Bioinformatics is the study of biological information and biological systems - such as of the relationships between the sequence, structure and function of genes and proteins. The subject has seen tremendous development in recent years, and there are ever-increasing needs for good understanding of quantitative methods in the study of proteins. "Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis" takes the novel approach of covering both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective. Provides a comprehensive introduction to the analysis of protein sequences and structures. Provides an integrated presentation of methodology, examples, exercises and applications. Emphasises the algorithmic rather than mathematical aspects of the methods described. Covers comparison and alignment of protein sequences and structures as well as protein structure prediction focusing on threading approaches. Written in an accessible yet rigorous style, suitable for biologists, mathematicians and computer scientists alike. Suitable both for developers and users of bioinformatics tools. Supported by a Web site featuring exercises, solutions, images, and computer programs.

"Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis" is ideally suited for advanced undergraduate and graduate students of bioinformatics, statistics, mathematics and computer science. It also provides an excellent introduction and reference source on the subject for practitioners and researchers.

Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins. The Ten Most Wanted Solutions in Protein Bioinformatics considers the ten most significant problems occupying those looking to identify the biological properties and functional roles of proteins. -Problem One considers the challenge involved with detecting the existence of an evolutionary relationship between proteins. -Two and Three studies the detection of local similarities between protein sequences and analysis in order to determine functional assignment. -Four, Five, and Six look at how the knowledge of the three-dimensional structures of proteins can be experimentally determined or inferred, and then exploited to understand the role of a protein. -Seven and Eight explore how proteins interact with each other and with ligands, both physically and logically. -Nine moves us out of the realm of observation to discuss the possibility of designing completely new proteins tailored to specific tasks. -And lastly, Problem Ten considers ways to modify the functional properties of proteins. After summarizing each problem, the author looks at and evaluates the current approaches being utilized, before going on to consider some potential approaches. introbul Features

Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure. The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

The aim of the Protein Reviews is to serve as a publication vehicle for review articles that focus on crucial current vigorous aspects of protein structure, function, evolution and genetics. The volumes will appear online before they are published in a printed book. Articles are selected according to their importance to the understanding of biological systems, their relevance to the unravelling of issues associated with health and disease or their impact on scientific or technological advances and developments. Volume 19 focusses on Purinergic receptors, also termed purinoceptors. These are plasma membrane proteins present in nearly all mammalian tissues. They participate in a number of cell functions that include proliferation and migration of neural stem cells, vascular reactivity, apoptosis and cytokine secretion and have been associated with learning and memory, feeding conduct, movement and sleep. They facilitate relaxation of smooth muscle of the gut in response to adenosine (P1 receptors) or ATP (P2 receptors). The chapters in this volume are authored by experts in the field. They deal with aspects of structure and biological activity of selected receptor proteins. The first chapter in this volume reviews the current research on the Mechanism of channel gating and regulation of the activity of calcium-activated chloride channel ANO1. This is followed by a chapter dealing with Structure and function of the two-component cytotoxins of Staphylococcus aureus and a chapter on Membrane Fusion and Infection involving the Influenza virus Hemagglutinin. The fourth chapter reviews the impact of arrhythmogenic mutations through the structural determination of the L-type voltage-gated calcium channel. Then there is a chapter that discusses some open questions pertaining to histone post-translational modifications and nucleosome organization in transcriptional regulation. The next chapter deals with regulation of the extracellular SERPINA5 (protein C inhibitor) penetration through cellular membranes. This is followed by a chapter on coding of Class I and II aminoacyl-tRNA synthetases; a chapter on regulation of nephrin phosphorylation in diabetes and chronic kidney injury and a chapter on The Structure-Forming Juncture in oxidative protein folding and the events in the ER. Finally the last chapter deals with the polyspecificity of anti-lipid antibodies and its relevance to the development of autoimmunity. This volume is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

