Translational Urinomics provides an overview of urine analysis using proteomics, metabolomics, transcriptomics or any combination thereof for the diagnosis and prognosis of diseases related to the urinary system and the kidneys. The text approaches urine biomarkers from a new perspective, incorporating up-to-date studies of mass-spectrometry-based biomarker discovery as well as the latest advances in personalized medicine. The integration of technology-driven techniques, such as OMICS also provides a unique opportunity for improved diagnostics accuracy of urinary-related diseases. For nephrologists and urologists looking for new approaches to well-known problems, this edited volume serves as a valuable guide.

This book provides a broad base of knowledge of G-protein-coupled receptors. Useful at both the university and industrial levels, this book is of particular interest to those who are developing therapeutic approaches to diseases using drugs that influence receptor activation.

This detailed volume explores a wide variety of applications of yeast surface display, an extensively used protein engineering technology. Beginning with detailed protocols for the construction and efficient selection/screening of yeast surface display libraries, as well as for the analysis of individual yeast-displayed protein variants, the book continues with protocols describing the selection of yeast surface display libraries for binding to mammalian cells or to extracellular matrix as well as protocols for a broad spectrum of specialized yeast surface display applications, demonstrating the versatility of this display platform. 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 methodologies, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Yeast Surface Display serves as a comprehensive resource that enables the implementation of this powerful and versatile technique in virtually any molecular biology laboratory, even in the absence of any prior yeast surface display experience.

Ubiquitin and Protein Degradation, Part B will cover chemical biology, ubiquitin derivatives and ubiquitin-like proteins, deubiquitinating enzymes, proteomics as well as techniques to monitor protein degradation. The chapters are highly methodological and focus on application of techniques.
*Second part of the Ubiquitin and Protein Degration series
*Topics include: E1 Enzymes, E2 Enzymes, E3 Enzymes, Proteasomes, and Isopeptidases

Intermediate filaments are a large family of proteins that are the cytoskeletal elements involved in a number of skin, liver, neuromuscular, cardiac, eye and hair diseases. Intermediate filament genes are regulated in a tissue-and cell type-specific manner and their polymerized protein products protects the cells and tissue they are part of against a variety of mechanical and nonmechanical stresses. This book provides a comprehensive resource of methodology essentials, describing a variety of essential tools and assays for studying intermediate filaments. The book provides user-friendly advice and protocols covering all aspects of intermediate filaments including protein isolation and structure, protein and gene regulation, relationship to disease and apoptosis, and associated proteins. Both mammalian and non-mammalian systems and animal models are covered, making this book a must-have for any investigator wishing to study IF genes or their protein products.
* Covers intermediate filaments from crystallography, protein chemistry, cell and molecular biology, microrheology, gene regulation, to animal models and human disease
* Practical and user-friendly with detailed "how-to-protocols and "tricks of the trade"
* Includes detailed tables of useful reagents, vendors and web links

De Novo Enzyme Design, the newest 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 includes the design of metal binding maquettes, insertion of non-natural cofactors, Cu metallopeptides, non-covalent interactions in peptide assemblies, peptide binding and bundling, heteronuclear metalloenzymes, florinated peptides, De Novo imaging agents, and protein-protein interaction.

The Protein Reviews series serves as a publication vehicle for reviews that focus on crucial contemporary and vital aspects of protein structure, function, evolution and genetics. Volumes are published online first, prior to publication in a printed book. Chapters are selected according to their importance to the understanding of biological systems, relevance to the unravelling of issues associated with health and disease, or impact on scientific or technological advances and developments. Volume 22 presents six review chapters authored by experts in related fields. The first chapter covers carotenoid-protein interactions. Chapter two addresses the non-continuum of eukaryotic transcriptional regulation. The third chapter reviews the structure of the regulatory and catalytic domains of the photoreceptor phosphodiesterase (PDE6) holoenzyme. Chapter four reviews the current knowledge on small molecule compounds that have been evaluated as rhodopsin modulators to be considered as leads for the development of novel therapies for retinitis pigmentosa. Chapter five deals with Plasticity-associated functionality and inhibition of the HIV protease. Finally, chapter six covers single-run catalysis and kinetic control of human telomerase holoenzyme. 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 second edition is dedicated to new and updated methodological approaches designed to study galectin function. Chapters examine 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 cutting-edge, Galectins: Methods and Protocols, Second Eidtion aims to be a useful practical guide to researches to help further their study in this field.

