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Biocatalysis, Enzyme Engineering and Biotechnology G P1: SFK/UKS P2: SFK BLBS102-c07 BLBS102-Simpson March 21, 2012 11:12 Trim: 276mm X 219mm Printer Name: Yet to Come 7 Biocatalysis, Enzyme Engineering and Biotechnology G. A. Kotzia, D. Platis, I. A. Axarli, E. G. Chronopoulou, C. Karamitros, and N. E. Labrou Preface Enzyme Utilisation in Industry Enzyme Structure and Mechanism Enzymes Involved in Xenobiotic Metabolism and Nomenclature and Classification of Enzymes Biochemical Individuality Basic Elements of Enzyme Structure Phase I The Primary Structure of Enzyme Phase II The Three-Dimensional Structure of Enzymes Phase III Theory of Enzyme Catalysis and Mechanism Acknowledgements Coenzymes, Prosthetic Groups and Metal Ion Cofactors References Kinetics of Enzyme-Catalysed Reactions Thermodynamic Analysis Abstract: Enzymes are biocatalysts evolved in nature to achieve Enzyme Dynamics During Catalysis the speed and coordination of nearly all the chemical reactions that Enzyme Production define cellular metabolism necessary to develop and maintain life. Enzyme Heterologous Expression The application of biocatalysis is growing rapidly, since enzymes The Choice of Expression System offer potential for many exciting applications in industry. The ad- Bacterial Cells vent of whole genome sequencing projects enabled new approaches Mammalian Cells for biocatalyst development, based on specialised methods for en- Yeast zyme heterologous expression and engineering. The engineering of Filamentous Fungi enzymes with altered activity, specificity and stability, using site- Insect Cells directed mutagenesis and directed evolution techniques are now Dictyostelium discoideum Trypanosomatid Protozoa well established. Over the last decade, enzyme immobilisation has Transgenic Plants become important in industry. New methods and techniques for en- Transgenic Animals zyme immobilisation allow for the reuse of the catalysts and the Enzyme Purification development of efficient biotechnological processes. This chapter Ion-Exchange Chromatography reviews advances in enzyme technology as well as in the techniques Affinity Chromatography and strategies used for enzyme production, engineering and immo- Enzyme Engineering bilisation and discuss their advantages and disadvantages. Tailor-Made Enzymes by Protein Engineering Rational Enzyme Design Directed Enzyme Evolution PREFACE Immobilised Enzymes Methods for Immobilisation Enzymes are proteins with powerful catalytic functions. They Adsorption increase reaction rates sometimes by as much as one million Covalent Coupling fold, but more typically by about one thousand fold. Catalytic Cross-linking activity can also be shown, to a limited extent, by biological Entrapment and Encapsulation molecules other than the ‘classical’ enzymes. For example, an- New Approaches for Oriented Enzyme Immobilisation: tibodies raised to stable analogues of the transition states of The Development of Enzyme Arrays a number of enzyme-catalysed reactions can act as effective Food Biochemistry and Food Processing, Second Edition. Edited by Benjamin K. Simpson, Leo M.L. Nollet, Fidel Toldra,´ Soottawat Benjakul, Gopinadhan Paliyath and Y.H. Hui. C 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc. 125 P1: SFK/UKS P2: SFK BLBS102-c07 BLBS102-Simpson March 21, 2012 11:12 Trim: 276mm X 219mm Printer Name: Yet to Come 126 Part 2: Biotechnology and Enzymology catalysts for those reactions (Hsieh-Wilson et al. 1996). In ad- above. ‘b’ denotes the sub-class, which usually specifies more dition, RNA molecules can also act as a catalyst for a number precisely the type of the substrate or the bond cleaved, e.g. by of different types of reactions (Lewin 1982). These antibod- naming the electron donor of an oxidation–reduction reaction or ies and RNA catalysts are known as abzymes and ribozymes, by naming the functional group cleaved by a hydrolytic enzyme. respectively. ‘c’ denotes the sub-subclass, which allows an even more precise Enzymes have a number of distinct advantages over conven- definition of the reaction catalysed. For example, sub-subclasses tional chemical catalysts. Among these are their high productiv- of oxidoreductases are denoted by naming the acceptor of the ity, catalytic efficiency, specificity and their ability to discrim- electron from its respective donor. ‘d’ is the serial number of the inate between similar parts of molecules (regiospecificity) or enzyme within its sub-subclass. An example will be analysed. optical isomers (stereospecificity). Enzymes, in general, work The enzyme that oxidises d-glucose using molecular oxygen under mild conditions of temperature, pressure and pH. This catalyses the following reaction: advantage decreases the energy requirements and therefore re- duces the capital costs. However, there are some disadvantages in the use of enzymes, such as high cost and low stability. These O O O O shortcomings are currently being addressed mainly by employ- O Glucose oxidase O + O2 + H2O2 ing protein engineering approaches using recombinant DNA O O O O technology (Stemmer 1994, Ke and Madison 1997). These ap- O O proaches