Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study.

Marine Enzymes Biotechnology: Production and Industrial Applications, Part I, Production of Enzymes provides a huge treasure trove of information on marine organisms. Nowadays, marine organisms are good candidates for enzymes production and have been recognized as a rich source of biological molecules that are of potential interest to various industries. Marine enzymes such as amylases, carboxymethylcellulases, proteases, chitinases, keratinases, xylanases, agarases, lipases, peroxidase and tyrosinases are widely used in the industry for the manufacture of pharmaceuticals, foods, beverages, and confectioneries, as well as in textile and leather processing, and in waste water treatment. The majority of the enzymes used in the industry are of microbial origin because microbial enzymes are relatively more stable than the corresponding enzymes derived from plants and animals.

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.

Intermediate Filament Proteins, the latest volume in the Methods in Enzymology series covers all the intermediate filaments in vertebrates and invertebrates, providing a unique understanding of the multiple different tissue-specific intermediate filaments. This volume also covers the latest methods that are currently being used to study intermediate filament protein function and dynamics. It will be an important companion for any experimentalist interesting in studying this protein family in their cell or organism model system.

Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions Part A & B, are the latest volumes in the Methods in Enzymology series, continuing the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods centered on the use of Electron Paramagnetic Resonance (EPR) techniques to study biological structure and function.

The Springer Handbook of Enzymes provides concise data on some 5,000 enzymes sufficiently well characterized and here is the second, updated edition. Their application in analytical, synthetic and biotechnology processes as well as in food industry, and for medicinal treatments is added. Data sheets are arranged in their EC-Number sequence. The new edition reflects considerable progress in enzymology: the total material has more than doubled, and the complete 2nd edition consists of 39 volumes plus Synonym Index. Starting in 2009, all newly classified enzymes are treated in Supplement Volumes."

This book provides comprehensive methods and protocols about enzyme design. The chapters are grouped by main topic, starting with methodologies describing library preparation and screening, state of the art techniques in directed evolution and rational design, followed by examples of immobilization of enzymes on sustainable polymers, as well as biocatalytic conversions mediated by homogenous enzymatic preparations or whole cells. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and timely, Enzyme Engineering: Methods and Protocols is an ideal guide for both the novice and the veteran researcher interested in biocatalysis. Chapter 13 is available open access under a CC BY 4.0 license.

This book presents the state-of-the-art advances and applications of nanozymes, the recently developing branch of enzymology that synthesizes and uses nanomaterials that mimic the function of traditional enzymes. During the past decade, the study of nanozymes has grown rapidly. Several new nanomaterials that exhibit enzymatic actions have been identified, along with new applications for their practical use. This book draws upon the work of experts from around the world and provides an in-depth analysis and cutting-edge overview of nanozymes, with an eye toward their present and future applications. Chapters are arranged in a logical order to provide physio-chemical characterization of nanozyme and basic mechanisms of their enzymatic actions. Focusing on current limitations of nanozymes and their reaction kinetics, the book presents a comprehensive discourse on nanozyme engineering that includes possible surface modifications to enhance nanozyme effectiveness. It also focuses on traditional and novel nanozyme applications, such as biosensing, drug delivery, and disease therapy, as well as their use as antibacterials. An important addition in this book is the summary of emerging literature on nanozyme toxicology. This book is intended as a ready reference for advanced undergraduate and graduate students doing research in nanotechnology; materials science; chemistry; and chemical, biological, biomedical, and food engineering. Research and development scientists, engineers, and technologists working in the chemical and biological/biomedical industries will gain much from the materials in this book for their industry practice. Presents a comprehensive discourse on nanozyme engineering that includes possible surface modifications to enhance nanozyme effectiveness. Discusses metal organic frameworks as nanozymes. Reviews on traditional and novel nanozyme applications, such as biosensing, drug delivery, disease therapy, and their use as antibacterials. Examines nanozyme toxicology. Dr. Sundaram Gunasekaran is a Professor in the Department of Biological Systems Engineering at the University of Wisconsin-Madison.

There has been enormous progress in our understanding of molybdenum and tungsten enzymes and relevant inorganic complexes of molybdenum and tungsten over the past twenty years. This set of three books provides a timely and comprehensive overview of the field and documents the latest research. Building on the first and second volumes that focussed on biochemistry and bioinorganic chemistry aspects, the third volume focusses on spectroscopic and computational methods that have been applied to both enzymes and model compounds. A particular emphasis is placed on how these important studies have been used to reveal critical components of enzyme mechanisms. This text will be a valuable reference to workers both inside and outside the field, including graduate students and young investigators interested in developing new research programs in this area.

