The edition details methods to study intrinsically disordered proteins (IDPs) including recent topics such as extremely high-affinity disordered complexes, kinetics that evade established concepts, liquid-liquid phase separation, and novel disorder-driven allosteric mechanisms. 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, Intrinsically Disordered Proteins: Methods and Protocols aims to help scientists with different backgrounds to further their investigations into these fascinating and dynamic molecules. Chapter 24 is available open access under a CC BY 4.0 license via link.springer.com. Chapters "40 and 42 " are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.

This volume focuses on protein analysis, and covers a wide array of uses of protein microarray for disease analysis. The chapters in this book discuss different stages of protein microarrays from their construction to their use, including different types of protein microarrays such as recombinant proteins, antibody, phage, and NAPPA protein microarrays, in planar format or in solution via beads arrays. 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. Comprehensive and cutting-edge, Protein Microarrays for Disease Analysis: Methods and Protocols is a valuable resource for graduate and post-doctoral fellows interested in protein microarrays, as well as senior researchers interested in gaining more insight into this developing field.

This volume contains a collection of innovative techniques for studying targeted protein degradation. Chapters guide readers through heterobifunctional proteolysis-targeting chimeras (PROTACs) approaches, E3 ligase, E3 ligase-induced ubiquitylation, proteomic approaches, novel degrader molecules, molecular glue, and stabilize binding interaction between a target and E3 ubiquitin ligase. 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, Targeted Protein Degradation: Methods and Protocols aims to ensure successful results in this emerging field of drug discovery.

Targeting protein degradation using small molecules is one of the most exciting small-molecule therapeutic strategies in decades and a rapidly growing area of research. In particular, the development of proteolysis targeting chimera (PROTACs) as potential drugs capable of recruiting target proteins to the cellular quality control machinery for elimination has opened new avenues to address traditionally 'difficult to target' proteins. This book provides a comprehensive overview from the leading academic and industrial experts on recent developments, scope and limitations in this dynamically growing research area; an ideal reference work for researchers in drug discovery and chemical biology as well as advanced students.

This book will address the growing roles of epigenetics in disease pathogenesis, and review the contribution of epigenetic modifications to disease onset and progression. The roles that epigenetics plays in facilitating effects of the environment on allergy and immunologic diseases will be reviewed. The book is divided into three parts - the first is an introduction to epigenetics and the methods that have been developed to study epigenetics, the second addresses epigenetics in allergic diseases and the third part will cover epigenetics in autoimmune diseases. With the rapid expansion of knowledge of how genes are regulated and how this regulation affects disease phenotypes, this book will be attractive to experienced researchers as well as those just launching an epigenetics research program. It will also be of interest to allergist, immunologists, rheumatologists and dermatologist who are engaged in clinical practice as a resource for understanding the basis for personalized and precision medicine. For example, the role that epigenetics plays in the pathogenesis in various allergic and autoimmune disorders and how this determines disease phenotypes will be covered extensively in this book. This book will thus help fill the gap in available resources on epigenetics in allergy and autoimmune diseases.

This volume provides readers with a comprehensive look at the latest techniques used to identify and characterize PDZ-mediated interactions. Chapters cover topics such as promiscuity, multimodularity, regulation, and viral recognition by PDZ domains. 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 thorough, PDZ Mediated Interactions: Methods and Protocols is a valuable resource for all researchers interested in learning more about this developing field.

Aging is an inevitable part of life and is becoming a worldwide social, economic and health problem. This is mainly due to the fact that the increasing proportion of individuals in the advanced age category have a higher probability of developing age-related disorders, such as type II diabetes mellitus, cardiovascular disorders, sarcopenia, and neurodegenerative conditions. New therapeutic approaches are still needed to decrease or slow the effects of such diseases. Advances in -omic technologies, such as genomics, transcriptomics, proteomics and metabolomics, have significantly advanced our understanding of disease in multiple medical areas, as the analysis of multiple molecular networks has simultaneously provided a more integrated view of disease pathways. It is hoped that emerging hits from these analyses might be prioritized for further screening as potential novel drug targets for increasing the human healthspan in line with the lifespan. In turn, this will lead to new therapeutic strategies as well as drug development projects by the pharmaceutical industry. This book presents a series of reviews describing studies that have resulted in identification of new potential drug targets for age-related disorders. Much of this information has come from -omic comparisons of healthy and disease states or from testing the effects of new therapeutic approaches. Authored by experts from around the globe, each chapter is presented in the context of specific chronic diseases or therapeutic strategies. This book is designed for researchers in the areas of aging and chronic disease, as well as clinical scientists, physicians and stakeholders in major drug companies.

