Biocatalysis

The whole range of biocatalysis, from a firm grounding in theoretical concepts to in-depth coverage of practical applications and future perspectives.
The book not only covers reactions, products and processes with and from biological catalysts, but also the process of designing and improving such biocatalysts.
One unique feature is that the fields of chemistry, biology and bioengineering receive equal attention, thus addressing practitioners and students from all three areas.Mittlerweile nutzen alle so genannten Life Sciences (z.B. Pharma- und Ernährungswissenschaften) die Möglichkeiten der Biokatalyse. Auch das Interesse der verarbeitenden Industrie an umweltverträglichen Prozessen wächst stetig. Da kommt es nicht von ungefähr, dass die Erforschung von Biokatalysatoren weiter vorangeschritten ist als die anderer Katalysatorentypen. Biocatalysis gibt einen aktuellen Überblick über das Wissen in diesem Gebiet, von den theoretischen Grundlagen bis hin zu Anwendungen und einem Ausblick in die Zukunft.

Bommarius und Riebel geht es in ihrem Buch nicht nur um Reaktionen, Produkte und Prozesse im Zusammenhang mit biologischen Katalysen und Katalysatoren. Sie erläutern auch den Prozess der Entwicklung und Verbesserung von Biokatalysatoren. Dabei schenken sie den Bereichen Chemie, Biologie und Biotechnologie die gleiche Aufmerksamkeit, so dass ihr Buch für Praktiker und Studenten aus allen drei Bereichen von Nutzen ist.
Biocatalysis gliedert sich in die Abschnitte "Grundlagen und Basis-Tools", "Fortgeschrittene Tools" sowie "Anwendungen". Im ersten Teil gehen die Autoren unter anderem auf die Stellung der Biokatalyse in der Biotechnologie ein, beschreiben Isolierung und Vorbereitung von Mikroorganismen und stellen molekularbiologische Tools für die Biokatalyse vor. Teil II beschreibt zum Beispiel die Enzymherstellung sowie Methoden zur Protein-Untersuchung und beschäftigt sich mit pharmazeutischen Anwendungen der Biokatalyse und der Bioinformatik. Im letzten Abschnitt geht es schließlich um künstliche Enzyme, das Design biokatalytischer Prozesse und um neue Möglichkeiten, die sich durch den Einsatz der Bioinformatik eröffnen.