Transformations using enzymes have been extensively investigated in the last two decades and the results promise great potential for this growing field, especially in the area of synthetic organic chemistry mainly due to of its many advantages. Accordingly, this book has attempted to bring out the advantages of using enzymes involving complex underivatized and unprotected substrates in non-polar media under homogenous and heterogeneous reaction conditions. Merits and demerits of using enzymes in terms of yields and selectivity/specificity are presented without any prejudice. Almost all the reactions dealt with are from the author's laboratory comprising diverse substrates, and the catalysis involves two important hydrolyzing enzymes, extensively examined for the reverse reactions. Thus, esterification involving lipses and glycosylation involving glycosidases were investigated with respect to various strategies like optimization of reaction conditions, response surface methodology and kinetics, carrying out reactions under solvent, non-solvent and super critical carbon dioxide conditions. In short, the work presented is to ensure the comprehension of the problems faced by the researchers in this area so as to work out further efficient strategies for carrying out enzymatic transformations in the laboratory successfully with better yields and specificity.

Extending the range of enzymatic catalysis by using non-aqueous media has now developed into a powerful approach in biochemistry and biotechnology. One peculiar feature which distinguishes it from the conventional enzymology (carried out in aqueous buffers) is that the awareness of different parameters that control and influence the behaviour of enzymes in such environments has emerged rather slowly. Science is about being able to repeat what somebody else has done. Absence of knowledge about such well-defined parameters/fac tors has sometimes made some workers rather cautious and diffident about using this approach in their laboratories. But for this, non-aqueous enzymol ogy would be more widely practised. It is these thoughts that made me feel that the availability of some well-defined protocols for various applications invol ving enzymes in non-aqueous environments would further catalyze the growth of this area. Hence this book, in which each chapter has some protocols in a specific area. The protocols are preceded by brief background material. The early chapters, which are of general importance, concern control of water ac tivity and stabilization via immobilization. Some subsequent chapters provide the protocols for transformations involving lipids and carbohydrates, peptide synthesis, and preparation of chiral compounds. The disproportionate focus on lipases is not a coincidence; this class of enzymes has been used more often than others in non-aqueous enzymology.

Protein Biosynthesis Interference in Disease offers a thorough discussion and overview of protein biosynthesis interference, its mechanisms of action, and influence over disease processes. This book examines the role of protein biosynthesis interference in Alzheimer's and other neurodegenerative conditions, cancer and inflammatory disorders, with specific attention paid to the biochemical dynamics of tryptamine, biogenic amines and aminoacyl-tRNA synthetases in these pathologies. Methods of regulating protein translation and interference mechanisms, including gene therapy, are presented, empowering biochemists, molecular biologists, disease researchers, and health professionals to understand the underlying factors of protein disease and improve patient outcomes.

A comprehensive, accessible, up-to-date catalog of enzymes and their uses in modern manufacturing.

Enzymes have long been used by industrial product makers as major catalysts to transform raw materials into end products. Now available in English for the first time, Industrial Enzymes and Their Applications is the only authoritative catalog of enzymes with in-depth coverage of their varied uses, the classes in which they are grouped, and which chemical reagents they have replaced on current mass production lines.

The first section surveys general enzyme characteristics and discusses their microbiological origin, including pH and temperature dependence of the activity and stability of each enzyme. The next section then examines the most important industrial enzymes in use today—including carbohydrate-hydrolyz-ing enzymes, proteases, ester cleavage-fat-hydrolyzing enzymes, and immobilized enzymes. The last section is devoted to specific applications of technical enzymes in such areas as food processing, beverage production, animal nutrition, leather, and textiles.

Industrial Enzymes and Their Applications offers instant access to a wealth of key enzyme data—an invaluable, wide-ranging resource for industrial chemists, biochemists, biochemical engineers, and students.

The field of Mitochondrial Medicine has been dominated by symptom constellation-based diagnostic categorization since the first clinical syndrome was described three decades ago. Now, as rapidly expanding knowledge has revealed that mitochondrial diseases may result from several hundred distinct gene disorders with extensive clinical and mutation heterogeneity, the most useful guide for clinical care and research embraces a gene-centric approach to each individual's disorder. Together with international colleagues, Dr. Marni Falk has developed the Mitochondrial Disease Sequence Data Resource (MSeqDR), an online, community curated, centralized data resource of mitochondrial disease data from a genomic perspective. Here, in the Mitochondrial Disease Genes Compendium, Dr. Marni Falk and a team of international experts have built off their work on MSeqDR to provide an all-in-one, readily accessible, and easy-to-use at point of care reference on 256 mitochondrial disease genes from a gene-based perspective. In this book, clinicians and researchers will find a complete overview of mitochondrial disease genes relevant across all specialties, cataloging and building context around clinical features and the genetic basis of each condition. Within, each "gene page" offers an in-depth, referenced view of the relevant clinical disease spectrum, including gene and protein descriptions, year discovered, inheritance pattern(s), age ranges affected, major clinical features and severity range, clinical pearls, known therapies, available support groups, animal models, and gene-specific basic, translational, or clinical research activities now underway. Links provided on each gene page direct readers to MSeqDR for new findings, up-to-date genomic variant data, and user friendly informatics tools accessible to general clinicians and sophisticated geneticists or bioinformaticians alike, ensuring access to updated information on each condition.

