Enzyme

Enzymes are applied in organic synthesis and in analytical chemistry, in industrial production processes of pharmaceuticals and in food processing. Finding a suitable enzyme for a desired transformation or with a de- fined specificity is not always an easy task. More than 3000 enzymes are well described to date. The Enzyme Handbook provides all the information for selecting the proper enzyme to perform defined transformations in a given environment. The Enzyme Handbook devotes a variable number of pages for each enzyme, depending on the amount of information available with the EC number as ordering criterion within a volume. Revised data sheets can be released for individual enzymes and newly characterized enzymes and they can easily be sorted into the binders at the appropriate place. Each data sheet is divided into 7 sections: - Nomenclature (EC number, Systematic name, Recom- mended name, Synonyms, CAS Reg. No.) - Reaction and specificity (Catalysed reaction, Reaction type, Natural substrates, Substrate spectrum, Product spectrum, Inhibitors, Cofactors/prosthetic groups, Metal compounds/salts, Turnover number, Specific activity, KM-value, pH-optimum, pH-range, Tem- perature optimum, Temperature range) - Enzyme structure (Molecular weight, Subunits, Glyco-/Lipoprotein) - Isolation/Preparation (Source organism, Source tissue, Localisation in source, Purification, Crystallization, Cloned, Renatured) - Stability (pH, Temperature, Oxidation, Organic sol- vent, General stability information, Storage) - Cross-References (to Structure Data Banks) - Literature references
Books dealing with the mechanisms of enzymatic reactions were written a generation ago. They included volumes entitled Bioorganic Mechanisms, I and II by T.C. Bruice and S.J. Benkovic, published in 1965, the volume entitled Catalysis in Chemistry and Enzymology by W.P. Jencks in 1969, and the volume entitled Enzymatic Reaction Mechanisms by C.T. Walsh in 1979. The Walsh book was based on the course taught by W.P. Jencks and R.H. Abeles at Brandeis University in the 1960's and 1970's. By the late 1970's, much more could be included about the structures of enzymes and the kinetics and mechanisms of enzymatic reactions themselves, and less emphasis was placed on chemical models. Walshs book was widely used in courses on enzymatic mechanisms for many years. Much has happened in the field of mechanistic enzymology in the past 15 to 20 years. Walshs book is both out-of-date and out-of-focus in todays world of enzymatic mechanisms. There is no longer a single volume or a small collection of volumes to which students can be directed to obtain a clear understanding of the state of knowledge regarding the chemicals mechanisms by which enzymes catalyze biological reactions. There is no single volume to which medicinal chemists and biotechnologists can refer on the subject of enzymatic mechanisms. Practitioners in the field have recognized a need for a new book on enzymatic mechanisms for more than ten years, and several, including Walsh, have considered undertaking to modernize Walshs book. However, these good intentions have been abandoned for one reason or another. The great size of the knowledge base in mechanistic enzymology has been a deterrent. It seems too large a subject for a single author, and it is difficult for several authors to coordinate their work to mutual satisfaction. This text by Perry A. Frey and Adrian D. Hegeman accomplishes this feat, producing the long-awaited replacement for Walshs classic text.
Experiments in the Purification and Characterization of Enzymes: A Laboratory Manual provides students with a working knowledge of the fundamental and advanced techniques of experimental biochemistry. Included are instructions and experiments that involve purification and characterization of enzymes from various source materials, giving students excellent experience in kinetics analysis and data analysis. Additionally, this lab manual covers how to evaluate and effectively use scientific data. By focusing on the relationship between structure and function in enzymes, Experiments in the Purification and Characterization of Enzymes: A Laboratory Manual provides a strong research foundation for students enrolled in a biochemistry lab course by outlining how to evaluate and effectively use scientific data in addition to offering students a more hands-on approach with exercises that encourage them to think deeply about the content and to design their own experiments. Instructors will find this book useful because the modular nature of the lab exercises allows them to apply the exercises to any set of proteins and incorporate the exercises into their courses as they see fit, allowing for greater flexibility in the use of the material.