This volume explores the latest methods used to study various aspects of TET proteins and their biology. Chapters in this book are divided into five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. 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 thorough, TET Proteins and DNA Demethylation: Methods and Protocols is a valuable resource that aims to help research scientists at all levels working in the fields of DNA demethylation dynamics. Chapters 3, 7 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book discusses the decoding of the lytic mechanism of an -helical pore-forming toxin, YaxAB, composed of two different subunits. Pore-forming toxins (PFTs) are among the most common bacterial toxins. They are produced by a variety of pathogens, which infect a wide range of organisms including plants, insects and humans. Yet the maturation of these particles and the structural changes required for pore formation are still poorly understood for many PFT families. Using a diverse panel of biochemical and structural techniques, including X-ray crystallography and cryo-electron microscopy, Dr. Brauning and colleagues have succeeded in identifying the mechanistic contributions of the two toxin components and elucidating the lytic state of the pore complex. The results of this thesis on the YaxAB system are applicable to orthologues from agriculturally relevant insect pathogens, and offer valuable structural and mechanistic insights to inform future bioengineering efforts.

This book explores the broad and diverse biological and physiological impacts of established and newly discovered cyclic di-nucleotide second messenger signaling systems, while also providing descriptions of the intriguing biochemical characteristics of multiple turnover enzymes and receptors. The respective chapters discuss the commonalities and diversity of cyclic di-GMP, cyclic di-AMP and recently discovered cyclic GMP-AMP signaling systems in manifold Gram-negative and Gram-positive bacteria. The global human pathogens Mycobacterium tuberculosis, Vibrio cholerae, Salmonella typhimurium, Escherichia coli and Streptococcus pneumoniae, the facultative human pathogen Pseudomonas aeruginosa, global plant pathogens as exemplified by Xanthomonas campestris and Burkholderia spp., and the omnipresent probiotic Lactobacilli, as well as environmentally important photoautotrophic cyanobacteria, the multicellular Myxococcus xanthus, and chemolithotrophic Acidithiobacillus are among the representatives of the microbial kingdom that are described. In turn, the various aspects of bacterial physiology affected by these signaling systems- e.g. biofilm formation and dispersal, the cell cycle, motility, virulence, production of antimicrobials, fundamental metabolism and osmohomeostasis - are discussed in detail in the context of different microorganisms. Dedicated chapters focus on the population diversity of cyclic dinucleotide signaling systems, their tendency to be horizontally transferred, the cyclic di-GMP signaling system in the social amoeba Dictyostelium, honorary cyclic (di)nucleotides, and the development of strategies for interfering with cyclic dinucleotide signaling in order to manipulate microbial behavior. Taken together, the chapters provide an authoritative source of information for a broad readership: beginners and advanced researchers from various disciplines; individuals seeking a broad overview of cyclic di-nucleotide signaling; and those who want to learn more about specific aspects. Also featuring reviews with a forward-looking perspective, the book offers a valuable source of inspiration for future research directions.

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.

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. 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, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.

This book examines detailed experimental and computational approaches for the analysis of many aspects vital to the understanding of membrane protein structure and function. Readers will receive guidance on the selection and use of methods for over-expression and purification, tools to characterize membrane proteins within different phospholipid bilayers, direction on functional studies, and approaches to determine the structures of membrane proteins. Detailed experimental steps for specific membrane proteins with critical notes allow the protocols to be modified to different systems. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of practical information and implementation advice that leads to excellent, reproducible results. Authoritative and up-to-date, Structure and Function Studies of Membrane Proteins serves as an ideal guide for biologists, biochemists, and biophysicists striving to further understand these essential proteins and their many biological roles.

