This book provides a coherent, clear, and uniform presentation of structural, genetic, molecular, and biochemical information available for the zona pellucida domain protein family, which impact pathologies such as infertility, deafness, and cancer. Furthermore it: * Details information about the structure and function of the ZP domain in ZPDC-proteins * Provides illustrations of the organization of ZPDC-proteins, the genes that encode the proteins, and examples of mutations in the ZP domain that cause diseases * Speculates as to the evolution of the ZP domain and potential therapeutics for diseases stemming from ZP domain mutations * Addresses mammalian and non-mammalian systems

The existence and functioning of intrinsically disordered proteins (IDPs) challenge the classical structure-function paradigm that equates function with a well-defined 3D structure. Uncovering the disordered complement of proteomes and understanding their functioning can extend the structure-function paradigm to herald new breakthroughs in drug development. Structure and Function of Intrinsically Disordered Proteins thoroughly covers the history up to the latest developments in this field.

After examining the principles of protein structure, the classical paradigm, and the history of structural disorder, the book focuses on physical techniques for the identification and characterization of IDPs. It discusses proteomic and bioinformatic approaches and shows how IDPs behave under crowding conditions in living cells. The next several chapters describe the structure, correlating biological processes, and molecular mechanisms of IDPs. The author also explores the evolutionary advancement of structural disorder in proteomes and possible ways of extending the structure-function paradigm to encompass both ordered and disordered states of proteins. He concludes with discussions on the involvement of IDPs in various diseases and how to establish rational drug design through detailed characterization of IDPs.

Although drug discovery rates have leveled off, new insight generated by the study of IDPs may offer fresh strategies for drug development. This work illustrates how these proteins defy the structure-function paradigm and play important regulatory and signaling roles.

The feld of proteomics moves rapidly. New methods, techniques, applications, standards, models and software appear almost on a daily basis. Accompanying this are plenty of texts on the experimental side of the feld and a few appearing on the informatic and data analysis side. This latterly includes one in the Methods in Molecular Biology series tackling the specifc analysis of "Mass spectrometry data in proteomics" in MMB vol. 376. This current collection builds on this, but takes a broader view of proteome data analysis covering data analysis essentials, but also the databases and data models, as well as practical consid- ations for analysing database search results, annotating genomes, and speeding up searches. It also digs deeper into some topics, such as decoy database searching and aspects of signal processing in proteomic mass spectrometry. The aim of the volume is to provide the reader with a mix of reviews and methodology chapters, which build from the essentials of database searching in proteomics, on through specifc data processing challenges to databases, data standards and data models.

This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics. Chapter 16 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume presents relevant background information to understanding the molecular basis governing unconventional protein secretion (UPS), and in particular explores the latest techniques and protocols that have been successfully applied for the study of this topic. Detailed chapters include an overview of conventional and unconventional secretory pathways along with multidisciplinary approaches and methods used for UPS analysis in different organisms. 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, Unconventional Protein Secretion: Methods and Protocols will be useful for all interested in the secretory pathway field as well as applications in cell biology, cell development, biomedical research, and healthcare.

Cytochromes P450 (CYPs) comprise a large superfamily of proteins that are of central importance in the detoxification or activation of a tremendous number of natural and synthetic hydrophobic xenobiotics, including many therapeutic drugs, chemical carcinogens and environmental pollutants. CYPs are important in mediating interactions between an organism and its chemical environment and in the regulation of physiological processes. Cytochrome P450 Protocols, Third Edition focuses on high-throughput methods for the simultaneous analysis of multiple CYPs, substrates or ligands. Although the emphasis is on CYPs of mammalian origin, it reflects an increasing interest in CYPs of bacterial species. Also included are chapters on cytochrome P450 reductase (the redox partner of CYPs) and the flavin-containing monooxygenases (FMOs), and metabolomic and lipidomic approaches for identification of endogenous substrates of CYPs ('de-orphanizing' CYP substrates). Written in the successful Methods in Molecular Biology (TM) 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, Cytochrome P450 Protocols, Third Edition provides a wide range of techniques accessible to researchers in fields as diverse as biochemistry, molecular biology, pharmacology, toxicology, environmental biology and genetics.

This volume provides an overview of the current successes as well as pitfalls and caveats that are hindering the design of membrane proteins. Divided into six parts, chapters detail membrane transporter, FoldX force field, protein stability, G-Protein Coupled Receptors (GPCR) structures, transmembrane helices, membrane molecular dynamics (MD) simulations, pH-dependent protonation states, membrane permeability, and passive transport. 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, Computational Design of Membrane Proteins aims to ensure successful results in the further study of this vital field. Chapter 4 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Revealing essential roles of the tumor microenvironment in cancer progression, this book provides a comprehensive overview of the latest research on the role of chemokines in the tumor microenvironment. Each chapter focuses on the chemokines patterns of expression, their regulation, and their roles in immune cell recruitment, as well as how they affect cancer immunity and tumorigenesis.Taken alongside its companion volumes, Tumor Microenvironment: The Role of Chemokines - Part B updates us on what we know about various aspects of the tumor microenvironment, as well as apprises us on future directions in the field. This book is essential reading for advanced cell biology and cancer biology students as well as scientists seeking an update on recent developments and research in the tumor microenvironment.