Written in a logical, easy-to-understand manner, Experiments in the Purification and Characterization of Enzymes: A Laboratory Manual is an indispensable resource for both students and instructors in the fields of biochemistry, molecular biology, chemistry, pharmaceutical chemistry, and related molecular life sciences such as cell biology, neurosciences, and genetics.

  • Offers project lab formats for students that closely simulate original research projects
  • Provides instructional guidance for students to design their own experiments
  • Includes advanced analytical techniques
  • Contains adaptable modular exercises that allow for the study proteins other than FNR, LuxG and LDH
  • Includes access to a website with additional resources for instructors
An authoritative review of the latest developments in the chemical biology of enzymes

In the first decade of the twenty-first century, enzymes and their multiple applications have played a critical role in the discovery and development of many new therapeutic agents.This book is a coordinated compilation of research expertise and current opinion uniquely focused on enzymes and their properties and applications.

Compiled by editors with a combined pharmaceutical experience of over sixty years, the text provides in-depth reviews of recent developments in selective topics on biosynthesis, biocatalysis, and chemical biology of enzymes as it applies to drug discovery, development, and manufacture.

The first in a multi-part series on enzymes, this volume features three sections:

  • New Approaches to Find and Modify Enzymes describes the emerging field of metagenomics, presents the practical applications of directed evolution to enzymes and pathways, and explores approaches for the discovery and design of biocatalysts

  • Biocatalytic Applications reviews specific applications of different reactions in producing active pharmaceutical ingredients and surveys recent developments employing enzymes in organic synthesis

  • Biosynthetic Applications goes over successful drug discoveries and developments by combinatorial biosynthesis and reviews the application of combinatorial biosynthesis among multiple compatible hosts

These timely discussions, which cover everything from chemical biology of enzymes, to the redesign of binding and catalytic specificities of enzymes, make this volume a valuable tool for keeping up to date. As such, it is an important read for researchers, students, and professors in the study of biotechnology, life sciences, biochemistry, enzymology, medicinal chemistry, and natural products.

This volume represents the proceedings of a NATO Advanced Studies Instituteheld near Barga (Italy), July 11-23, 1988, involving over 90 participants from more than twelve countries of Europe, North America and elsewhere. It was not our intention at this meeting to present a complete up-to-the-minute review of current research in enzyme catalysis but t·ather, in accord wi th the intended spiri t of NATO ASis, to gi ve an opportunity for advanced students and researchers in a wide variety of disciplines to meet tagether and study the problern from different points of view. Hence the lectures cover topics rauging from the purely theoretical aspects of chemical reaction kinetics in condensed matter through practical experimental approaches to enzyme structure, dynamics and mechanism, including the new experimental opportunities arising from genetic engineering techniques. Our approachwas unashamedly physical, both because the more biochemical aspects of enzymology are amply covered elsewhere and because progress in our understanding and application of the molecular basis of enzymic processes must ultimately come from advances in physical knowledge. We tried to cover as wide a spectrum as possible, and succeeded in gathering an expert and enthusiastic team of speakers, but there . are some inevitable omissions. In particular, and with hindsight, our discussions might have been enriched by more detailed coverage of general aspects of chemical catalysis - but readers requiring this background should find adequate references herein.
Fully updated and expanded-a solid foundation for understanding experimental enzymology.
This practical, up-to-date survey is designed for a broad spectrum of biological and chemical scientists who are beginning to delve into modern enzymology. Enzymes, Second Edition explains the structural complexities of proteins and enzymes and the mechanisms by which enzymes perform their catalytic functions. The book provides illustrative examples from the contemporary literature to guide the reader through concepts and data analysis procedures. Clear, well-written descriptions simplify the complex mathematical treatment of enzyme kinetic data, and numerous citations at the end of each chapter enable the reader to access the primary literature and more in-depth treatments of specific topics.
This Second Edition of Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis features refined and expanded coverage of many concepts, while retaining the introductory nature of the book. Important new features include:
* A new chapter on protein-ligand binding equilibria
* Expanded coverage of chemical mechanisms in enzyme catalysis and experimental measurements of enzyme activity
* Updated and refined discussions of enzyme inhibitors and multiple substrate reactions
* Coverage of current practical applications to the study of enzymology
Supplemented with appendices providing contact information for suppliers of reagents and equipment for enzyme studies, as well as a survey of useful Internet sites and computer software for enzymatic data analysis, Enzymes, Second Edition is the ultimate practical guide for scientists and students in biochemical, pharmaceutical, biotechnical, medicinal, and agricultural/food-related research.
Enzymes are giant macromolecules which catalyse biochemical reactions. They are remarkable in many ways. Their three-dimensional structures are highly complex, yet they are formed by spontaneous folding of a linear polypeptide chain. Their catalytic properties are far more impressive than synthetic catalysts which operate under more extreme conditions. Each enzyme catalyses a single chemical reaction on a particular chemical substrate with very high enantioselectivity and enantiospecificity at rates which approach “catalytic perfection”. Living cells are capable of carrying out a huge repertoire of enzyme-catalysed chemical reactions, some of which have little or no precedent in organic chemistry.