New Techniques for Studying Biomembranes describes some of the latest methods used to investigate the dynamic distribution of specific lipids in membranes and their effects on other membrane components. The contributors present important discoveries with respect to lipid analysis and lipid interactions with membrane proteins. Various methods, which have been used to study lipid bilayer structure and lipid organization in membranes, include both in vitro and in vivo membrane systems, and study membrane proteins in various membrane systems. Key Features: Reviews both in vivo and in vitro analytical technologies and methods for studying membrane structure and function Explores how lipid bilayers and membrane proteins interact Includes contributions from an international team of researchers actively studying membrane structure and function Identifies various diseases whose causes are related to membrane proteins Related Titles: Christopher R. Jacobs, Hayden Huang, and Ronald Y. Kwon. Introduction to Cell Mechanics and Mechanobiology (ISBN 978-0-8153-4425-4) Wendell Lim and Bruce Mayer. Cell Signaling: Principles and Mechanisms (ISBN 978-0-8153-4244-1) Stephen Rothman. Proteins Crossing Membranes: A Scientist's Memoir (978-0-3670-7449-4)

There are many mononuclear iron containing enzymes in nature that utilize molecular oxygen and transfer one or both oxygen atoms of O2 to substrates. These enzymes catalyze many processes including the biosynthesis of hormones, the metabolism of drugs, DNA and RNA base repair and, the biosynthesis of antibiotics. Therefore, mononuclear iron containing enzymes are important intermediates in bioprocesses and have great potential in the commercial biosynthesis of specific products since they often catalyze reactions regioselectively or stereospecifically. Understanding their mechanism and function is important and will assist in searches for commercial exploitation. In recent years, advances in experimental as well as theoretical methodologies have made it possible to study the mechanism and function of these enzymes and much information on their properties has been gained. This book highlighting recent developments in the field is, therefore, a timely addition to the literature and will interest a broad readership in the fields of biochemistry, inorganic chemistry and computational chemistry. The Editors, leaders in the field of nonheme and heme iron containing monoxygenases, have filled the book with topical review chapters by leaders in the various sub-disciplines.

Oxidative Stress: Eustress and Distress presents current knowledge on oxidative stress within the framework of redox biology and translational medicine. It describes eustress and distress in molecular terms and with novel imaging and chemogenetic approaches in four sections: A conceptual framework for studying oxidative stress. Processes and oxidative stress responses. Signaling in major enzyme systems (oxidative eustress), and damaging modification of biomolecules (oxidative distress). The exposome addresses lifelong exposure and impact on health, nutrient sensing, exercise and environmental pollution. Health and disease processes, including ischemia-reperfusion injury, developmental and psychological disorders, hepatic encephalopathy, skeletal muscle disorders, pulmonary disease, gut disease, organ fibrosis, and cancer. Oxidative Stress: Eustress and Distress is an informative resource useful for active researchers and students in biochemistry, molecular biology, medicinal chemistry, pharmaceutical science, nutrition, exercise physiology, analytical chemistry, cell biology, pharmacology, clinical medicine, and environmental science.

Carbonic Anhydrases provides an interdisciplinary review of the burgeoning carbonic anhydrase (CA) research area, spanning from CAs classification (biochemical and structural features) to drug design and pharmacology of CA inhibitors and activators, finally touching on the biotechnological applications of these metalloenzymes. The book adopts a clear step-by-step approach and introduction to this intricate and highly interdisciplinary field. A diverse range of chapters from international experts speak to CA classification and distribution, the mechanisms of action and drug design of inhibitors and activators, the druggability of the various isoforms in the treatment of a multitude of diseases, and threats to human health. Carbonic Anhydrases provides biology, biochemistry, and medicinal chemistry students and researchers a thorough discussion and update on the evergreen and expanding research area of CAs.

The Springer Handbook of Enzymes provides concise data on some 5,000 enzymes sufficiently well characterized and here is the second, updated edition. Their application in analytical, synthetic and biotechnology processes as well as in food industry, and for medicinal treatments is added. Data sheets are arranged in their EC-Number sequence. The new edition reflects considerable progress in enzymology: the total material has more than doubled, and the complete 2nd edition consists of 39 volumes plus Synonym Index. Starting in 2009, all newly classified enzymes are treated in Supplement Volumes."