This book brings together recent, international contributions to the study of gluten proteins from leading experts in the field. Gluten proteins have gained greater importance due not only to their fundamental role in determining technological quality of wheat end products, but also to the apparently increased number of people showing different degrees of gluten intolerance or allergy. Along with classical subjects such as gluten genetics, quality and rheology, The Gluten Proteins covers new tools and research fields, including the use of proteomics and genomics. Furthermore, information dedicated to intolerances and allergies is included and opens the possibility to widen future research opportunities, promoting cooperation between wheat breeders, medical researchers and gluten chemists and geneticists. The Gluten Proteins provides an authoritative source of information for researchers, professionals and postgraduate students wishing to increase their knowledge of the molecular bases of gluten functionality and nutritional role, as well as touching on possible future research opportunities.

Omics is an emerging and exciting area in the field of science and medicine. Numerous promising developments have been elucidated using omics (including genomics, transcriptomics, epigenomics, proteomics, metabolomics, interactomics, cytomics and bioinformatics) in cancer research. The development of high-throughput technologies that permit the solution of deciphering cancer from higher dimensionality will provide a knowledge base which changes the face of cancer understanding and therapeutics.

This is the first book to provide such a comprehensive coverage of a rapidly evolving area written by leading experts in the field of omics. It complies and details cutting-edge cancer research that covers the broad advances in the field and its application from cancer-associated gene discovery to drug target validation. It also highlights the potential of using integration approach for cancer research.

This unique and timely book provides a thorough overview of developing omics, which will appeal to anyone involved in cancer research. It will be a useful reference book for graduate students of different subjects (medicine, biology, engineering, etc) and senior scientists interested in the fascinating area of advanced technologies in cancer research.

Readership: This is a precious book for all types of readers cancer researchers, oncologists, pathologists, biologists, clinical chemists, pharmacologists, pharmaceutical specialists, biostatisticians, and bioinformaticists who want to expand their knowledge in cancer research."

This volume explores current technologies used to investigate the formation, insertion, and function of metalloclusters associated with proteins. Chapters describe relevant topics about Fe-S cluster metabolism are explored through genetic, biochemical, spectroscopic methods. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Fe-S Proteins: Methods and Protocols aims to be a useful practical guide to researchers to help further their study in this field.

Based upon a workshop entitled "The Small HSP World" held in Quebec 2-5 October 2014. Twenty-five scientists provided chapters for the book. The chapters are from the best scientists currently working in this field. These colleagues include Arrigo, Benesch, Benjamin, Buchner-Haslbeck-Weinkauf, Benndorf, Boelens, Carra, Chang, Currie, Ecroyd, Emanuelsson, Fu, Garrido, Golenhofen, Gusev, Hightower, Kampinga, Lavoie, MacRae, Quinlan, Tanguay, Vierling, Vigh, Weeks and Wu. Briefly, the book starts with the structure of small heat shock proteins, moving to their functions and finishing with their involvement in diseases. Although this is quite broad, the structural aspect will be the unifying theme of the book.

Focusing on model systems for the study of structure, folding, and association in the membrane, Membrane Proteins: Folding, Association, and Design presents an overview of methods that can be applied to these intricate systems. The volume is divided into four detailed sections, covering association of transmembrane helices, interactions with the lipid bilayer, NMR methods, as well as a variety of engineering approaches. 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 practical, Membrane Proteins: Folding, Association, and Design serves as an ideal guide for researchers reaching for the tantalizing possibility of designing novel membrane proteins with tailored functionality.

"Provides a lot of reading pleasure and many new insights." —Journal of Molecular Structure

"This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." —Contemporary Physics

"A very useful introduction . . . more interesting to read than the often dry equation-based texts." —Journal of the American Chemical Society

Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics.