This volume explores current technologies used to investigate the formation, insertion, and function of metalloclusters associated with proteins. Chapters describe relevant topics about Fe-S cluster metabolism are explored through genetic, biochemical, spectroscopic methods. 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, Fe-S Proteins: Methods and Protocols aims to be a useful practical guide to researchers to help further their study in this field.

This book reviews the latest trends in glycobiotechnology, it offers an authoritative discussion about future directions of glycoengineering, and it provides a comprehensive overview about the current and emerging approaches to identify, quantify and characterize glycosylated proteins. Divided into 14 chapters, the book outlines recombinant glycoprotein expression in mammalian cells, insect cells, yeast, and bacterial systems. It covers the chemical and enzymatic syntheses of glycans and glyconjugates, and addresses the impact of glycosylation on protein function for the development of biologicals including vaccines. In the final chapters of the book, readers will discover more about the state-of-the-art in glycomics, glycoproteomics and glycan array technologies.

This second edition provides new and updated methods on the principles underlying modern protein analysis, from statistical issues to gel-based and mass spectrometry-based applications. Chapters detail protein quantification as basis for realisation of quantitative studies, gel-based and mass spectrometry-based quantification techniques, TMT, IPTL, PRM, MALDI Imaging, SILAC, PTM analysis, DIA, cross-linking, and the up-to-date topics of software and data analysis. 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, Quantitative Methods in Proteomics, Second Edition aims to provide comprehensive and competent overview in the important and still growing field of quantitative proteomics.

This volume compiles new experimental approaches and concepts focusing mostly, but not solely, on ways to manipulate and regulate Ras activity and its downstream signaling output. Chapters detail standard methodologies, biochemical methods, Ras processing trafficking and localization, Ras signaling and inhibition, and in vivo models for studying Ras function. 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 accessible, Ras Activity and Signaling: Methods and Protocols aims to provide support and guidance to lab workers in their work on Ras GTPases and in the design of new projects requiring novel methodologies.

Upstream processing refers to the production of proteins by cells genetically engineered to contain the human gene which will express the protein of interest. The demand for large quantities of specific proteins is increasing the pressure to boost cell culture productivity, and optimizing bioreactor output has become a primary concern for most pharmaceutical companies. Each chapter in Cell Culture and Upstream Processing is taken from presentations at the highly acclaimed IBC conferences as well as meetings of the European Society for Animal Cell Technology (ESACT) and Protein Expression in Animal Cells (PEACe) and describes how to improve yield and optimize the cell culture production process for biopharmaceuticals, by focusing on safety, quality, economics and operability and productivity issues. Cell Culture and Upstream Processing will appeal to a wide scientific audience, both professional practitioners of animal cell technology as well as students of biochemical engineering or biotechnology in graduate or high level undergraduate courses at university.

The origin of life has been investigated by many researchers from various research fields, such as Geology, Geochemistry, Physics, Chemistry, Molecular Biology, Astronomy and so on. Nevertheless, the origin of life remains unsolved. One of the reasons for this could be attributed to the different approaches that researchers have used to understand the events that happened on the primitive Earth. The origins of the main three members of the fundamental life system, as gene, genetic code and protein, could be only separately understood with these approaches. Therefore, it is necessary to understand the origins of gene, the genetic code, tRNA, metabolism, cell structure and protein not separately but comprehensively under a common concept in order to understand the origin of life, because the six members are intimately related to each other. In this monograph, the author offers a comprehensive hypothesis to explain the origin of life under a common concept. At the same time, the author offers the [GADV] hypothesis contrasting it with other current hypotheses and discusses the results of analyses of genes/proteins and the experimental data available in the exploration of the current knowledge in the field. This book is of interest for science students, researchers and the general public interested in the origin of life.

The book Heat Shock Proteins in Cancer Therapeutics provides the most comprehensive review on contemporary knowledge on the role of HSP in various types of cancer therapeutics. Using an integrative approach, the contributors provide a synopsis of the most current updates on the state of HSP in cancer therapeutics. The heat shock response pathway is a highly conserved cellular process. Heat shock factors are a master transcriptional regulator responsible for expression of several important heat shock proteins, which can effectively protect critical client proteins from misfolding and degradation, thus maintaining intracellular integrity under stressed conditions. Recent studies have demonstrated the direct connections between heat shock response players and tumor cell survival, validating heat shock response players as novel molecular targets in anticancer treatment. Although many hurdles in clinical application still need to be effectively addressed, such as undesirable drug toxicity and off target effects; narrow therapeutic window; poor PK/PD profiles, etc. Recent reports on synergistic drug combination, advanced prodrug design, smart nanoparticle packaging, and RNA aptamer selection offer promising solutions to overcome these challenges. Future advancements in this fast-growing area can potentially lead to the next generation of cancer therapeutics. Key basic and clinical research laboratories from major universities, academic medical hospitals, biotechnology and pharmaceutical laboratories around the world have contributed chapters that review present research activity and importantly project the field into the future. The book is a must read for graduate students. medical students, basic science researchers and postdoctoral scholars in the fields of Cancer Biology, Oncology, Translational Medicine, Clinical Research, Biotechnology, Cell & Molecular Medicine, Pharmaceutical Scientists and Researchers involved in Drug Discovery.

