The book focuses on the current research of the relation between protein phosphorylation and meat quality, reviews the influence mechanism of protein phosphorylation on meat quality, and summarizes the improvement of meat quality by regulating protein phosphorylation. It could help to clarify some dilemmas and encourage further research in this field, aiming for effective application of protein phosphorylation in meat quality in the near future. The book is written for researchers and graduate students in the field of meat science, food chemistry and molecular biology etc.

This book focuses on histone mutations, especially those mutations closely related to cancer. Genetic mutations and epigenetic alterations contribute to the development of a variety of cancers: recent genetic studies have identified e.g. H3K27M and H3G34R/V mutation in over 75% of DIPG cases, H3.3K36M mutation in more than 90% of chondroblastoma cases, and H3G34W/L mutation in over 90% of giant cell tumors of bone. Given the high incidence and tumorigenesis effects of histone H3 mutations, they are also referred to as oncohistones. This book highlights the advances made in the area over the past 10 years, and offers a state-of-the-art summary of epigenetic alternation, gene expression, protein structure, drug discovery, immunotherapy, and mouse modeling of histone H3 mutations in various tumors. Chiefly intended to provide researchers and graduate students with an overall picture of these mutations, it will also be of interest to researchers in basic oncology, clinical oncology, and epigenetics, as well as academics and clinical oncology practitioners.

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.

This second edition volume expands on the previous edition with updated research and techniques to help laboratory workers design and implement a successful purification strategy, emphasize critical aspects on practical problems, and answers questions encountered at the lab bench. The chapters in this book are divided into five parts: Part One discusses an overview of screening and design of purification strategies and covers initial aspects on high-throughput screening, methods development, and media selection; Parts Two and Three explore low- and high-resolution methods, with emphasis on affinity chromatography; Part Four describes analytical techniques of purified proteins; and Part Five presents selected examples and case studies to discuss the aforementioned. 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 comprehensive, Protein Downstream Processing: Design, Development, and Application of High and Low-Resolution Methods, Second Edition is an ideal source of information to advanced students, junior researchers, and scientists involved in health sciences, cellular and molecular biology, biochemistry, biotechnology, and other related areas in both academia and industry.

This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.

This volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This second edition focuses on various techniques to investigate aspects of the TNF Superfamily members in health and disease. Chapters detail protocols on the signaling process of TNF family members, technical examples to investigating the role of TNF family members in physiopathologies, modulation of TNF signaling by pathogens, experimental applications of TNF-reporter mice, methodologies for various assays of TNF family members and the production of recombinant molecules. 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 accessible, The TNF Superfamily: Methods and Applications, Second Edition serves to aid researchers investigating this key family of proteins.

This book gathers selected studies on the industrial applications of glycoside hydrolases (GHs), presenting an updated classification of these enzymes, and discussing their structure, mechanisms, and various approaches to improve their catalytic efficiency. Further, it explains the various industrial applications of glycoside hydrolases in food, effluent treatment, biofuel production, and the paper and pulp industries. Lastly, the book provides a comparative analysis of glycoside hydrolases and discusses the role of metagenomics in the discovery of industrially important enzymes. As such it is a thought-provoking, instructive and informative resource for biochemists, enzymologists, molecular biologists and bioprocess technologists.

This second edition presents an up-to-date chapters describing the most relevant and novel techniques employed to study the opioid receptors. Chapters detail transcriptional and post-transcriptional analysis, cellular detection of opioid receptors, analysis of signaling events modulated by opioid receptors, model systems to studying opioid receptor-mediated functions, and behavioral effects mediated by opioid receptors. 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, Opioid Receptors: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Covering a wide-ranging facet of a "gold-standard" targeted mass spectrometry (MS) method for the consistent detection and accurate quantification of preselected proteins in complex biological matrices, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics: A Comprehensive View describes: The knowledge-based development of highly efficient SRM methodology including assay workflow, selection of proteins, peptides, transitions and its validation, and quality assessment Available bioinformatic tools - for both pre-acquisition method development and post-MS acquisition data analysis and data repositories Various relative and absolute quantification techniques SRM-MS' widespread applications in biomarker development and in clinical studies, as well as in the analysis of various posttranslational modifications (PTMs) Current challenges and contemporary trends to overcome those difficulties In addition, it features the historical development of modern-day mass spectrometry with its vivid applications and also covers basic MS instrumentation, ionization techniques, and various proteomics approaches. Comprehensive discussion, extensive references at the end of each chapter, and the list of review articles in the bibliography offer invaluable resources for advanced readings. Researchers from the undergraduate to postgraduate level and beyond in both academic or industry settings studying and working on mass spectrometry and/or proteomics will benefit from this book.