The popular textbook Introduction to Enzyme and Coenzyme Chemistry has been thoroughly updated to include information on the most recent advances in our understanding of enzyme action, with additional recent examples from the literature used to illustrate key points. A major new feature is the inclusion of two-colour figures, and the addition of over 40 new figures of the active sites of enzymes discussed in the text, in order to illustrate the interplay between enzyme structure and function.

This new edition provides a concise but comprehensive account from the perspective of organic chemistry, what enzymes are, how they work, and how they catalyse many of the major classes of enzymatic reactions, and will continue to prove invaluable to both undergraduate and postgraduate students of organic, bio-organic and medicinal chemistry, chemical biology, biochemistry and biotechnology.

The kinetic mechanisms by which enzymes interact with inhibitors and activators, collectively called modifiers, are scrutinized and ranked taxonomically into autonomous species in a way similar to that used in the biological classification of plants and animals. The systematization of the mechanisms is based on two fundamental characters: the allosteric linkage between substrate and modifier and the factor by which a modifier affects the catalytic constant of the enzyme. Combinations of the physically significant states of these two characters in an ancestor-descendant-like fashion reveal the existence of seventeen modes of interaction that cover the needs of total, partial and fine-tuning modulation of enzyme activity. These interactions comprise five linear and five hyperbolic inhibition mechanisms, five nonessential activation mechanisms and two hybrid species that manifest either hyperbolic inhibition or nonessential activation characteristics depending on substrate concentration. Five essential activation mechanisms, which are taxonomically independent of the mentioned basic species, complete the inventory of enzyme modifiers. Often masked under conventional umbrella terms or treated as anomalous cases, all seventeen basic inhibition and nonessential activation mechanisms are represented in the biochemical and pharmacological literature of this and the past century, either in the form of rapid or slow-onset reversible interactions, or as irreversible modification processes.

The full potential of enzyme inhibitors and activators can only be appreciated after elucidating the details of their kinetic mechanisms of action exploring the entire range of physiologically significant reactant concentrations. This book highlights the wide spectrum of allosteric enzyme modification in physiological occurrences as well as in pharmacological and biotechnological applications that embrace simple and multiple enzyme-modifier interactions. The reader is guided in the journey through this still partly uncharted territory with the aid of mechanistically-oriented criteria aimed at showing the logical way towards the identification of a particular mechanism.

