This is the third volume in a series on membrane protein transfer. Membrane protein transport underlies the topological disposition of many proteins within cells and it is this disposition that allows for the co-ordination of the central cellular processes, such as metabolism.

Why a Second Edition?
The Second Edition provides practical answers to the general question, "How can I obtain useful sequence information from my protein or peptide?" rather than the more specific question asked in the first edition, "How can I obtain the N-terminal sequence?" Important new methods include ways of dealing with blocked N termini, computer analysis of protein sequences, and the recent revolution in mass spectrometry.
Key Features
Highlights of the Second Edition:
* Mass spectrophotometric characterization of proteins and peptides
* N-terminal sequencing of proteins with blocked N termini
* Internal amino acid sequence analysis after protease digestion in-gel and on-blot
* Improved microscale peptide purification methods
* Computer analysis of protein sequences
* New protocols tested and refined through everyday use in authors' laboratories
* Updated reference chapter covering all aspects of protein microsequencing

Proteomics in Biology, Part B, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in proteomics.

Proteomics, like other post-genomics tools, has been growing at a rapid pace and has important applications in numerous fields of science. While its use in animal and veterinary sciences is still limited, there have been considerable advances in this field in recent years, in areas as diverse as physiology, nutrition and food of animal origin processing. This is mainly as a consequence of a wider availability and better understanding of proteomics methodologies by animal and veterinary researchers. This book provides a comprehensive, state-of-the-art account of the status of farm-animal proteomics research, focusing on the principles behind proteomics methodologies and its specific applications and offering clear example.

Polycomb Group Proteins is a comprehensive volume detailing the mechanisms that are key to the management of genome function in many different contexts, from embryonic stem cells to terminal differentiation. The book discusses the regulation of cell lineages, cell proliferation, apoptosis, X chromosome inactivation, and most major genome programming choices. In the last few years, the biochemical understanding of PRC1-type complexes has greatly expanded in terms of the number of components involved and the intricacies of their interactions. The functionalities of these various complexes and their components are not all well understood, but recent work has shown an important division of labor and roles in the recruitment of stable binding in the ability to lay the groundwork of histone modifications and in the epigenetic maintenance of repressed states. In an effort to provide clarity in this topical research area, the book provides a cluster of chapters that deal with variant PRC1 complexes, their taxonomy, their components, their interactions, and what is known of their functions.

A look at the methods and algorithms used to predict protein structure

A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology.

With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure predictionThe structure prediction flagship assessment (CASP) and the protein structure initiative (PSI)Definitions of recurring substructures and the computational approaches used for solving sequence problemsDifficulties with contact map prediction and how sophisticated machine learning methods can solve those problemsStructure prediction methods that rely on homology modeling, threading, and fragment assemblyHybrid methods that achieve high-resolution protein structuresParts of the protein structure that may be conserved and used to interact with other biomoleculesHow the loop prediction problem can be used for refinement of the modeled structuresThe computational model that detects the differences between protein structure and its modeled mutant

Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.

This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.

Hsp90 in Cancer: Beyond the Usual Suspects, the latest volume in the Advances in Cancer Research series, focuses on the multifunctional molecular chaperone Hsp90 which regulates the post-translational stability and function of a broad repertoire of client proteins and discusses some of the lesser-known aspects of how Hsp90 and its related family members enable oncogenic transformation and malignant progression.

Recent advances in protein structural biology, coupled with new developments in human genetics, have opened the door to understanding the molecular basis of many metabolic, physiological, and developmental processes in human biology. Medical pathologies, and their chemical therapies, are increasingly being described at the molecular level. For single-gene diseases, and some multi-gene conditions, identification of highly correlated genes immediately leads to identification of covalent structures of the actual chemical agents of the disease, namely the protein gene products. Once the primary sequence of a protein is ascertained, structural biologists work to determine its three-dimensional, biologically active structure, or to predict its probable fold and/or function by comparison to the data base of known protein structures. Similarly, three-dimensional structures of proteins produced by microbiological pathogens are the subject of intense study, for example, the proteins necessary for maturation of the human HIV virus. Once the three-dimensional structure of a protein is known or predicted, its function, as well as potential binding sites for drugs that inhibit its function, become tractable questions. The medical ramifications of the burgeoning results of protein structural biology, from gene replacement therapy to "rational" drug design, are well recognized by researchers in biomedical areas, and by a significant proportion of the general population. The purpose of this book is to introduce biomedical scientists to important areas of protein structural biology, and to provide an insightful orientation to the primary literature that shapes the field in each subject.
The chapters in this volume cover aspects of protein structural biology which have led to the recognition of fundamental relationships between protein structure and function.