Preface v

Acknowledgments vii

1 Introduction to Biocatalysis 1

1.1 Overview:The Status of Biocatalysis at the Turn of the 21st Century 2

1.2 Characteristics of Biocatalysis as a Technology 6

1.3 Current Penetration of Biocatalysis 11

1.4 The Breadth of Biocatalysis 14

2 Characterization of a (Bio-)catalyst 19

2.1 Characterization of Enzyme Catalysis 20

2.2 Sources and Reasons for the Activity of Enzymes as Catalysts 23

2.3 Performance Criteria for Catalysts, Processes, and Process Routes 30

3 Isolation and Preparation of Microorganisms 43

3.1 Introduction 44

3.2 Screening of New Enzyme Activities 46

3.3 Strain Development 48

3.4 Extremophiles 52

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

4.3 Gene Isolation, Detection, and Verification 67

4.4 Cloning Techniques 77

4.5 (Over)expression of an Enzyme Function in a Host 81

5 Enzyme Reaction Engineering 91

5.1 Kinetic Modeling: Rationale and Purpose 92

5.2 The Ideal World: Ideal Kinetics and Ideal Reactors 94

5.3 Enzymes with Unfavorable Binding: Inhibition 97

5.4 Reactor Engineering 105

5.5 Enzyme Reactions with Incomplete Mass Transfer: Influence of Immobilization 113

5.6 Enzymes with Incomplete Stability: Deactivation Kinetics 119

5.7 Enzymes with Incomplete Selectivity: E-Value and its Optimization 126

6 Applications of Enzymes as Bulk Actives: Detergents, Textiles, Pulp and Paper, Animal Feed 135

6.1 Application of Enzymes in Laundry Detergents 136

6.2 Enzymes in the Textile Industry: Stone-washed Denims, Shiny Cotton Surfaces 140

6.3 Enzymes in the Pulp and Paper Industry: Bleaching of Pulp with Xylanases or Laccases 145

6.4 Phytase for Animal Feed: Utilization of Phosphorus 152

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

7.2 Enzymes as Catalysts in the Fine Chemicals Industry 170

7.3 Enzymes as Catalysts in the Food Industry 187

7.4 Enzymes as Catalysts towards Crop Protection Chemicals 195

7.5 Enzymes for Large-Scale Pharma Intermediates 197

8 Biotechnological Processing Steps for Enzyme Manufacture 209

8.1 Introduction to Protein Isolation and Purification 210

8.2 Basics of Fermentation 212

8.3 Fermentation and its Main Challenge: Transfer of Oxygen 218

8.4 Downstream Processing: Crude Purification of Proteins 223

8.5 Downstream Processing: Concentration and Purification of Proteins 231

8.6 Examples of Biocatalyst Purification 237

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

9.3 Methods of Enzyme Determination 253

9.4 Enzymatic Mechanisms: General Acid–Base Catalysis 258

9.5 Nucleophilic Catalysis 261

9.6 Electrophilic catalysis 269

10 Protein Engineering 281

10.1 Introduction: Elements of Protein Engineering 282

10.2 Methods of Protein Engineering 283

10.3 Glucose (Xylose) Isomerase (GI) and Glycoamylase: Enhancement of Thermostability 289

10.4 Enhancement of Stability of Proteases against Oxidation and Thermal Deactivation 293

10.5 Creating New Enzymes with Protein Engineering 295

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

11 Applications of Recombinant DNA Technology: Directed Evolution 309

11.1 Background of Evolvability of Proteins 310

11.2 Process steps in Directed Evolution: Creating Diversity and Checking for Hits 314

11.3 Experimental Protocols for Directed Evolution 319

11.4 Successful Examples of the Application of Directed Evolution 325

11.5 Comparison of Directed Evolution Techniques 331

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

12.3 State of Knowledge of Functioning of Enzymes in Solvents 344

12.4 Optimal Handling of Enzymes in Organic Solvents 351

12.5 Novel Reaction Media for Biocatalytic Transformations 355

12.6 Solvent as a Parameter for Reaction Optimization (“Medium Engineering”) 366

13 Pharmaceutical Applications of Biocatalysis 373

13.1 Enzyme Inhibition for the Fight against Disease 374

13.2 Enzyme Cascades and Biology of Diseases 380

13.3 Pharmaceutical Applications of Biocatalysis 393

13.4 Applications of Specific Biocatalytic Reactions in Pharma 402

14 Bioinformatics 413

14.1 Starting Point: from Consequence (Function) to Sequence 414

14.2 Bioinformatics: What is it, Why do we Need it, and Why Now? (NCBI Homepage) 415

14.3 Tools of Bioinformatics: Databases, Alignments, Structural Mapping 418

14.4 Applied Bioinformatics Tools, with Examples 422

14.5 Bioinformatics for Structural Information on Enzymes 429

14.6 Conclusion and Outlook 431

15 Systems Biology for Biocatalysis 433

15.1 Introduction to Systems Biology 434

15.2 Genomics, Proteomics, and other -omics 435

15.3 Technologies for Systems Biology 438

15.4 Metabolic Engineering 449

16 Evolution of Biocatalytic Function 457

16.1 Introduction 458

16.2 Search Characteristics for Relatedness in Proteins 461

16.3 Evolution of New Function in Nature 466

16.4 α/β-Barrel Proteins as a Model for the Investigation of Evolution 474

17 Stability of Proteins 487

17.1 Summary: Protein Folding, First-Order Decay, Arrhenius Law 488

17.2 Two-State Model: Thermodynamic Stability of Proteins (Unfolding) 491

17.3 Three-State Model: Lumry–Eyring Equation 493

17.4 Four-State Model: Protein Aggregation 496

17.5 Causes of Instability of Proteins: ∆G < 0, γ(t), A 501

17.6 Biotechnological Relevance of Protein Folding: Inclusion Bodies 505

17.7 Summary: Stabilization of Proteins 506

18 Artificial Enzymes 511

18.1 Catalytic Antibodies 512

18.2 Other Proteinaceous Catalysts: Ribozymes and Enzyme Mimics 521

18.3 Design of Novel Enzyme Activity: Enzyme Models (Synzymes) 523

18.4 Heterogenized/Immobilized Chiral Chemical Catalysts 526

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

19.2 Processing of Fine Chemicals or Pharmaceutical Intermediates in an Enzyme Membrane Reactor 549

19.3 Production of Enantiomerically Pure Hydrophobic Alcohols: Comparison of Different Process Routes and Reactor Configurations 556

