This book seeks to fill in the current technology gap with a specific collection of technologies developed for the study of protein function at a proteome scale. Chapters explore topics from protein functions to other aspects of protein analysis, especially in post-translational modification, as most proteomes use this mechanism in some capacity to carry out their unique role in cellular regulation. By comparing functional proteomes, this presents a bridge to other levels of system biology research including genomics and metabolomics in order to provide readers with a relatively complete picture for how one might study the biological system of their interest. 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, Functional Proteomics: Methods and Protocols collects these novel technologies in the hope that new frontiers in biological research will be created, important drug targets can be identified, and clinically validated biomarkers and diagnostic tests can be further developed.

After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative mRNP code . These cis-regulatory RNA elements can be found in the 5 and 3 untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5 and 3 UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3 end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA.

This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases."

G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.

During the past decade we have witnessed several major dis coveries in the area of protein synthesis and post-translational modification of protein molecules. In this volume, many of the lat est research developments in these fields are reported by the dis tinguished international group of scientists who presented their state-of-the-art results at the 13th Linderstr0m-Lang Conference held at God0Ysund, Norway, June 14-18, 1983. We feel that the presentation here of so wide a variety of articles on both the molecular and the cellular aspects of protein synthesis will be of considerable value to many scientists working in the area who were unable to attend, as well as to many who are active in related areas. In addition to the research papers, the contents of the six scientific sessions held during the conference have been summarized by the respective session chairmen. These individual summaries provide insightful syntheses of all the recent progress in each field, identify which current problems remain of special inter est, and suggest what the future may hold in the several areas of protein synthesis research covered. Though this volume obviously cannot provide a complete survey of all important ongoing research on the molecular and cellular biology of translational and post-translational events, we are confi dent that it will facilitate a much better understanding of many im portant contemporary problems in research on protein synthesis, including cell differentiation, translational accuracy, protein modifi cation, intracellular transport, and membrane turnover."

This volume provides an overview of modern and emerging methods for production, analysis, and utility of peptide libraries. Chapter focus on methods and techniques for synthesis, genetic expression, hybrid synthesis-expression, examples of modern utility of these libraries, de novo discovery of reactions, hybrid organic-inorganic materials and, emerging tools for the analysis of these libraries by method of genetic selection and next-generation sequencing. 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, Peptide Libraries: Methods and Protocols seeks to serve both professionals and novices with its well-honed methodologies.

The purpose of the preface is to explain the book's objectives and how to use it; give warnings, disclaimers, and the like.* The main objective of Protein and Peptide Analysis by Mass Spec trometry is quite straightforward-to present authoritative, up-to-date, and practical accounts of the use of mass spectrometry in the analysis of pep tides and proteins. How to use it? Every reader will have their own particular interests and will surely be drawn toward the chapters that cover these interests. Within the remaining chapters, however, techniques are described with analytical possibilities that such a reader can then only guess at. So, read the book fully. Again, as is customary in the Methods in Molecular Biology series, the chapter format (Introduction, Materials, Methods, and Notes) allows the authors to introduce the techniques, to explain their relevance and applicability, and, above all, to provide detail-detail that represents each author's accumulated experience and enables the reader to use and benefit from these methods. So, read the book fully, and read it diligently. Warnings and disclaimers: Mass spectrometry today offers the pro tein chemist ready access to a wealth of information that is otherwise avail able only with great difficulty, or perhaps not at all. With this goal in sight, any warnings and disclaimers will almost surely be ignored. So, a warning anyway; the use of mass spectrometry might be habit forming."

Divided into two convenient sections, Protein Kinase Technologies collects contributions from experts in the field examining recent methodologies and techniques generally applicable to protein kinase research as well as to individual protein kinases which require special attention in neuroscience. These chapters will not only be practical instructions useful for readers' daily work in setting up and performing research but also thought-provoking and enjoyable reviews of recent advancements of individual protein kinases in neuroscience. Written for the highly successful Neuromethods series, this work contains the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and accessible, Protein Kinase Technologies seeks to foster cross-talk among investigators who study different protein kinases, and will also be beneficial for the entry of new investigators into this pivotal field.

In Fluorescent Protein-Based Biosensors: Methods and Protocols, experts in the field have assembled a series of protocols describing several methods in which fluorescent protein-based reporters can be used to gain unique insights into the regulation of cellular signal transduction. Genetically encodable fluorescent biosensors have allowed researchers to observe biochemical processes within the endogenous cellular environment with unprecedented spatiotemporal resolution. As the number and diversity of available biosensors grows, it is increasingly important to equip researchers with an understanding of the key concepts underlying the design and application of genetically encodable fluorescent biosensors to live cell imaging. 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, Fluorescent Protein-Based Biosensors: Methods and Protocols promises to be a valuable resource for researchers interested in applying current biosensors to the study of biochemical processes in living cells as well as those interested in developing novel biosensors to visualize other cellular phenomena.

Whole new areas of immunological research are emerging from the analysis of experimental data, going beyond statistics and parameter estimation into what an applied mathematician would recognise as modelling of dynamical systems. Stochastic methods are increasingly important, because stochastic models are closer to the Brownian reality of the cellular and sub-cellular world.