Stresses easy-to-use molecules

• Provides sample calculations and figures
• Includes four complete FORTRAN codes

Helps researchers in proteomics and oncology work together to understand, prevent, and cure cancer

Proteomic data is increasingly important to understanding the origin and progression of cancer; however, most oncologic researchers who depend on proteomics for their studies do not collect the data themselves. As a result, there is a knowledge gap between scientists, who devise proteomic techniques and collect the data, and the oncologic researchers, who are expected to interpret and apply proteomic data. Bridging the gap between proteomics and oncology research, this book explains how proteomic technology can be used to address some of the most important questions in cancer research.

"Proteomic Applications in Cancer Detection and Discovery "enables readers to understand how proteomic data is acquired and analyzed and how it is interpreted. Author Timothy Veenstra has filled the book with examples--many based on his own firsthand research experience--that clearly demonstrate the application of proteomic technology in oncology research, including the discovery of novel biomarkers for different types of cancers.

The book begins with a brief introduction to systems biology, explaining why cancer is a systems biology disease. Next, it covers such topics as: Mass spectrometry in cancer researchApplication of proteomics to global phosphorylation analysisSearch for biomarkers in biofluidsRise and fall of proteomic patterns for cancer diagnosticsEmergence of protein arraysRole of proteomics in personalized medicine

The final chapter is dedicated to the future prospects of proteomics in cancer research.

By guiding readers through the latest proteomic technologies and their applications in cancer research, "Proteomic Applications in Cancer Detection and Discovery" enhances the ability of researchers in proteomics and researchers in oncology to collaborate in order to better understand cancer and develop strategies to prevent and treat it.

A comprehensive introduction to the art and science used by the biochemist and process engineer in the design and optimization of large-scale protein-purification processes. Covers the basics of proteins' properties, the unit operations involved in protein purification as well as important related issues of process design, integration with upstream operations, cost and timing to market. Includes an abundance of figures and tables.

This book represents the most current, comprehensive, and authoritative study of integrins on the market today. It provides an overview of the diverse biological functions of integrins, including: The structure and functions of integrin cytoplasmic domains, the role of b2 integrins in leukocyte adhesion, the role of platelet membrane fibrinogen receptor glycoprotein IIb-IIIa (aIIbb3) in thrombosis and hemostasis, the functions of aV integrin family, the role of integrins in signal transduction, the role of integrins in carcinoma cells, the role of integrins in internalization of microbial pathogens through the binding of Yersinia pseudotuberculosis invasin protein, the role of integrins in the skin, the integrin function in early vertebrate development using amphibian embryos. Key selling features: the structure and functions of integrin cytoplasmic domains the role of b2 integrins in leukocyte adhesion the role of platelet membrane fibrinogen receptor glycoprotein IIb-IIIa (aIIbb3) in thrombosis and hemostasis the functions of aV integrin family the role of integrins in signal transduction

The broad range of G protein-coupled receptors (GPCRs) encompasses all areas of modern medicine and have an enormous impact on the process of drug development. Using disease-oriented methods to cover everything from screening to expression and crystallization, G Protein-Coupled Receptors in Drug Discovery describes the physiological roles of GPCRs and their involvement in various human diseases. The book presents current approaches in drug discovery that include target selection, establishment of screening and functional assays. It also covers recombinant GPCR expression for drug screening and structural biology, different methods for structural characterization of GPCRs, and the importance of bioinformatics. The book has been carefully edited to avoid overlapping information, some duplication has been intentionally permitted so that each chapter can function as an independent unit. Providing in-depth discussions on structure and dynamics of GPCRs, this book outlines the importance of the GPCRs to drug discovery in general and drug targets specifically. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.

This detailed collection gathers both established and recent technical procedures to study the Endosomal Sorting Complex Required for Transport (ESCRT) complexes in a wide range of biological systems: Archaea, A. thaliana, U. maydis, S. cerevisiae, S. pombe, C. elegans, D. melanogaster, and mammalian cells. Opening with a section on imaging techniques, the book continues with chapters covering biochemical approaches presenting strategies for production and characterization of recombinant ESCRT proteins, or of specific ESCRT protein domains, as well as genetic and proteomic experimental approaches. Written for the highly successful Methods in Molecular Biology series, chapters include introduction 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 practical, The ESCRT Complexes: Methods and Protocols serves as a compact guide for researchers interested in establishing an integrated approach to investigate the ESCRT machinery functions in cell biology.