20 Comparison of Biological and Chemical Catalysts for Novel Processes 569

20.1 Criteria for the Judgment of (Bio-)catalytic Processes 570

20.2 Position of Biocatalysis in Comparison to Chemical Catalysts for Novel Processes 575

20.3 Pathway Engineering through Metabolic Engineering 586

Index 593

PART I: FUNDAMENTALS AND BASIC TOOLS
Position of biocatalysis within biotechnology
Characterization of a (bio-)catalyst
Isolation and preparation of microorganisms
Molecular biology tools for biocatalysis
Enzyme reaction engineering
Applications of enzymes as bulk actives: detergents, textile, pulp and paper, animal feed
Applications of enzymes as catalyst:Chemicals, fine chemicals, food, pharmaceuticals
PART II: ADVANCED TOOLS
Biotechnological processing steps for enzyme manufacture
Methods for the investigation of proteins
Protein Engineering
Applications of recombinant DNA technology: Directed evolution
Biocatalysis in non-conventional media
Pharmaceutical applications of biocatalysis
Bioinformatics
Systems biology for biocatalysis
PART III: APPLICATIONS
Evolution of biocatalytic function
Stability of proteins
Artificial enzymes
Design of biocatalytic processes
Comparison of biocatalysts with homogeneous and heterogeneous chemical catalysts
New functions through application of bioinformatics
Genomics and proteomics: applications "...the book is excellent and could be read cover to cover or used for reference and I strongly recommend it to anyone interested in the field of biocatalysis whether they be graduate students just entering the field or more experienced practitioners."
Organic Process Research & Development

"This guidebook is warmly recommended to scientists in academia, industry and authorities engaged in biocatalysis because one unique feature of primary importance is that the interdisciplinary fields of chemistry, biology and bioengineering receive equal attention, thus, addressing both practioners and students from all three areas."
AFS

"The book nicely brings together the essentials of biocatalysis including reactions, the products and processes that utilize the methodology, and techniques for improving biocatalysts."
Catalyst

"I strongly recommend it to advanced students, experienced chemists, biologists, and engineers interested in or actively working in biocatalysis, as it is a rich source of information and offers an excellent opportunity to get an insight into neighbouring areas of expertise."
Angewandte Chemie I.E.

"The content of the book is excellent...the book is excellent and could be read cover to cover or used for reference and I strongly recommend it to anyone interested in the field of biocatalysis..."
Organic Process Research & Development

"With their book "Biocatalysis" Bommarius and Riebel successfully bridge the gap between textbooks and original research papers. The book is recommended for advanced students, experienced chemists and engineers interested in the area of industrial biocatalysis."
CHEMBIOCHEM

"...a timely and detailed summary of the important recent developments in the rapidly moving fields pertinent to harnessing the efficiency and specificity of biological catalysts. It will definitely assist research scientists' efforts to improve their own chemical transformations."
Synthesis
"Biocatalysis" ist ein interessantes und hervorragendes Lehrbuch zum Thema Biokatalyse...sehr interessantes Lesevergnügen...absolut lesenswert...Grundlagen zur Zellbiologie aber auch zum Thema Bioinformatik, Enzymkinetik und vielen weiteren Gebieten runden das gelungene Gesamtbild ab. Das Buch ist wahrlich eine Hilfe für Ingenieure, welche sich auf Biokatalyse spezialisieren wollen und im Umfeld zwischen Biologie, Biochemie und Chemie bestehen wollen."
www.organische-chemie.ch

"Ein durchaus empfehlenswertes Buch, das besonders diejenigen anspricht, die bereits vertiefte Kenntnisse in der molekularen Biologie, der (bio-)chemischen Synthese und Analytik besitzen und der englischen Fachsprache mächtig sind."
Mitteil. der FG Umweltchemie und Ökotoxikologie der GDCh

"Mit "Biocatalysis" liegt ein Werk vor, in dem die Autoren sorgsam die Balance halten, zwischen Lehrbuchwissen und aktuellen Forschungsergebnissen. Dadurch findet der Leser zeitökonomisch den Einstieg und vielmehr den Zugang auch in die aktuellsten Themen der Biokatalyse ohne sich durch den aktuellen Publikationsdschungel arbeiten zu müssen..."
Chemie-Online

"Biocatalysis" gibt einen aktuellen Überblick über das Wissen in diesem Gebiet, von den Grundlagen bis hin zu Anwendungen und einem Ausblick in die Zukunft."
Bioworld

"Den Autoren ist mit der Vorlage dieses Buches gelungen, ein typisches interdisziplinäres Wissenschaftsthema unter Berücksichtigung von allen Aspekten - Forschung, Entwicklung, Verfahrenstechnik, Produktion sowie prozeßbegleitende Technologien - in hervorragender Weise vorzustellen. Entscheidend für die Qualität und die Wichtung der adressierten Themen ist dabei, dass in hohem Maße die Erfahrungen aus der industriellen Verfahrensentwicklung einfließen." Arzneimittel-Forschung/Drug Research