This book is a passionate account of the scientific breakthroughs that led to the solution of the first protein structures and to the understanding of their function at atomic resolution. The book is divided into self-standing chapters that each deal with a protein or protein family. The subject is presented in a fluid, non-technical style that will engage student and scientists in biochemistry, biophysics, molecular and structure biology and physiology.

This book will provide current understandings about two ubiquitously expressed metabotropic GPCRs, G-coupled purinoreceptor type 2 (P2Y) and Takeda G-protein-coupled bile acid receptor 5 (TGR5). G protein coupled receptors (GPCRs) are the largest family of proteins implicated in majority of cellular responses. The two receptor sub-families play a central role in many physiological functions as well as in many pathological conditions. This book offers up-to-date information on the physiological functions, signaling pathways and regulatory mechanisms of P2Y and TGR5 receptors. In addition, this book provides a comprehensive overview about the abnormalities of P2Y/TGR5 receptors and their contribution in the development and progression of pathological conditions. It also covers the currently available natural, chemical and pharmacological agents targeting these two receptor families and their therapeutic implications in P2Y and TGR5 associated disorders. This book is a valuable source for beginners and researchers to follow the rapidly progressing field of these two GPCR subfamily members.

Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: * Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria * Physiological importance and consequences of aggregation for the bacterial cell * Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble * Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids * Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.

This is the second volume in a series on membrane protein transfer. Membrane protein transport underlies the topological disposition of many proteins within cells and it is this disposition that allows for the co-ordination of the central cellular processes, such as metabolism.

This volume covers past and present western blot techniques, such as diffusion blotting, slice blotting, blotting of high and low molecular weight proteins, single cell blotting and automated blotting. 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. Thorough and cutting-edge, Western Blotting: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.

This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks. This book is organized into four parts and covers the basic framework and major resources for analysis of protein sequence, structure, and function; approaches and resources for analysis of protein PTMs, protein-protein interactions (PPIs) and protein networks, including tools for PPI prediction and approaches for the construction of PPI and PTM networks; and bioinformatics approaches in proteomics, including computational methods for mass spectrometry-based proteomics and integrative analysis for alternative splice isoforms, for functional discovery. 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 or computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein Bioinformatics: From Protein Modifications and Networks to Proteomics is a valuable resource for readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods, and future trends in protein and proteomic data analysis in systems biology. This book is useful to researchers who work in the biotechnology and pharmaceutical industries, and in various academic departments, such as biological and medical sciences and computer sciences and engineering.

This volume provides the most commonly used methods and protocols to study the apoptotic and non-apoptotic roles of CD95. Chapters explore molecular, biochemical, cellular methods and animal models to in order to better understand the biological functions of this cytokine. 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 practical, CD95: Methods and Protocols aims to foster original research on CD95/CD95L couple.

Amino Acids, Peptides and Proteins comprises a comprehensive and critical review of significant developments at the biology/chemistry interface. Compiled by leading researchers in their subject, this volume incorporates current trends and emerging areas for example new bioconjugates of metal complexes with peptides and derivatization of peptides for improved detection by mass spectrometry. Appealing broadly to researchers in academia and industry, it will be of great benefit to any researcher wanting a succinct reference to developments now and looking to the future.

This detailed volume explores the continuing techniques of studying RNA-protein complexes and interactions as research in these areas expand. After an introductory chapter, the book continues with ways to purify RNA-protein complexes assembled in cells or in isolated cellular extracts, methods for measuring various biochemical activities of RNA-interacting proteins or ribonucleoproteins, biochemical methods for measuring direct RNA-protein contact, as well as various new or innovative methods pertinent to the subject. Written for the highly successful Methods in Molecular Biology series, chapters contain brief 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 up-to-date, RNA-Protein Complexes and Interactions: Methods and Protocols provides a set of useful protocols, both basic and advanced, designed to inspire researchers working with RNA and RNA-interacting proteins.