This book offers comprehensive information on all aspects of ELISA, starting with the fundamentals of the immune system. It also reviews the history of analytical assays prior to the advent of ELISA (enzyme-linked immunosorbent assay) and addresses the materials of choice for the fabrication of the platforms, possible biomolecular interactions, different protocols, and evaluation parameters. The book guides readers through the respective steps of the analytical assay, while also familiarizing them with the possible sources of error in the assay. It offers detailed insights into the immobilization techniques used for protein attachment, as well as methods for evaluating the assay and calculating the key parameters, such as sensitivity, specificity, accuracy and limit of detection. In addition, the book explores the advantages and shortcomings of the conventional ELISA, as well as various approaches to improving its performance. In this regard, merging and integrating other technologies with widely known ELISAs have opened new avenues for the advancement of this immunoassay. Accordingly, the book provides cutting-edge information on integrated platforms such as ELISpot, plasmonic ELISAs, sphere-/bead-based ELISAs, paper-/fiber-based ELISAs and ELISA in micro-devices.

This thorough book aims to present the methods that have enabled the success of peptides and proteins in a wide variety of applications. It opens with a section on chemical tools applied to the production or engineering of peptides and proteins, and concludes with a collection of chapters on biological approaches used to engineer structure and function in peptides and proteins. As a book in the Springer Protocols Handbooks series, chapters include the kind of detailed descriptions and tips necessary for successful results in practice. Authoritative and practical, Peptide and Protein Engineering: From Concepts to Biotechnological Applications will be of great use to scientists in academia and industry seeking a better understanding of the emerging principles and methodologies in peptide and protein engineering.

Written by a pioneer in the development of spin labeling in biophysics, this expert book covers the fundamentals of nitroxide spin labeling through cutting-edge applications in chemistry, physics, materials science, molecular biology, and biomedicine. Nitroxides have earned their place as one of the most popular organic paramagnets due to their suitability as inhibitors of oxidative processes, as a means to polarize magnetic nuclei, and, in molecular biology, as probes and labels to understand molecular structures and dynamics AS DRAGS FOR CANCER AND OTHER DISEASES. Beginning with an overview of the basic methodology and nitroxides' 145-year history, this book equips students with necessary background and techniques to undertake original research and industry work in this growing field.

This book presents a new view of the mechanism of functional expression of ATP-driven motors (proteins or protein complexes). It is substantially different from the prevailing idea that the motor converts chemical energy to mechanical work. To facilitate understanding, the differences between the new and prevailing views are explained using many illustrations. The book is of interest to those who are not convinced of the notion of chemo-mechanical coupling. The claims presented are the following: The system, which comprises not only the motor but also water, does no mechanical work during the ATP hydrolysis cycle; a protein is moved or a protein in the complex is rotated by the entropic force generated by water. The highlight of the explanation in the book is that the mechanism of unidirectional rotation of the central shaft in F1-ATPase is discussed in detail on the basis of this new view. The hydration entropy of each subunit to which a specific chemical compound (ATP, ADP and Pi, Pi, or nothing) is bound, the hydration entropy of the 3 3 complex, and the dependence of the hydration entropy of F1-ATPase on the orientation of the subunit play essential roles.

In this book, the major paradigm-shifting discoveries made in the past century on key cellular nanomachines are described in great detail: their complex yet precise and elegant design and function, as well as the diseases linked to their dysfunction and the therapeutic approaches to overcome them. The major focus of this book is the "porosome" nanomachine, the universal secretory portal in cells. This is an ideal book for students, researchers, and professionals in the fields of nanoscience and nanotechnology.

This book summarizes all the important aspects of CRLs (Cullin-RING E3 Ubiquitin Ligases), while providing details of mechanistic specifics that go beyond protein ubiquitination and neddylation. Ubiquitin ligases, including the CRLs, which are activated by neddylation, play an important role in diverse biological processes and are involved in various human diseases, particularly cancer. The book covers various topics, such as CRL structure, biology, genetics, its regulation by neddylation, its pivotal role in human disease, and its potential in drug discovery and targeted therapies. The book appeals to biochemists and biologists working in other fields, and, given the importance of CRLs in all aspects of cell biology and the great promise of targeting these complexes for therapy, is a valuable resource anyone interested in modern biology or medicine.