"Bommarius und Riebel präsentieren mit Biocatalysis nun ein Werk, das alle wichtigen Aspekte der Biokatalyse abdeckt. Die größte Herausforderung bestand sicher darin, aus dem umfangreichen Datenbestand die wesentlichen Fakten herauszufiltern - mit ausgezeichnetem Ergebnis. ... Positiv fällt weiterhin auf, dass jedem Kapitel eine Zusammenfassung vorangestellt ist und viele aktuelle Beispiele biokatalytischer Verfahren mit dazugehörigen Hintergrundinformationen vorgestellt werden. ... Ich kann dieses Buch fortgeschrittenen Studenten sowie erfahrenen Chemikern, Biologen und Ingenieuren, die an Biokatalyse interessiert sind oder biokatalytische Methoden verwenden, sehr empfehlen."
Angewandte Chemie und Angewandte Chemie I.E.

"Mit dem Buch 'Biocatalysis - Fundamentals and Applications' schließen die Autoren die Kluft zwischen Forschungsergebnissen in der Biokatalyse und deren industrieller Anwendung sowie den dahinter stehenden Grundlagen aus Biochemie, organischer Synthese, Molekularbiologie, Kinetik und Reaktionstechnik. Durch ihre Erfahrung aus der Industrie ... eignen sich die Autoren für dieses Ziel bestens. ... Das Buch bietet eine gelungene Übersicht über den aktuellen Stand der Enzymtechnologie und wendet sich dabei hauptsächlich an fortgeschrittene Studenten und den forschenden Biokatalytiker. ... ist dieses Buch sicherlich eine Bereicherung für den 'biokatalytischen' Buchmarkt."
Nachrichten aus der Chemie
Andreas S. Bommarius obtained his diploma in Chemistry from the Technical Universtiy in Munich, Germany, and, in 1989, his PhD in Chemical Engineering from Massachusetts Institute of Technology (MIT) in Cambridge, MA,USA. In 1990, he joined Degussa as head of the Biocatalysis Laboratory and pilot plant. Since 2000 he is affiliated at Georgia Institute of Technology in Atlanta, Georgia, USA, as professor in the Schools of Chemical and Biomolecular Engineering and Chemistry and Biochemistry. His main research interests are novel redox enzyme systems, stability of protein biocatalysts, as well as novel catalysts through directed evolution.

Bettina R. Riebel obtained her diploma in Biology at the University of Cologne, Germany, and her PhD in Biochemistry at the University of Dusseldorf, Germany. She then occupied postdoctoral associate positions with Roche Diagnostics (then Boehringer Mannheim) in Penzberg and at the Research Center Julich. As of 2000, she is part of the Institute of Pathology in the School of Medicine at Emory University in Atlanta, Georgia, USA, where her main research interests are in host-pathogen relationships, and specifically in tyrosine kinases and cell signaling.
Long awaited, "Biocatalysis - Fundamentals and Applications" is finally available: Covering the whole range, from a firm grounding in theoretical concepts to in-depth coverage of the practical aspects and future
perspectives.
The book not only covers reactions, products and processes using biocatalysts, but also methods of designing and improving them. One unique feature is that chemistry, biology and bioengineering receive equal attention, thus addressing practitioners and students from all three fields.

Table of Contents
1. Introduction to Biocatalysis
2. Characterization of a (Bio-)catalyst
3. Isolation and Preparation of Microorganisms
4. Molecular Biology Tools for Biocatalysis
5. Enzyme Reaction Engineering
6. Applications of Enzymes as Bulk Actives: Detergents, Textiles, Pulp and Paper, Animal Feed
7. Applications of Enzymes as Catalysts: Basic Chemicals, Fine Chemicals, Food, Crop Protection, Bulk Pharmaceuticals
8. Biotechnological Processing Steps for Enzyme Manufacture
9. Methods for the Investigation of Proteins
10. Protein Engineering
11. Applications of Recombinant DNA Technology: Directed Evolution
12. Biocatalysis in Non-conventional Media
13. Pharmaceutical Applications of Biocatalysis
14. Bioinformatics
15. Systems Biology for Biocatalysis
16. Evolution of Biocatalytic Function
17. Stability of Proteins
18. Artificial Enzymes
19. Design of Biocatalytic Processes
20. Comparison of Biological and Chemical Catalysts for Novel Processes