This detailed collection explores techniques involved in the main strategies of nanopore sensing, such as translocation, analyte trapping, and interactions with external binding sites. Opening with a section on nanopore design and nanopore production, the book continues with parts devoted to various biological nanopores, nanopore engineering, and their uses in single molecule sensing, computational methods to study intrinsic nanopore behavior, characterizing the specific translocation activity of a vesicle particle through a nanopore, as well as the use of the technique droplet interface bilayer (DIB) in nanopore and membrane biophysical studies. 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 practical, Nanopore Technology: Methods and Protocols, with its focus on nanopore technology and biomolecule characterization, will hold the interest of the biophysicists, biochemists, bioengineers, and molecular biologists who are working toward further understanding this key field of research.

Following the announcement of the draft sequence of the human genome and the completion of many others, attention is now increasingly turning to the analysis of the proteins encoded by genomes - proteomics. This is a rapidly emerging research area and this book reviews recent developments in proteomics and compares them with current genomics technologies. The book is written by experts, from academia and industry, who review their area in a concise yet easy to understand style, providing a comprehensive review volume that integrates genomics with proteomics. This is the first book to address the subject at an undergraduate level.

Protein engineering has proved to be one of the more fruitful technological approaches in biotechnology, being both very powerful and able to generate valuable intellectual property. This book aims to present examples in which the application of protein engineering has successfully solved problems arising in industrial biotechnology. There is a section on its use to enhance purification of recombinant proteins. The use of protein engineering to modify the activity or the stability of industrial enzymes from lipases to proteases, from carboxypeptidases to glucanases and glucosidases, and from pectin modifying enzymes to enzymes able to degrade recalcitrant compounds is extensively covered. It is shown how areas as diverse as agrofood technology, fine chemistry, detergents, bioremediation and biosensors receive significant contributions from protein and solvent engineering.
The application of protein engineering to health care is also covered, from the development of new vaccines to new potential therapeutic proteins. A specific notation is given to protein engineering in the development of target molecules for drug discovery.
International in scope, the many contributions are drawn from academia and industry. The text should be of interest to students and researchers in industrial biotechnology as well as to everybody interested in basic research in protein structure, molecular genetics, bio-organic chemistry, biochemistry, agrobiotechnology, pharmaceutical sciences and medicine.

Recognizing the urgent need for an up-to-date review of new and innovative research on growth hormone (GH) secretagogues, this exclusive work furnishes the state of the art on the mechanisms of action, design, synthesis, evaluation, and clinical applications of GH secretagogues, including orally active and xenobiotic GH-releasing compounds. Beginning with a thorough historical perspective on the discovery and evolution of GH-releasing peptides (GHRPs) as therapeutic agents, Growth Hormone Secretagogues in Clinical Practice -analyzes structural requirements for GH secretagogue efficacy -demonstrates the use of mathematical models to predict differential values of individual stimuli for GH secretion from the pituitary -reports on the development of a simple screening system based on polyclonal antibodies -discusses laboratory synthesis of agonistic analogs intended for human and veterinary use -proposes applications in managing conditions such as Turner's syndrome, acromegaly, diabetic retinopathy, glomerulosclerosis, tumors, and cancer -provides physiological evidence for the effects of GHRP on behavior with a series of trials involving voluntary and forced exercise -describes a new diagnostic test for evaluating pituitary function in slowly growing children and aging adults -explores the interactions of GH secretagogues with other hormones and endogenous substances from sex steroids to interferons -and much more!

"Provides practical information on the application of capillary electrophoresis (CE) to protein analysis, with an emphasis on developing and optimizing CE techniques in the laboratory. Includes separation methods bases on mass, charge, isoelectric point, molecular sieving, and affinity interactions."