This book offers an authoritative review of biopharmaceuticals and their clinical relevance. Biopharmaceuticals have been showing high therapeutic potential by means of biological and biosimilar medicines, particularly for the treatment of cancer, chronic diseases (e.g. diabetes, Crohn's disease, psoriasis and rheumatoid arthritis), neurodegenerative disorders (e.g. multiple sclerosis), and they have also been contributing to the progress of innovative therapies such as assisted reproductive medicine. Since the eighties, several biopharmaceuticals have been approved and, due to patents expiration, many biosimilars are also marketed. In this book, readers will find the most relevant updated information about the main clinical applications of pharmaceutical biotechnology. The authors provide expert analysis about the industrial challenges of recombinant proteins and the different classes of biopharmaceuticals, including monoclonal antibodies, vaccines, growth factors and stem cells. Topics such as bioprinting technologies in tissue engineering, gene therapy and personalized medicine are also covered in this book. Professionals, students and researchers interested in this field will find this work an important account.

This book is a collection of principles and current practices in omics research, applied to skeletal muscle physiology and disorders. The various sections are categorized according to the level of biological organization, namely, genomics (DNA), transcriptomics (RNA), proteomics (protein), and metabolomics (metabolite). With skeletal muscle as the unifying theme, and featuring contributions from leading experts in this traditional field of research, it highlights the importance of skeletal muscle tissue in human development, health and successful ageing. It also discusses other fascinating topics like developmental biology, muscular dystrophies, exercise, insulin resistance and atrophy due to disuse, ageing or other muscle diseases, conveying the vast opportunities for generating new hypotheses as well as testing existing hypotheses by combining high-throughput techniques with proper experiment designs, bioinformatics and statistical analyses. Presenting the latest research techniques, this book is a valuable resource for the physiology community, particularly researchers and grad students who want to explore the new opportunities for omics technologies in basic physiology research.

This book presents a comprehensive overview of important immune molecules and their structure-function relationships. The immune system is highly complex, consisting of a network of molecules, cells, tissues and organs, and the immune reaction is involved in various physiological as well as pathological processes, including development, self-tolerance, infection, immunity, and cancer. Numerous molecules participate in immune recognition, inhibition and activation, and these important immune molecules can be roughly divided into cell surface receptors, intracellular receptors and intracellular signaling molecules. The study of how these immune molecules function at molecular level has laid the foundation for understanding the immune system. The book provides researchers and students with the latest research advances concerning the structural biology of key immune molecules/pathways, and offers immunologists essential insights into how these immune molecules function.

This book demonstrates the potential of urine as a biomarker resource for early disease detection, covering the related theory, strategies, tools and findings. Biomarkers are measurable changes associated with diseases. Blood, as a critical part of its internal environment, is closely monitored and controlled by the body to maintain homeostasis, especially in the early stages of diseases. In contrast, urine, as a form of waste excreted by the body, collects a variety of substance changes. Accordingly, urine can offer an ideal resource for early biomarker discovery. In addition, urine is more stable than blood in vitro, and is easy to store and analyze. The book discusses exciting preliminary applications of urine biomarkers for diseases affecting major biological systems. Its main goal is to make scientists, clinicians and medical companies aware of this important, exciting, undeveloped, and profitable field.

Using both epidemiological and model organism approaches, we have gained new insights into the physiological and molecular aspects of aging, which has led to significant advancements in potential anti-aging strategies. Reviews on Biomarker Studies in Aging and Anti-Aging Research presents a series of reviews in various aspects of aging and age-related disease research along with several methods which have shown progress as potential anti-aging approaches. The book is aimed at researchers in the areas of aging and chronic disease, as well as to clinical scientists, physicians and major drug companies. It provides important information on disease mechanisms, and each chapter is presented in the context of the aging process, specific chronic diseases or different therapeutic areas.