The knowledge of Th17 cells and other cell populations which secrete IL-17A, and/or IL-22 has expanded tremendously since the publication of the first edition "Th17 Cells: Role in Inflammation and Autoimmune Disease" in 2008. The present volume has been completely revised with the addition of new chapters on the IL-17 receptor family and signaling, and an in-depth review of IL-22 and innate lymphoid cells. The differentiation of na ve T cells into regulatory T cells and Th17 cells as well as the plasticity of Th17 cells is discussed. The role of IL-22 in cutaneous inflammation including psoriasis has been reviewed. In addition, the volume contains critical updates on autoimmunity, organ transplantation, tumor immunology and genetic mouse models for mechanistic studies. Lastly, the latest clinical progress in neutralizing antibodies to IL-17A, IL-17RA not only confirms the therapeutic promise foreseen in 2008, but also improves our knowledge of the pathogenesis of autoimmune diseases. In summary, this is a timely update and important review of the clinical and experimental aspects of IL-17, IL-22 and their producing cells.

This detailed volume provides methods and techniques for detection after blotting. Chapters guide readers through a number of variations on the theme of protein transfer to solid support followed by detection, presenting adaptations of traditional techniques, and original methods of protein blotting. 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.Practical and authoritative, Detection of Blotted Proteins: Methods and Protocols presents numerous techniques based on the Western blot, providing detailed, readily reproducible methods, tips, and alternatives directly and easily transferable to the laboratory setting.

This unique text introduces students and researchers to the world of misfolded proteins, toxic oligomers, and amyloid assemblages, and the diseases of the brain that result. During the past few years the connections between failures in protein quality control and neurological disorders have been reinforced and strengthened by discoveries on multiple fronts. These findings provide novel insights on how amyloidogenic oligomers and fibrils form, interconvert from one state to another, and propagate from cell to cell and region to region. Starting with protein folding and protein quality control basics, the reader will learn how misfolded proteins can cause diseases ranging from prion diseases to Alzheimer's disease and Parkinson's disease to Huntington's disease, amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Authoritative but written in a clear and engaging style, Fundamentals of Neurodegeneration and Protein Misfolding Disorders addresses one of today's forefront areas of science and medicine. The text emphasizes the new groundbreaking biophysical and biochemical methods that enable molecular-level explorations and the conceptual breakthroughs that result. It contains separate chapters on each of the major disease classes. Special emphasis is placed on those factors and themes that are common to the diseases, especially failures in synaptic transmission, mitochondrial control, and axonal transport; breakdowns in RNA processing; the potential role of environmental factors; and the confounding effects of neuroinflammation. The book is ideal for use in teaching at the advanced undergraduate and graduate levels, and serves as a comprehensive reference for a broad audience of students and researchers in neuroscience, molecular biology, biological physics and biomedical engineering.

The Annexins is focused on a specific family of calcium and membrane-binding proteins, annexins, ubiquitously spread within living organisms, including animals, plants and fungi. The volume covers important areas of annexinology. The characterization of structural-functional relationship within the annexin family of proteins, together with emerging transgenic animal models, provides an up-to-date overview of potential physiological roles of annexins. Growing evidence of participation of annexins in human diseases, called annexinopathies, related to disturbances in signal transduction, vesicular traffic, ion homeostasis and energy metabolism within the cell.
The book will attract a broad scientific audience, not only scientists interested in annexins, but also others involved in multidisciplinary studies, as well as undergraduate and postgraduate students. It can be used in courses relating to special topics such as calcium homeostasis, calcium-binding proteins, membrane structure and transport properties, various signal transduction pathways, and membrane trafficking.

The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Aggregation: Methods and Protocols aims to be useful and practical guide to new researchers and experts looking to expand their knowledge.

Lipid peroxidation is an important cellular process which can lead to detrimental effects if it is not regulated efficiently. Lipid hydroperoxide is formed in an initial step of lipid peroxidation. Lipid hydroperoxide is also known as a potential source of singlet oxygen. Harmful aldehydes are formed when the lipid hydroperoxide is degraded. The formed aldehyde has high reactivity against thiol or amine moieties. Therefore, it could act as a signaling molecule, which might induce the changing of gears inside a cell. Recent studies have shown that lipid hydroperoxide or a slightly modified product of the lipid hydroperoxide reacts with biomolecules such as proteins and aminophospholipids, which leads to formation of amide-type adducts. Amide-type adducts could be one of markers for oxidative stress and could also be an important player in some diseases. In this book, the chemistry and biochemistry of lipid hydroperoxide along with their conjugates with biomolecules are described.

The second volume continues to fill the gap in protein review and protocol literature. It does this while summarizing recent achievements in the understanding of the relationships between protein misfoldings, aggregation, and development of protein deposition disorders. The focus of Part B is the molecular basis of differential disorders.