Marine bioprospecting is a highly topical subject - in both applied and basic research - but, as yet, the marine ecosystem is a relatively unexplored source of natural bioactive substances with potential therapeutic activity. This book addresses the use of marine enzymes in biocatalysis through a series of chapters from leading scientists within academic and industrial fields. Biocatalytic processes can take advantage of the habitat-related properties of marine enzymes, such as salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and so on, whilst also taking into consideration substrate specificity and affinity. These evolved properties are linked to the metabolic functions of the enzymes and to the ecological aspects of the natural source. New properties can also be discovered at the molecular level of catalysis, particularly concerning the stereochemical characteristics of products.

Marine enzymes for biocatalysis initially examines the nature and level of interest in marine biological diversity, and outlines the fundamentals of biocatalysis. It goes on to detail sources of marine enzymes, and to analyse examples from both chemical and stereochemical viewpoints of catalysis, including microbial enzymes and animal or plant sources. The book goes on to explore the future potential of marine bioprospecting in biocatalysis.
  • Compiles studies from leading scientists in a direct and accessible format. Includes practical descriptions of results, adding further details not often covered in formal articles
  • Takes a molecular view which fully explains the enzymatic aspects of reactions, particularly regarding biocatalytic characteristics and descriptions of bioprocesses
  • Selects examples of chemical and stereochemical aspects of enzymatic action with respect to known terrestrial counterparts
Humans are exposed to foreign compounds such as drugs, household products and environmental chemicals by swallowing or breathing. Also, food is considered a foreign compound. Such foreign compounds can be non-essential and non-functional to life, and commonly are referred to as xenobiotics. Some xenobiotics are not toxic; however, many of them are potentially toxic or become toxic after conversion to metabolic intermediates. A considerable number of foreign compounds belong to non-polar, lipophilic substances. Lipophilic compounds are not soluble in water. Metabolic conversion of lipophilic foreign compounds to facilitate their removal from the body is essentially carried out by biochemical reactions catalyzed by two classes of metabolizing enzymes, namely, activation enzymes and detoxification enzymes.

Activation enzyme-catalyzed functionalization reaction introduces a functional group to a lipophilic compound. Functionalization modifies many foreign compounds to form reactive intermediates capable of interacting with cellular components (proteins, DNA and lipids), leading to a variety of conditions for diseases. Functionalized compounds are further metabolized through detoxification enzyme-catalyzed reactions, which result in an increase in the solubility of parent compounds and an inactivation of metabolic intermediates, thus facilitating their excretion from the body. To minimize the exposure of potentially toxic metabolic intermediates, it is essential to keep them at a minimum level.

Extensive investigations have revealed that foreign compound-metabolizing enzymes exhibit genetic polymorphisms. Variations in their activities can produce different results as to the susceptibility to potential toxic effects. Moreover, the expressions of activation enzymes and detoxification enzymes are inducible. A number of chemical compounds are capable of acting as modulators for these two classes of enzymes. These findings have lead to the proposal of modulating metabolizing enzymes as a useful approach for human health benefits. Importantly, many of these chemical compounds are present in human daily diets.

There are many advances that have been made in the past decades towards the understanding of functions and implications of activation enzymes and detoxification enzymes. An organized, concise overview is needed for the readers who are initially exposed to this important subject, particularly for students and researchers in the areas of biomedical sciences, biochemistry, nutrition, pharmacology and chemistry. This book is intended to serve this purpose as an introduction to the subject. Furthermore, major topics in the book, excluding catalytic reactions and structural properties, may have interest to other readers who have knowledge of basic sciences and understanding enzyme related information.

The book discusses subjects associated with foreign compound metabolizing enzymes with emphasis on biochemical aspects, including lipophilic foreign compounds, catalytic properties, reactive intermediates, biomedical and biochemical effects, genetic polymorphisms, enzyme inducibility, enzyme modulation for health benefits, dietary related enzyme modulators, and structural characteristics of enzyme inducers.