Protein Transcription is a key element of cellular and organ regulation. This volume covers structure and function of all major elements associated with transcription.
*Mechanism of RNA polymerase I Transcription
*Structure and function of RNA Polymerase II
*Structure and function of the TFIID complex
*Functional properties of Chromatin Remodeling Enzymes
*Posttranslational modification

The Protein Reviews series serves as a publication vehicle for reviews that focus on crucial contemporary and vital aspects of protein structure, function, evolution and genetics. Volumes are published online first, prior to publication in a printed book. Chapters are selected according to their importance to the understanding of biological systems, relevance to the unravelling of issues associated with health and disease, or impact on scientific or technological advances and developments. Volume 21 presents eight review chapters authored by experts in the related fields. The first chapter covers the enzyme squalene monooxygenase and lipid levels and its relevance in health and disease. Chapter two presents a systematic analysis of the structural and functional aspects of heteromeric solute carriers. The third chapter provides a review of the role of CI- in type IV collagen assembly, function, and disease, including future directions for studies. This is followed by a summary in chapter four about the recent progress on defining the roles of the Slit-Robo signaling in bone metabolism and the possible roles of the interaction between Robo and neural epidermal growth factor-like proteins. Chapter five discusses recent data about the evolutionary aspects on structural differences between humans and the nematode in relation to previous knowledge of core proteins and GAG-attachment sites in Chn and CS proteoglycans of C.elegans and humans. The sixth chapter summarizes the immunochemical character of the IGHV1-69-derived RFs and the recognition mechanism of the IGHV1-69-derived RFs. Chapter seven covers regulated alternative translocation and its role as an emerging mechanism to regulate transmembrane proteins. Finally, chapter eight reviews current progress on IL-36 protein and biology and novel investigative tools. This volume is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

In this first book to provide an overview of applications of proteomics in the discovery of new diagnostic, prognostic and therapeutic targets, a team of international specialists from research institutions, hospitals and companies contribute with their specific expertise. They cover a wide range of example applications for the most important diseases, such as heart and cardiovascular disorders, cancer, pharmatoxicology, infectious diseases and diseases of the nervous system.
Denis Hochstrasser is an eminent scientist in the field of bioinformatics and proteomics and one of the founders of the Swiss Prot Databank as well as of the Swiss biotech company Genebio.

This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer's, Parkinson's, and preeclampsia. 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, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.

In the post-genomic era, several plant species have been sequenced and massive genomic information is now available which contributed to expand the development of novel technical strategies for the study of additional levels of biological information of plant species. This book focuses on the "omics" approaches together with systems analysis of several different plant species, which have revealed very interesting variations on the cellular responses at the protein, transcript and metabolite levels in response to changes environmental conditions. The volume covers recent technological advances in the area of "omics" and synthesizes recent findings of the field of plant "omics" and systems biology together along with techniques that can be applied for such studies.