This volume provides a comprehensive set of protocols that can be used by any research lab to investigate diverse functional and structural properties of Single Stranded DNA Binding Proteins (SSBs) from eubacterial, archaeal, eukaryotic, mitochondrial and viral systems. 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, Single Stranded DNA Binding Proteins aims to be a useful practical guide to researchers to help further their study in this field.

This book is specifically about the application of the extremely powerful interaction between the protein avidin or its homologues and the vitamin biotin and some of its homologues. With excellent descriptions of laboratory protocols written by expert researchers, this volume is equally perfect for the student or the professional laboratory scientist.

Site-specific mutagenesis of DNA, developed some thirty years ago, has proven to be one of the most important advances in biology. By allowing the site-specific replacement of any amino acid in a protein with one of the other nineteen amino acids, it ushered in the new era of "Protein Engineering." The field of protein engineering has, however, evolved rapidly since then and the last fifteen years have witnessed remarkable advances through the use of new chemical, biochemical and molecular biological tools towards the synthesis and manipulation of proteins. The chapters included in this book reflect the rapid evolution of protein engineering and its many applications in basic research, biotechnology, material sciences and therapy. This book will provide the reader with an introduction to state-of the-art concepts and methods and will be of use to anyone interested in the study of proteins, in academia as well as in industry.

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.

Presents methods for determining the secondary and tertiary structure of proteins. The issues covered here involve theoretical/empirical approaches for predicting protein structure; a review using protein ligand interactions to study surface properties of proteins; use of fluorescence techniques to study structure and dynamics of proteins; and limited proteolysis with monoclonal antibodies to understand how specific structural features confer biological function.

This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.

This book focuses on the development of stapled peptides, a novel molecular modality used to regulate aberrant intracellular protein-protein interactions (PPIs). The author designs and presents a novel helical peptide stabilization methodology by constructing a chiral cross-linker moiety, namely "chiral center induced peptide helicity (CIH)". The book demonstrates that a precisely positioned carbon chiral center on tether can decisively determine the secondary structure of a peptide, and that the R-configured peptide is helical, while the S-configured peptide is non-helical. Further, it reports that helicity-enhanced R isomer peptides displayed significantly enhanced cell permeability and target binding affinity, as well as tumor inhibition efficiency, in comparison to S isomer peptides. The book will not only advance readers' understanding of the basic principle of stapled peptides, but also accelerate the clinical transformation of stapled peptide drugs.

This detailed new edition presents the latest developments of the main pillars of protein analysis, namely sample preparation, separation, and characterization. Core areas in this volume are protocols for the analysis of post-translational modifications and protein interaction partners, followed by sophisticated procedures to enrich for extracellular vesicles and organelles, along with several types of protein immuno-assays complemented by various methods for the characterization of antibodies and host-cell protein analysis. Last but not least, a few standard sample preparation protocols and recent advances concerning immuno-chemical detection of proteins are included as well. 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 up-to-date, Proteomic Profiling: Methods and Protocols, Second Edition serves as an ideal reference for students of biochemistry, biomedicine, biology, and genomics and will be an invaluable source for the experienced, practicing scientist as well.

This new edition features research from nearly 60 of the profession's most distinguished international authorities. Recognizing emerging developments in biopolymer systems research with fully updated and expanded chapters, the second edition discusses the biopolymer-based multilayer structures and their application in biosensors, the progress made in the understanding of protein behaviour at the air-water interface, experimental findings in ellipsometry and reflectometry, and recent developments concerning protein interfacial behaviour in microfabricated total analysis systems and microarrays. With over 3000 references, this is an essential reference for professionals and students in surface, pharmaceutical, colloid, polymer, and medicinal chemistry; chemical, formulation, and application engineering; and pharmacy.

This book discusses the unique ion channels and transporters found within the epithelial tissues of various organs, including the kidney, intestine, pancreas and respiratory tract. Authors focus on demonstrating the crucial roles that each of these channels and transporters play in transepithelial ion and fluid transport across epithelia, as well as in maintaining homeostasis. It allows readers to gain an understanding of the fundamentals of ion transport, in terms of function, modelling, regulation, trafficking, structure and pharmacology. This is the second of three volumes highlighting the importance of epithelial ion channels and transporters in basic physiology and pathophysiology of human diseases. This volume focuses on a wide array of epithelial tissues and the use of organoids to study epithelial function. Furthermore, clinical researchers and basic scientists from various fields provide a medical perspective on the physiology of a number of tissues and organs of the body including the pancreas, intestine, sweat glands, mammary gland, inner ear epithelia, retinal pigment epithelia of the eye, choroid plexus, and the ectodermal epithelia in dental enamel formation. This volume aims to 'round out' the reader's journey from basic science to the laboratory bench and clinical management of molecular diseases, making Volume 2 a must-read for students and scientists in the field of physiology, as well as for clinicians.