All enzymes are remarkable since they have the ability to increase the rate of a chemical reaction, often by more than a billion fold. Allosteric enzymes are even more amazing because they have the additional ability to change their rate in response to cellular activators or inhibitors. This enables them to control the pathway in which they are the regulatory enzyme. Since the effector molecules represent the current status of the cell for a given metabolic pathway, this results in very responsive and balanced metabolic states, and makes it possible for cells and organisms to be appropriately dynamic, and responsive, in a changing environment. This book provides a logical introduction to the limits for enzyme function, as dictated by the factors that are the limits for life. This book presents a complete description of all the mechanisms used for changing enzyme activity. Eight enzymes are used as model systems, because they have been studied extensively. Wherever possible, the human form of the enzyme is used to illustrate the regulatory features.

While authors often emphasize the few enzymes that have the most remarkable catalytic rates, this survey of enzymes has led to the author’s appreciation of some important general conclusions:

1. Most enzymes are not exceptionally fast; they are always good enough for their specific catalytic step.

2. Although enzymes could always be much faster if they changed so as to bind their substrates more weakly, actual enzymes must be able to discriminate in favor of their special substrate, and therefore they have sacrificed speed to obtain better binding. This means that specific control of individual metabolic steps is more important than overall speed.

3. Results for many hundreds of enzymes establish that a lower limit for a normal catalytic activity is 1 s-1. Most enzymes have a catalytic rate between 10 and 300 s-1.

4. Allosteric regulation always results in a change in the enzyme's affinity for its substrate. Even V-type enzymes (named for their large change in catalytic velocity) always have a corresponding change in affinity for their substrate.

Thomas Traut has a PhD in molecular biology, and has studied enzymes since 1974. As a professor at the University of North Carolina at Chapel Hill he has focused on enzyme regulation, and taught advanced enzymology to graduate students. Important findings from his research helped to define the mechanism of allosteric control for dissociating enzymes. In this group the active form of the enzyme is normally oligomeric (trimer, tetramer, hexamer, etc.) and the dissociated subunit has little or no activity. With the solution of crystal structures for these enzymes by other laboratories, it became established that these dissociating enzymes had the active site at the interface of two adjacent subunits. Therefore, only the oligomer could have a complete active site. Since binding of the substrate, or of an effector, stabilizes two adjacent subunits in contact, this from of regulation is an efficient form of conformational control.

Additional studies helped to establish the correspondence between the subunit size of an enzyme and the number of independent ligand binding sites. Modules are the smallest units of folded protein structure. They are normally 3 - 7 kDa in size, and can bind one ligand. Catalytic sites, or regulatory sites, are frequently formed by two adjacent modules. The total size of a protein subunit then gives a good estimate of the number of such different ligand binding sites.

Leading experts from all over the world present an overview of the use of enzymes in industry for:

- the production of bulk products, such as glucose, or fructose
- food processing and food analysis
- laundry and automatic dishwashing detergents
- the textile, pulp and paper and animal feed industries
- clinical diagnosis and therapy
- genetic engineering.

The book also covers identification methods of new enzymes and the optimization of known ones, as well as the regulatory aspects for their use in industrial applications.

Up to date and wide in scope, this is a chance for non-specialists to acquaint themselves with this rapidly growing field.

'...The quality...is so great that there is no hesitation in recommending it as ideal reading for any student requiring an introduction to enzymes. ...Enzymes in Industry - should command a place in any library, industrial or academic, where it will be frequently used.'
The Genetic Engineer and Biotechnologist

'Enzymes in Industry' is an excellent introduction into the field of applied enzymology for the reader who is not familiar with the subject. ... offers a broad overview of the use of enzymes in industrial applications. It is up-to-date and remarkable easy to read, despite the fact that almost 50 different authors contributed. The scientist involved in enzyme work should have this book in his or her library. But it will also be of great value to the marketing expert interested in the present use of enzymes and their future in food and nonfood applications.'
Angewandte Chemie

'This book should be available to all of those working with, or aspiring to work with, enzymes. In particular academics should use this volume as a source book to ensure that their 'new' projects will not 'reinvent the wheel'.'
Journal of Chemical Technology and Biotechnology
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