In an intriguing series of experiments carried out many years ago, a common scientific belief, feted by no less than three Nobel prizes, was brought into question. The observations were about proteins-the molecules that the genetic code specifies and that are in one way or another central to all of life's activities. The experiments however were not about what proteins do, but how they are moved, in particular how they are moved from where they are made to where they act. The results of these studies conflicted with the standard view of how this happens, and thus became controversial. The standard view, the vesicle theory of protein secretion, envisions proteins being carried within and out of cells en masse in membrane-bound sacs or vesicles. The controversial experiments demonstrated that to the contrary individual protein molecules cross the relevant membranes as a result of their own motion. This was thought to be impossible at the time. Proteins Crossing Membranes is a personal narrative that tells the story of the controversy. Among other things, the author illustrates that scientists, like the rest of us, can rigidly hold onto their beliefs despite evidence that they are misguided. Key Features Reviews the data in support and critical of the vesicle theory of protein secretion Explores the ways scientists respond to evidence that challenges a favored theory Documents the author's personal experiences in this conflict-laden situation

Compiles the recent agricultural-biocatalysis research results by interdisciplinary teams from international institutes for chemistry, biochemistry, biotechnology, and materials and chemical engineering, Investigates important agricultural-biocatalytic topics related to biochemical conversions or bioremediation, modern biological and chemical applications Covers the research on plant and soil enzymes, herbicide tolerant traits, biochemical conversions, including aspects from bioremediation, plant viruses, and evaluation of the agricultural enzymes market.

Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. Our current level of understanding fails the basic, practical test - designing and making artificial systems with catalytic efficiencies to rival those of natural enzymes. Chemists and bio-scientists are well aware of this problem, and "artificial enzymes" have been a "hot topic" for many years. However, until now, there has been no book devoted specifically to this subject. This is the first book to provide a critical introduction to, and overview of, this exciting area. It is aimed at students and more senior researchers with specialist or general interests in the field. The book starts with a systematic overview of the most important properties of natural enzymes, with special emphasis on mechanisms and efficiency of catalysis. This is followed by a summary of the mechanisms involved in the major classes of reaction they catalyze, and spells out the logical progression from simple mechanistic models for particular reactions to the first, rudimentary artificial enzymes catalyzing them. Catalytic efficiency is the key criterion for inclusion. An analysis of the strengths and limitations of the classical design-based approach to catalysis by enzyme mimics leads on to a discussion of recent advances which use selection methods coupled with iterative techniques for creating and improving catalysts by natural methods. The comparison of natural and artificial catalysts requires a quantitative understanding based on the interpretation of kinetic measurements. Key skills in data interpretation are introduced in a guided approach that connects the formal treatment of kinetic measurements with their chemical and biological interpretation.

Humans contain more than 20 Rho type GTPases. This volume not only presents a detailed phylogenetic analysis of Rho proteins, but also discusses the possible origins of the human members. Such an analysis of human Rho GTPases has not previously been attempted.

The book includes an overview of how Rho GTPases become activated which is complemented by an extensive Chapter by Darerca Owen and Helen Mott who unravel the beautiful molecular details given to us by the many structural studies of Rho GTPases.

The key areas currently being investigated in relation to these ubiquitous proteins are described for both in vitro and in vivo systems. These are presented in a format that ensures the reader can approach the topic with minimal background knowledge, while ultimately bringing the subject to the level of an expert. Timely and highly authoritative, this volume illuminates newer findings, particularly as they relate to Rho proteins in vertebrate biology.

Experimental Analysis of Enzyme Mechanism Using Isotope Effects, Volume 596, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Chapters in this comprehensive update include Measurement of enzyme binding isotope effects, Chemical ligation and isotope labeling to locate dynamic effects, Measurement of heavy enzyme isotope effects, Extracting kinetic isotope effects from a global analysis of reaction progress curves, KIE of metabolic flux and enzymes, Solvent and Primary KIE on Flavin Enzymes, and The Rapid Determination of Primary Deuterium Isotope Effects on Enzyme-Catalyzed Proton Transfer at Carbon in 50/50 HOH/DOD. Readers who are interested in applying or understanding this research will find useful methods currently used for measuring isotope effects on solution and enzyme reactions.

Fe-S Cluster Enzymes, Part A, Volume 595 is the first of two volumes focused on Fe-S cluster enzymes. New topics of note in this series include Electrochemistry of Fe/S Proteins, Genetic, biochemical and biophysical methods for studying Fe-S proteins and their assembly, Fluorescent reporters to track Fe-S cluster assembly and transfer reactions, Mechanism-based strategies for structural characterization of radical SAM reaction intermediates, Purification and Characterization of Recalcitrant Cobalamin-Dependent Radical S-adenosylmethionine Methylases, A polymerase with potential: the Fe-S cluster in Human DNA Primase, In Vitro Studies of Cellular Iron-sulfur Cluster Biosynthesis, Trafficking and Transport, and Fe-S cluster Hsp70 Chaperones: the ATPase cycle and protein interactions.