In recent years, interest in proteins has surged. This resurgence has been driven by the expansion of the post-genomic era when structural genomics and proteomics require new techniques in protein chemistry and new applications of older techniques. Protein chemistry methods are used by nearly every discipline of biomedical research. Many techniques have been used in less traditional ways with exciting results. Modern Protein Chemistry: Practical Aspects describes the practical side of advanced techniques in protein chemistry. The book gives researchers an excellent "cost-benefit" analysis of these techniques. The contributors have been selected for their prominence in their specific fields and because they run laboratories that actively collaborate with other scientists. Researchers and practitioners, both beginners and experienced, who are looking for new ideas and who are interested in applying these more advanced methods will be assisted in their work by these commentaries. This guide provides hands-on information to complement theoretical understanding. The theory behind these methods can be found in existing books and in the original literature. However, no other guide will help you make a practical evaluation of these methods and their value to your work.

This practical guide offers concise coverage of the scientific and pharmaceutical aspects of protein delivery from controlled release microparticulate systems-emphasizing protein stability during encapsulation and release.

Individual organisms are de?ned by their genetic code. During development andasaresponsetoexternalstimulithegeneticinformationistranslated into awell-de?nedanswerresultingintheexpressionandmodi?cationofproteins. The processes that control protein-protein interactions (PPI) are presently mostly described in terms of individual protein-protein interactions. In vivo suchinteractions are partof complex molecular interaction networksthat are highlydynamicintimeandspace.Onthebasisofquantitative experiments, it would be possible to understand such complex biological systems leading to anunravelingofthesenetworksandallowingthemtobecaughtinquantitative and predictive models. This textbook illustrates the rise of a relatively new area of biology. The shifting of research from the structural assembly of cells and whole org- isms to metabolic diversity led to the beginning of interactomics. This ?eld hasarisenfromtheincreasingimportanceofmolecularbiologyandbioch- istry in basic research as well as in prognostics and prevention of diseases in connection withbiomarker development. The behavior, morphology, and response to stimuli in biological systems arepredetermined bytheinteractionsbetweentheircomponents.Theseint- actions, as we observe them now, are therefore shaped by genetic variations and selective pressure. With the understanding of molecular interactions the biologyisgettingeasier tosurvey.Thecharacterizationofproteininteractions cancontribute to the understanding ofmany processes in nature. Knowledgeofthedifferenttypesofbiologicalmacromoleculesandincre- ingnumbersofwholegenomicstudiesfacilitatetheelucidationofcellularp- cesses. Whether it is genomics, transcriptomics, proteomics, interactomics, or metabolomics, the full complement of genomic information at different levels can be compared between different organisms to reveal similarities or differences and even to provide consensus models.

Electron transfer is the simplest of chemical reactions in that it does not normally involve the breaking and making of bonds. It is also of fundamental importance in biology, especially in the electron transport of chains of respiration and photosynthesis, but also in a wide range of other reactions not directly involved in energy coupling.

Recent findings have implied a distinct therapeutic potential for drugs targeting Transient Receptor Potential (TRP) channels in a wide variety of diseases, many with no existing satisfactory treatment options. Thus, the TRP superfamily of ion channels has attracted a great deal of well-deserved attention. TRP Channels in Drug Discovery provides a thorough collection of the most up-to-date reviews and protocols on the subject, coming from top experts in the field. Volume I presents a series of state-of-the-art minireviews on the most interesting TRP channels (from TRPA1 to TRPV4), as well as TRP-related protocols involving airways and the genitourinary tract. Written for the Methods in Pharmacology and Toxicology (TM) series, this work includes the kind of detailed description and key implementation advice that ensures successful results in the lab. Comprehensive and cutting-edge, TRP Channels in Drug Discovery serves as an ideal reference for graduate students in academic laboratories as well as for pharmaceutical scientists developing new drugs and clinicians interested in novel drugs in the pipeline.