This second edition of Membrane Protein Purification and Crystallization, A Practical Guide is written for bench scientists working in the fields of biochemistry, biology, and proteomic research. This guide presents isolation and crystallization techniques in a concise form, emphasizing the critical aspects unique to membrane proteins. It explains the principles of the methods and provides protocols of general use, permitting researchers and students new to this area to adapt these techniques to their particular needs. This edition is not only an update but is comprised mainly of new contributions. It is the first monograph compiling the essential approaches for membrane protein crystallization, and emphasizes recent progress in production and purification of recombinant membrane proteins.
Key features
* Provides general guidelines and strategies for isolation and crystallization of membrane proteins
* Gives detailed protocols that have wide application, and low specialized equipment needs
* Emphasizes recent progress in production and purification of recombinant membrane proteins, especially of histidine-tagged and other affinity-epitope-tagged proteins
* Summarizes recent developments of Blue-Native PAGE, a high resolution separation technique, which is independent of the use of recombinant techniques, and is especially suited for proteomic analyses of membrane protein complexes
* Gives detailed protocols for membrane protein crystallization, and describes the production and use of antibody fragments for high resolution crystallization
* Presents a comprehensive guide to 2D-crystallization of membrane proteins

This volume serves to aid researchers working in the recombinant protein production field by describing a wide number of protocols and examples. Chapters describe recombinant protein production in different expression systems, prokaryotic and eukaryotic expression systems, purification protocols, characterization of insoluble proteins and a general overview of interesting applications of insoluble proteins. 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, Insoluble Proteins: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field.

A wide range of researchers are currently investigating different properties and applications for copper-containing proteins. Biochemists researching metal metabolism in organisms ranging from bacteria to plants to animals are working in a completely different area of discovery than scientists studying the transportation and regulation of minerals and small molecule nutrients. They are both working with copper-containing proteins, but in very different ways and with differing anticipated outcomes.

Protein carbonylation has attracted the interest of a great number of laboratories since the pioneering studies at the Earl Stadtman s lab at NIH started in early 1980s. Since then, detecting protein carbonyls in oxidative stress situations became a highly efficient tool to uncover biomarkers of oxidative damage in normal and altered cell physiology. In this book, research groups from several areas of interest have contributed to update the knowledge regarding detection, analyses and identification of carbonylated proteins and the sites where these modifications occur. The scientific community will benefit from these reviews since they deal with specific, detailed technical approaches to study formation and detection of protein carbonyls. Moreover, the biological impact of such modifications in metabolic, physiologic and structural functions and, how these alterations can help understanding the downstream effects on cell function are discussed. * Oxidative stress occurs in all living organisms and affects proteins and other macromolecules: Protein carbonylation is a measure of oxidative stress in biological systems * Mass spectrometry, fluorescent labelling, antibody based detection, biotinylated protein selection and other methods for detecting protein carbonyls and modification sites in proteins are described * Aging, neurodegenerative diseases, obstructive pulmonary diseases, malaria, cigarette smoke, adipose tissue and its relationship with protein carbonylation * Direct oxidation, glycoxidation and modifications by lipid peroxidation products as protein carbonylation pathways * Emerging methods for characterizing carbonylated protein networks and affected metabolic pathways

Protein Physics is a lively presentation of the most general problems of protein structure, folding and function from the physics and chemistry perspective, based on lectures given by the authors. It deals with fibrous, membrane and, most of all, with the best studied water-soluble globular proteins, in both their native and denatured states. The major aspects of protein physics are covered systematically, physico-chemical properties of polypeptide chains; their secondary structures; tertiary structures of proteins and their classification; conformational transitions in protein molecules and their folding; intermediates of protein folding; folding nuclei; physical backgrounds of coding the protein structures by their amino acid sequences and protein functions in relation to the protein structure. The book will be of interest to undergraduate and graduate level students and researchers of biophysics, biochemistry, biology and material science.
* Designed for a wide audience of undergraduate and graduate students, as well as being a reference for researchers in academia and industry
* Covers the most general problems of protein structure, folding, and function and introduces the key concepts and theories
* Deals with fibrous, membrane and especially water-soluble globular proteins, in both their native and denatured states
* Summarizes and presents in a systematic form the results of several decades of world wide fundamental research on protein physics, structure and folding
* Examines experimental data on protein structure in the post-genome era

