Volume I highlights the association of the cellular prion protein (PrPC) with copper and zinc, the potential roles of PrPC in Alzheimer's disease and cancers, insoluble PrPC, PMCA, molecular and cellular mechanisms of PrPSc formation and clearance, possible co-factors involved in the conversion of PrPC into PrPSc, infectious and pathogenic forms of PrP, cell biology of prions, prion strains and their interference, as well as yeast prions and their inheritable and structural traits. This unique volume will take you through the fascinating chronicle of prions in mammals, yeast, and fungi.

This volume focuses on mono-ADP-ribosylation and enzymes that use NAD+ including Sirtuins, PARPs, and bacterial and eukaryotic ADP-ribosyltransferases. The chapters in this book are organized into eight parts, and offer detailed descriptions of key protocols used to study topics such as in vitro techniques for ADP-ribosylation substrate identification; biochemical and biophysical assays of PAR-WWE domain interactions; monitoring expression and enzyme activity of ecto-ARTCs; HPLC-based enzymes assays for Sirtuins; and identifying target RNAs of PARPs. 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, ADP-ribosylation and NAD+ Utilizing Enzymes: Methods and Protocols is a valuable resource for anyone interested in this developing and expanding 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.

The contents of this book focus on the recent investigations in molecular bi- ogywhereapplicationsoftopologyseemtobeverystimulating. Thevolumeis based on the talks and lectures given by participants of the three-month p- gram"TopologyinCondensedMatter,"whichwasheldintheMaxPlanck- stitut fur Physik komplexer Systeme, Dresden, Germany, 8May-31July 2002, under the scienti?c direction of Professors M. Kl eman, S. Novikov and - self. The aim of this program was to discuss recent applications of topology to several areas in condensed matter physics and molecular biology. The ?rst volume "Topology in Condensed Matter" is concerned with m- ern applications of geometrical and topological techniques to such new and classic ?elds of physics like electron theory of metals, theory of nano-crystals, aperiodic and liquid crystals, quantum computation and so on. This volume is published simultaneously in "Springer Series in Solid-State Physics." The present volume gives an exposition of the role of topology in the theory of proteins and DNA. The last thirty years a?rmed very e?cient - plications of modern mathematics, especially topology, in physics. The union of mathematics and physics was very stimulating for both sides. On the other hand, the impact of mathematics in biology has been rather limited. H- ever here also some interesting results were obtained. In particular, there are applications of knot theory in the theory of circular closed DNA. The - cent discoveries in molecular biology indicate future successful applications of topology."

This volume provided methods and protocols on recombinant protein production in different plant systems, downstream processing, and strategies to optimize protein expression. Chapters guide readers through recombinant protein production in important plant systems, protein recovery and purification, different strategies to optimise productivity, cloning and fusion protein approaches, and the regulation and freedom to operate analysis of plant-produced proteins. 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, Recombinant Proteins in Plants: Methods and Protocols aims to be useful to newcomers and experienced researchers interested in expanding their expertise in the field of plant-based protein production. Chapters 6, 8 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Ubiquitination and Protein Stability - Part B, Volume 619, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this updated volume presenting interesting chapters written by an international board of authors. Topics of note include chapters on Assays of SUMO protease function in mammalian cells, In vitro analysis of proteasome-associated USP14 activity for substrate degradation and deubiquitylation, Methods to study proteasome regulatory particle assembly, Native mass spectrometry approaches to study the proteasome, Single-molecule methods to study the ubiquitin-proteasome system, Assays for the function of ubiquitin in the mammalian endocytic pathway, and much more.

This book provides timely reviews of several protein complexes that regulate gene expression and chromatin dynamics. Examples of such complexes include: nucleosome assembly complexes, ATP-dependent chromatin remodeling complexes, histone acetyltransferase complexes, histone deacetylase complexes, heterochromatin complexes, SMC complexes and transcription elongation complexes. These chapters will bring experts in the field up to date on several aspects of chromosome biology and will provide an exiting introduction to the field for new chromatin researchers.

Thousands of proteins have been identified to be acetylated. