16.3.1.2
Catalytic Promiscuity
469
16.3.2
Gene Duplication
470
16.3.3
Horizontal Gene Transfer (HGT)
471
16.3.4
Circular Permutation
474
16.4
α/β
-Barrel
Proteins as a Model for the Investigation of Evolution
474
16.4.1
Why Study
α/β
-Barrel
Proteins?
474
16.4.2
Example of Gene Duplication:
Mandelate
and a-Ketoadipate Pathways
475
16.4.2.1
Description of Function
480
16.4.3
Exchange of Function in the Aromatic Biosynthesis Pathways:
Trp
and
His Pathways
481
17
Stability of Proteins
487
17.1
Summary: Protein Folding, First-Order Decay, Arrhenius Law
488
17.1.1
The Protein Folding Problem
488
17.1.2
Why do Proteins Fold?
489
17.2
Two-State Model: Thermodynamic Stability of Proteins (Unfolding)
491
17.2.1
Protein Unfolding and Deactivation
491
17.2.2
Thermodynamics of Proteins
491
17.3
Three-State Model: Lumry-Eyring Equation
493
17.3.1
Enzyme Deactivation
493
17.3.2
Empirical Deactivation Model
494
17.4
Four-State Model: Protein Aggregation
496
17.4.1
Folding, Deactivation, and Aggregation
496
17.4.2
Model to Account for Competition between Folding and Inclusion Body
Formation
498
17.4.2.1
Case
1:
In Vitro
-
Protein Synthesis Unimportant
498
17.4.2.2
Case
2:
In Vivo
-
Protein Synthesis Included
499
17.5
Causes of Instability of Proteins:
AG
< 0,
γ(ί),
A
501
17.5.1
Thermal Inactivation
502
17.5.2
Deactivation under the Influence of Stirring
503
17.5.3
Deactivation under the Influence of Gas Bubbles
504
17.5.4
Deactivation under the Influence of Aqueous/Organic Interfaces
505
17.5.5
Deactivation under the Influence of Salts and Solvents
505
17.6
Biotechnological Relevance of Protein Folding: Inclusion Bodies
505
17.7
Summary: Stabilization of Proteins
506
17.7.1
Correlation between Stability and Structure
507
XXII Contents
18
Artificial
Enzymes
511
18.1
Catalytic Antibodies
512
18.1.1
Principle of Catalytic Antibodies: Connection between Chemistry and
Immunology
512
18.1.2
Test Reaction Selection, Haptens, Mechanisms, Stabilization
514
18.1.2.1
Mechanism of Antibody-Catalyzed Reactions
516
18.1.2.2
Stabilization of Charged Transition States
517
18.1.2.3
Effect of Antibodies as Entropy Traps
517
18.1.3
Breadth of Reactions Catalyzed by Antibodies
518
18.1.3.1
Fastest Antibody-Catalyzed Reaction in Comparison with Enzymes
518
18.1.3.2
Antibody-Catalyzed Reactions without Corresponding Enzyme
Equivalent
518
18.1.3.3
Example of a Pericyclic Reaction: Claisen Rearrangement
518
18.1.3.4
Antibody Catalysts with Dual Activities
518
18.1.3.5
Scale-Up of an Antibody-Catalyzed Reaction
520
18.1.3.6
Perspective for Catalytic Antibodies
520
18.2
Other Proteinaceous Catalysts: Ribozymes and Enzyme Mimics
521
18.2.1
Ribozymes:
RNA
World before Protein World?
521
18.2.2
Proteinaceous Enzyme Mimics
521
18.3
Design of Novel Enzyme Activity: Enzyme Models (Synzymes)
523
18.3.1
Introduction
523
18.3.2
Enzyme Models on the Basis of the Binding Step: Diels-Alder Reaction
523
18.3.3
Enzyme Models with Binding and Catalytic Effects
525
18.4
Heterogenized/Immobilized Chiral Chemical Catalysts
526
18.4.1
Overview of Different Approaches
526
18.4.2
Immobilization with Polyamino Acids as Chiral Polymer Catalysts
526
18.4.3
Immobilization on Resins or other Insoluble Carriers
527
18.4.4
Heterogenization with Dendrimers
528
18.4.5
Retention of Heterogenized Chiral Chemical Catalysts in a Membrane
Reactor
529
18.4.6
Recovery of Organometallic Catalysts by Phase Change: Liquid-Liquid
Extraction
531
18.5
Tandem Enzyme Organometallic Catalysts
532
19
Design of Biocatalytic Processes
539
19.1
Design of Enzyme Processes: High-Fructose Corn Syrup (HFCS)
540
19.1.1
Manufacture of HFCS from Glucose with Glucose Isomerase (GI):
Process Details
540
19.1.2
Mathematical Model for the Description of the Enzyme Kinetics of
Glucose Isomerase (GI)
541
19.1.3
Evaluation of the Model of the GI Reaction in the Fixed-Bed Reactor
543
19.1.4
Productivity of a Fixed-Bed Enzyme Reactor
547
Contents XXIII
19.2 Processing
of Fine Chemicals or Pharmaceutical Intermediates in an
Enzyme Membrane Reactor
549
19.2.1
Introduction
549
19.2.2
Determination of Process Parameters of a Membrane Reactor
550
19.2.2.1
Case
1:
Leakage through Membrane, no Deactivation
551
19.2.2.2
Case
2:
Leakage through the Membrane and Deactivation of Enzyme
552
19.2.2.3
Design Criterion for EMRs
552
19.2.3
Large-Scale Applications of Membrane Reactors
553
19.2.3.1
Enantiomerically Pure 1-Amino Acids for Infusion Solutions and as
Building Blocks for New Drugs
553
19.2.3.2
Aqueous-Organic Membrane Reactors
554
19.2.3.3
Other Processes in Enzyme Membrane Reactors
554
19.3
Production of Enantiomerically Pure
Hydrophobie
Alcohols:
Comparison of Different Process Routes and Reactor Configurations
556
19.3.1
Isolated Enzyme Approach
556
19.3.2
Whole-Cell Approach
559
19.3.3
Organometallic Catalyst Approach
561
19.3.4
Comparison of Different Catalytic Reduction Strategies
563
20
Comparison of Biological and Chemical Catalysts for Novel Processes
569
20.1
Criteria for the Judgment of (Bio-Jcatalytic Processes
570
20.1.1
Discussion: Jacobsen s Five Criteria
570
20.1.2
Comment on Jabobseris Five Criteria
572
20.2
Position of Biocatalysis in Comparison to Chemical Catalysts for Novel
Processes
575
20.2.1
Conditions and Framework for Processes of the Future
575
20.2.2
Ibuprofen (Painkiller)
577
20.2.3
Indigo (Blue Dye)
578
20.2.4
Menthol (Peppermint Flavoring Agent)
580
20.2.4.1
Separation of Diastereomeric Salt Pairs
580
20.2.4.2
Homogeneous Catalysis with Rh-BINAP
580
20.2.4.3
Lipase-Catalyzed Resolution of Racemic Menthol Esters
582
20.2.5
Ascorbic Acid (Vitamin C)
583
20.2.5.1
The Traditional
Reichstein-Grüssner
Synthesis
584
20.2.5.2
Two-Step Fermentation Process to 2-Ketogulonic Acid with Chemical
Step to Ascorbic Acid
584
20.2.5.3
One-Step Fermentation to 2-Ketogulonic Acid with Chemical Step to
Ascorbic Acid
585
20.3
Pathway Engineering through Metabolic Engineering
586
20.3.1
Pathway Engineering for Basic Chemicals: 1,3-Propanediol
586
20.3.2
Pathway Engineering for Pharmaceutical Intermediates:
cis-Aminoindanol
588
Index
593
|
| any_adam_object | 1 |
| author | Bommarius, Andreas Sebastian Riebel, Bettina |
| author_facet | Bommarius, Andreas Sebastian Riebel, Bettina |
| author_role | aut aut |
| author_sort | Bommarius, Andreas Sebastian |
| author_variant | a s b as asb b r br |
| building | Verbundindex |
| bvnumber | BV016522299 |
| classification_rvk | VE 7040 VK 8700 VN 7340 VN 8900 WD 5000 WD 5050 WF 9720 |
| classification_tum | CIT 970f CHE 825f |
| ctrlnum | (OCoLC)248372268 (DE-599)BVBBV016522299 |
| dewey-full | 660.634 |
| dewey-hundreds | 600 - Technology (Applied sciences) |
| dewey-ones | 660 - Chemical engineering |
| dewey-raw | 660.634 |
| dewey-search | 660.634 |
| dewey-sort | 3660.634 |
| dewey-tens | 660 - Chemical engineering |
| discipline | Chemie / Pharmazie Biologie Chemie Chemie-Ingenieurwesen Biotechnologie |
| format | Book |
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| id | DE-604.BV016522299 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:11:30Z |
| institution | BVB |
| isbn | 3527303448 |
| language | German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010211018 |
| oclc_num | 248372268 |
| open_access_boolean | |
| owner | DE-20 DE-91G DE-BY-TUM DE-M49 DE-BY-TUM DE-1046 DE-19 DE-BY-UBM DE-526 DE-83 DE-703 DE-29T DE-634 DE-91S DE-BY-TUM DE-11 DE-523 |
| owner_facet | DE-20 DE-91G DE-BY-TUM DE-M49 DE-BY-TUM DE-1046 DE-19 DE-BY-UBM DE-526 DE-83 DE-703 DE-29T DE-634 DE-91S DE-BY-TUM DE-11 DE-523 |
| physical | XXIII, 611 S. graph. Darst. |
| publishDate | 2004 |
| publishDateSearch | 2004 |
| publishDateSort | 2004 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Bommarius, Andreas Sebastian Verfasser aut Biocatalysis [fundamentals and applications] A. S. Bommarius ; B. R. Riebel Weinheim Wiley-VCH 2004 XXIII, 611 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biokatalyse Biokatalyse (DE-588)4393622-2 gnd rswk-swf Biokatalysator (DE-588)4006842-0 gnd rswk-swf Biokatalyse (DE-588)4393622-2 s DE-604 Biokatalysator (DE-588)4006842-0 s 1\p DE-604 Riebel, Bettina Verfasser aut http://www3.ub.tu-berlin.de/ihv/001717247.pdf Inhaltsverzeichnis Digitalisierung UB Augsburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010211018&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Bommarius, Andreas Sebastian Riebel, Bettina Biocatalysis [fundamentals and applications] Biokatalyse Biokatalyse (DE-588)4393622-2 gnd Biokatalysator (DE-588)4006842-0 gnd |
| subject_GND | (DE-588)4393622-2 (DE-588)4006842-0 |
| title | Biocatalysis [fundamentals and applications] |
| title_auth | Biocatalysis [fundamentals and applications] |
| title_exact_search | Biocatalysis [fundamentals and applications] |
| title_full | Biocatalysis [fundamentals and applications] A. S. Bommarius ; B. R. Riebel |
| title_fullStr | Biocatalysis [fundamentals and applications] A. S. Bommarius ; B. R. Riebel |
| title_full_unstemmed | Biocatalysis [fundamentals and applications] A. S. Bommarius ; B. R. Riebel |
| title_short | Biocatalysis |
| title_sort | biocatalysis fundamentals and applications |
| title_sub | [fundamentals and applications] |
| topic | Biokatalyse Biokatalyse (DE-588)4393622-2 gnd Biokatalysator (DE-588)4006842-0 gnd |
| topic_facet | Biokatalyse Biokatalysator |
| url | http://www3.ub.tu-berlin.de/ihv/001717247.pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010211018&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT bommariusandreassebastian biocatalysisfundamentalsandapplications AT riebelbettina biocatalysisfundamentalsandapplications |
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