aim at improving various properties such as thermosta- β-D-Glucose D-Glucono-1,5-lactone bility, specificity and catalytic efficiency. The advent of designer biocatalysts enables production of not only process-compatible Scheme 7.1. enzymes, but also novel enzymes able to catalyse new or unexploited reactions (Schmidt-Dannert et al. 2000, Umeno and Arnold 2004). This is just the start of the enzyme technology era. Hence, its systematic name is d-glucose: oxygen oxidoreduc- tase, and its systematic number is EC 1.1.3.4. The systematic names are often quite long, and therefore, ENZYME STRUCTURE AND MECHANISM short trivial names along with systematic numbers are often Nomenclature and Classification of Enzymes more convenient for enzyme designation. These shorter names are known as recommended names. The recommended names Enzymes are classified according to the nature of the reaction consist of the suffix ‘–ase’ added to the substrate acted on. For they catalyse (e.g. oxidation/reduction, hydrolysis, synthesis, example for the enzyme mentioned above, the recommended etc.) and sub-classified according to the exact identity of their name is glucose oxidase. substrates and products. This nomenclature system was estab- It should be noted that the system of nomenclature and classi- lished by the Enzyme Commission (a committee of the Inter- fication of enzymes is based only on the reaction catalysed and national Union of Biochemistry). According to this system, all takes no account of the origin of the enzyme, that is from the enzymes are classified into six major classes: species or tissue it derives. 1. Oxidoreductases, which catalyse oxidation–reduction reac- tions. Basic Elements of Enzyme Structure 2. Transferases, which catalyse group transfer from one molecule to another. The Primary Structure of Enzyme 3. Hydrolases, which catalyse hydrolytic cleavage of C–C, Enzymes are composed of l-α-amino acids joined together by C–N, C–O, C–S or O–P bonds. These are group transfer a peptide bond between the carboxylic acid group of one amino reactions but the acceptor is always water. acid and the amino group of the next. 4. Lyases, which catalyse elimination reactions, resulting in the cleavage of C–C, C–O, C–N, C–S bonds or the for- mation of a double bond, or conversely adding groups to R1 R2 R1 H H double bonds. ⏐ ⏐ ⏐ ⏐ ⏐ ⎯ ⎯ ⎯ ⎯ H2O ⎯ ⎯ ⎯ ⎯ ⎯ 5. Isomerases, which catalyse isomerisation reactions, e.g., H2N C COOH H2N C COOH H2N C C= N C COOH racemisation, epimerisation, cis-trans-isomerisation, tau- ⏐ ⏐ ⏐ ⏐ H H H O R tomerisation. 2 6. Ligases, which catalyse bond formation, coupled with the Peptitde bond hydrolysis of a high-energy phosphate bond in ATP or a Scheme 7.2. similar triphosphate. The Enzyme Commission system consists of a numerical clas- sification hierarchy of the form ‘E.C. a.b.c.d’ in which ‘a’ rep- There are 20 common amino acids in proteins, which are spec- resents the class of reaction catalysed and can take values from ified by the genetic code; in rare cases, others occur as the prod- 1 to 6 according to the classification of reaction types given ucts of enzymatic modifications after translation. A common P1: SFK/UKS P2: SFK BLBS102-c07 BLBS102-Simpson March 21, 2012 11:12 Trim: 276mm X 219mm Printer Name: Yet to Come 7 Biocatalysis, Enzyme Engineering and Biotechnology 127 feature of all 20 amino acids is a central carbon atom (Cα)to first amino acid and the free amino group of the second amino which a hydrogen atom, an amino group (–NH2) and a carboxy acid. The first amino acid in any polypeptide sequence has a free group (–COOH) are attached. Free amino acids are usually zwit- amino group and the terminal amino acid has a free carboxyl terionic at neutral pH, with the carboxyl group deprotonated and group. The primary structure is responsible for the higher levels the amino group protonated. The structure of the most common of enzyme’s structure and therefore for the enzymatic activity amino acids found in proteins is shown in Table 7.1. Amino (Richardson 1981, Price and Stevens 1999). acids can be divided into four different classes depending on the structure of their side chains, which are called R groups: non- The Three-Dimensional Structure of Enzymes polar, polar uncharged, negatively charged (at neutral pH) and positively charged (at neutral pH; Richardson 1981). The prop- Enzymes are generally very closely packed globular structures erties of the amino acid side chains determine the properties of with only a small number of internal cavities, which are normally the proteins they constitute. The formation of a succession of filled by water molecules. The polypeptide chains of enzymes peptide bonds generates the ‘main chain’ or ‘backbone’. are organised into ordered, hydrogen bonded regions, known The primary structure of a protein places several constrains as secondary structure (Andersen and Rost 2003). In these or- on how it can fold to produce its three-dimensional structure dered structures, any buried carbonyl oxygen forms a hydro- (Cantor 1980, Fersht 1999). The backbone of a protein consists gen bond with an amino NH group.
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