This book presents an in-depth overview on the topic of protein synthesis, covering all areas of protein science, including protein targeting, secretion, folding, assembly, structure, localization, quality control, degradation, and antigen presentation. Chapters also include sections on the history of the field as well as summary panels for quick reference. Numerous color illustrations complement the presentation of material. This book is an essential reference for anyone in biochemistry and protein science, as well as an excellent textbook for advanced students in these and related fields.
Key Features
* Basic principles and techniques
* Targeting adn sorting sequences
* Protein export in bacteria
* Membrane protein integration into ER and bacterial membranes
* Protein translocation across the ER
* Disulfide bond formation in prokaryotes and eukaryotes
* Quality control in the export pathway
* Import of proteins into organelles
* The secretory pathway
* Vesicular transport
* Spectacular color throughout

A cofactor is a component part of many enzymes and functions by uniting with another molecule in order to become active.
The use of cofactors to supplement the native amino acids of a protein is essential to maintain the chemical capabilities necessary for organisms to survive. This volume focuses on the significant advances of the past decade in identifying and describing new cofactors--either small molecules or those derived posttranslationally.

This volume explores the basic issues of "allostery" and "network" that are fundamental to studying this field. Chapters in this book look at how the basic "machine-like" proteins, that are similar to "human machines," need to be organized, architecturally, to relate to different organizational layers. Chapters cover topics such as methodological/computational factors focused on links between allostery and network formalism; the presence of oscillating modes transversing the structure and underlying network wiring of the allosteric process; the "action at distance" by transduction of signals across an organized network structure; and the P53 protein located at the cross-road of cell cycle regulation, genome integrity, and cancer development. 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 practical, Allostery: Methods and Protocols is a valuable resource for any scientists and researcher interested in learning more about this developing field.

This volume explores strategies and detailed protocols for the preparation of macromolecular complexes and their characterization in view of structural analysis. The chapters in this book are separated into three parts: Part One focuses on sample preparation, and covers strategies for recombinant expression of multiprotein complexes in prokaryotic and eukaryotic hosts, for genome engineering using the CRISPR/Cas9 system and for production of specific binders such as reformatted antibodies and artificial binding proteins. Part Two looks at the biophysical methods that can provide useful indicators for sample optimization, and often complement structural information obtained with core technologies for structure determination-x-ray crystallography and cryo-electron microscopy-by quantitative solution data. Part Three discusses the characterization of multiprotein complexes in a cellular environment using the latest technologies and in vivo approaches. 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, Multiprotein Complexes: Methods and Protocols is a valuable resource for structural and molecular biologists who need to prepare multi-components for their applications, and for other scientists working on macromolecular assemblies from other angles that need to know the latest approaches that the field has to offer.

"Proteins: Structure and Function" is a comprehensive introduction to the study of proteins and their importance to modern biochemistry. Each chapter addresses the structure and function of proteins with a definitive theme designed to enhance student understanding. Opening with a brief historical overview of the subject the book moves on to discuss the 'building blocks' of proteins and their respective chemical and physical properties. Later chapters explore experimental and computational methods of comparing proteins, methods of protein purification and protein folding and stability.The latest developments in the field are included and key concepts introduced in a user-friendly way to ensure that students are able to grasp the essentials before moving on to more advanced study and analysis of proteins. An invaluable resource for students of Biochemistry, Molecular Biology, Medicine and Chemistry providing a modern approach to the subject of Proteins. It provides an accessible introduction to the principles of protein structure and function. It is beautifully illustrated throughout in full colour. End of chapter includes problems, references to further reading and a full glossary of terms. It features website including web-based tutorials, problems and additional content.

This is the first compilation of protein lipidation enzymes. This volume summarizes recent dramatic developments regarding enzymes responsible for protein lipidation, a process critical for a number of physiological functions, including cell proliferation and morphology. Inhibitors of protein lipidation have recently been shown to be useful as anticancer drugs. Enzymatic mechanisms, mutational analysis, and structural studies are presented.
Key Features
* The enzymatic mechanisms of protein lipidation
* Three-dimensional structures of protein farnesytransferase, protein geranylgeranytransferase II, and n-myristoryltransferase

This volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. 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 Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.