Anatomy of Gene Regulation is the first book to present the parts and processes of gene regulation at the three-dimensional level. Vivid structures of nucleic acids and their companion proteins are revealed in full-color, three dimensional form. Beginning with a general introduction to three-dimensional structures, the book looks at the organization of the genome, the structure of DNA, DNA replication and transcription, splicing, protein synthesis, and ultimate protein death. This concise and unique synthesis and its accompanying web site offer insight into gene regulation, and into the development of methods to interfere with regulation at diseased states.

This detailed collection explores techniques involved in the main strategies of nanopore sensing, such as translocation, analyte trapping, and interactions with external binding sites. Opening with a section on nanopore design and nanopore production, the book continues with parts devoted to various biological nanopores, nanopore engineering, and their uses in single molecule sensing, computational methods to study intrinsic nanopore behavior, characterizing the specific translocation activity of a vesicle particle through a nanopore, as well as the use of the technique droplet interface bilayer (DIB) in nanopore and membrane biophysical studies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Nanopore Technology: Methods and Protocols, with its focus on nanopore technology and biomolecule characterization, will hold the interest of the biophysicists, biochemists, bioengineers, and molecular biologists who are working toward further understanding this key field of research.

This book focuses on C-type lectin receptors, a newly emerging family of pattern-recognition receptors (PRRs) and a crucial part of the human innate immune system. Above all, the authors highlight these receptors' role in the recognition of pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) - one of the first steps in responding to foreign and potentially dangerous structures in the human body. The respective chapters chiefly examine various C-type lectin receptors, their corresponding ligands, and signalling. In addition to offering immunologists and clinicians important insights from the latest research, they may also provide novel points of departure for future drug development.

This book merges approaches in understanding the function of the light-gated ion channels known as channelrhodopsin together with methods addressing how channelrhodopsins can be used to address biomedical questions on a cellular or organismal level. Since the first molecular identification of channelrhodopsins, a broad range of tools have been created and new approaches developed to both better understand the molecular determinants of channelrhodopsin function as well as to use these and homologous proteins from a variety of species as tools to better understand physiological processes, which this volume addresses. Additionally, channelrhodopsins have become instrumental as a potential treatment for disease states. 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, Channelrhodopsin: Methods and Protocols provides a resource for those interested in honing their current expertise in this vital area of study as well as potentially branching out into new directions.

This book details the synthesis and assembly of polypeptide materials across length scales, i.e. proteins and peptides, their precursors, conjugates, and derivatives. A particular emphasis is made on measurement tools and procedures for material characterization, both physicochemical and functional. 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, Polypeptide Materials: Methods and Protocols serves to reflect the inter-disciplinary nature of molecular biology as well as the importance of developing innovative measurement methods to advance this vital area of research.

This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. 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, RNA Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.

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. Volume 20, Purinergic Receptors, has ten chapters. The first five chapters deal with various aspects of membrane binding. The first chapter focuses on the phox-homology (PX) domain, which is a phosphoinositide-binding domain conserved in all eukaryotes and present in forty-nine human proteins. The next chapter deals with the modeling of PH domains/phosphoinositides interactions. This is followed by a chapter on BAR domain proteins regulate Rho GTPase signaling. The BAR (Bin-Amphiphysin-Rvs) domain is a membrane lipid binding domain present in a wide variety of proteins, often proteins with a role in Rho-regulated signaling pathways. The fourth article presents AP180 N-terminal homology (ANTH) and Epsin N-terminal homology (ENTH) domains and discusses their physiological functions and involvement in disease. The fifth article reviews the polyphosphoinositide-binding domains and presents insights from peripheral membrane and lipid-transfer proteins. This is followed by a chapter on the physiological functions of phosphoinositide-modifying enzymes and their interacting proteins in Arabidopsis, then by a chapter on the molecular mechanisms of Vaspin action in various tissues such as adipose tissue, skin, bone, blood vessels, and the brain. The eighth chapter deals with exceptionally selective substrate targeting by the metalloprotease anthrax lethal factor followed by an article on Salmonella, E. coli, and Citrobacter type III secretion system effector proteins that alter host innate immunity. The last chapter presents New techniques to study intracellular receptors in living cells, with insights into RIG-I-like receptor signaling. Volume 20 is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

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 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 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.

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 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 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.