"Galectins: Methods and Protocols "is the first book solely dedicated to methodological approaches designed to study galectin function. The galectin family represents one of the most pleiotropic families, with individual members having been implicated in various aspects of nearly every biological process described, from RNA splicing to complex regulatory circuits that orchestrate adaptive immunity. Given the diverse roles of galectins in a variety of biological systems, studying these glycan binding proteins often requires the assimilation of diverse technical skills to fully appreciate their biological function. Their nearly ubiquitous expression and ability to bind highly modifiable carbohydrate ligands, in addition to a variety of other regulatory proteins, allows these glycan binding proteins (GBPs) to possess the capacity to regulate a wide variety of biological processes. Individual chapters are dedicated to examining salient features of galectin functions. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Galectins: Methods and Protocols "seeks to serve both professionals and novices with a useful framework when examining galectin function for many years to come."

This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of 'transformer proteins'; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. 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. Cutting-edge and authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.

This volume compiles methodologies used for detailed studies of histone variants, from their basic properties to their functional roles in chromatin and as vectors of epigenetic information. Its four sections cover experimental approaches to probe the biochemistry of histone variants and variant nucleosomes; their dynamics throughout the cell cycle and at specific genomic locations; their functional impact on chromosome organization and genome stability; and their importance in development, disease and evolution. Written in the highly successful Methods in Molecular Biology series format, chapters include lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, illustrations on the expected results, and tips on troubleshooting and avoiding known pitfalls. This anthology brings together contributions from many of the most highly recognized investigators in this community. Cutting-edge and thorough, Histone Variants: Methods and Protocols is a valuable resource for anyone interested in exploring the experimental and collaborative possibilities in this evolving field.

Over the last decades, amino acids have been found to be of importance in many fields of science. Apart from their biological function, this family of organic compounds has been employed in the synthesis of a vast variety of salts, with impact on areas such as materials science, pharmaceutical or physical research. This covers a wide range, from the discovery of important ferroelectrics or non-linear optical materials to nutrients, flavor enhancers or drugs. This book describes amino acids and their salts with cations, anions and inorganic compounds from a chemical, physical and crystallographical point of view. Additional data on structural properties, crystal growth and the relation of structure and physical properties of amino acid salts is discussed.

This volume provides up-to-date scientific achievements from the world's top researchers. Recombinant Proteins from Plants: Methods and Protocols, Second Edition guides readers through protocolsfor use with a variety of plant expression systems. Various aspects of production are covered including vector selection and cloning; product improvements for stability, glycosylation, and antibiotic-free selection; extraction and scale-up; and analysis of transgenic plants and their recombinant proteins. Written for the 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, Recombinant Proteins from Plants: Methods and Protocols, Second Edition is an ideal reference for those who are interested in plant molecular biology and molecular farming.

This volume provides a comprehensive study of this key method of gel-based proteomics. Chapters in Difference Gel Electrophoresis: Methods and Protocols detail methods on principles of differential protein labeling, two-dimensional gel electrophoresis, techniques on optimized proteomic workflows, advanced mass spectrometry for protein identification, application of basic biological research, and applied biomarker discovery. 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, Difference Gel Electrophoresis: Methods and Protocols aims to ensure successful results in the further study of this vital field.

"Biophysical Characterization of Proteins in Developing Biopharmaceuticals" is concerned with the analysis and characterization of the higher-order structure (HOS) or conformation of protein based drugs. Starting from the very basics of protein structure this book takes the reader on a journey on how to best achieve this goal using the key relevant and practical methods commonly employed in the biopharmaceutical industry today as well as up and coming promising methods that are now gaining increasing attention.

As a general resource guide this book has been written with the intent to help today s industrial scientists working in the biopharmaceutical industry or the scientists of tomorrow who are planning a career in this industry on how to successfully implement these biophysical methodologies. In so doing a keen focus is placed on understanding the capability of these methodologies in terms of what information they can deliver. Aspects of how to best acquire this biophysical information on these very complex drug molecules, while avoiding potential pitfalls, in order to make concise, well informed productive decisions about their development are key points that are also covered.
Presents the reader with a clear understanding of the real world issues and challenges in using these methods.Highlights the capabilities and limitations of each method.Discusses how to best analyze the data generated from these methods.Points out what one needs to look for to avoid making faulty conclusions and mistakes.In total it provides a check list or road map that empowers the industrial scientists as to what they need to be concerned with in order to effectively do their part in successfully developing these new drugs in an efficient and cost effective manner."