This volume presents established bioinformatics tools and databases for function prediction of proteins. Reflecting the diversity of this active field in bioinformatics, the chapters in this book discuss a variety of tools and resources such as sequence-, structure-, systems-, and interaction-based function prediction methods, tools for functional analysis of metagenomics data, detecting moonlighting-proteins, sub-cellular localization prediction, and pathway and comparative genomics databases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step instructions of how to use software and web resources, use cases, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Function Prediction: Methods and Protocols is a valuable and practical guide for using bioinformatics tools for investigating protein function

This book presents pioneering findings on the characterization of cellular regulation and function for three recently identified protein posttranslational modifications (PTMs): lysine malonylation (Kmal), glutarylation (Kglu) and crotonylation (Kcr). It addresses three main topics: (i) Detecting Kmal substrates using a chemical reporter, which provides important information regarding the complex cellular networks modulated by Kmal; (ii) Identifying Kglu as a new histone PTM and assessing the direct impact of histone Kglu on chromatin structure and dynamics; and (iii) Revealing Sirt3's value as a regulating enzyme for histone Kcr dynamics and gene transcription, which opens new avenues for examining the physiological significance of histone Kcr. Taken together, these studies provide information critical to understanding how these protein PTMs are associated with various human diseases, and to identifying therapeutic targets for the dysregulation of these novel protein markers in various human diseases.

The main purpose of this volume is to provide a focused analysis of the function of the G protein-coupled signaling pathways that operate in the interconnected network of retinal neurons as they detect and encode the information carried by light. The organization of this volume will generally follow the path of signal flow in the retina. First we will describe recent advances in understanding the phototransduction cascade of rod and cone photoreceptors, which use signaling cascade based on the GPCR rhodopsin to transduce incident light into neural activity. Chapters will be devoted to unique specializations of the two major types of photosensitive cells that comprise the predominant input for our spatial and color vision. Subsequently, the mechanisms of synaptic information encoding by retinal ON bipolar cells will be described, where the GPCR mGluR6 plays a fundamental role. Chapters in this section will examine macromolecular organization of the mGluR6 signaling pathway as well as current understanding of its function. The functional characteristics of this signaling mechanism will be explored in detail. Additionally, this section will cover the role of dopamine receptors in modulating signal transmission between photoreceptors and ON-bipolar cells. Finally, chapters will be focused on the output neurons of the inner retina, ganglion cells, where the components of the emerging GPCR melanopsin cascade in intrinsically photosensitive ganglion cells will be detailed. Collectively these mechanisms allow the retina to represent visual space over a wide range of light intensities.

Leading researchers are specially invited to provide a complete understanding of a key topic within the multidisciplinary fields of physiology, biochemistry and pharmacology. In a form immediately useful to scientists, this periodical aims to filter, highlight and review the latest developments in these rapidly advancing fields.

The incentive for putting together Volume 4 of this series was to review the wealth of new information that has become available in prokaryotic organisms in protein export and membrane biogenesis. Just in the last several years, protein translocation has now been efficiently reconstituted using defined components and the mechanism by which proteins are moved across membrane bilayers is now being examined at a higher resolution. In addition, because of a new technical breakthrough using osmolytes, it is now possible to reconstitute a number of channel proteins, ATPase, receptors, and transporters. In many cases, it is possible to successfully predict the membrane topology of these types of proteins using both "hydrophobicity analysis" and the "positive inside" rule.
In this volume, two chapters focus on protein translocation across membranes ("Biochemical Analyses of Components Comprising the Protein Translocation Machinery of E. Coli; Protein Translocation Genetics"), while several others on how proteins assemble into the ineer membrane of E. Coli ("Membrane Protein Assembly; Membrane Insertion of Small Proteins: Evolutionary and Functional Aspects; Pigment-Protein Complex Assembly in Rhodobacter sphaeroides and Rhodobacter Capsulatus"). Other sections review recent progress on transporters ("Identification and Reconstitution of Anion Exchange Mechanisms in Bacteria; Helic Packing in the C-Terminal Half of Lactose Permease") and signal transduction ("Mechanism of Transmembrane Signaling in Osmoregulation") as well as the assembly of prints into the outer membrane ("Export and Assembly of Outer Membrane Proteins in E. coli"). Although the emphasis of the book is on proteins, the role of phospholipids in controlling various cell surface processes is reviewed ("Role of Phospholipids in coli Cell Function"). I should point out the reason for the rapid progress in bacteria research is because of the possibility to apply biochemistry and genetics in this organism.

This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book.

In "Single Molecule Studies of Proteins," expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.

Protein Glycosylation provides clear, up-to-date, and integrated coverage of key topics in this field. Particular emphasis is placed on the biosynthetic pathways that result in a wide variety of identified protein-bound oligosaccharides. Protein Glycosylation begins with an overview of the chemical structures of mono- and oligosaccharides, to provide a scientific basis for the later chapters. The book includes discussions on the purification, function, and enzyme kinetics of selected glycosidases and glycotransferases, as well as a review of the roles of oligosaccharides in glycoprotein function and the in vivo role of glycoproteins themselves. Finally, the in vitro synthesis of glycoproteins is presented, together with future directions in glycobiology. Protein Glycosylation serves as an excellent text for upper-level undergraduate and graduate students as well as a reference for those scientists whose training is not in glycobiology but who are moving into this field.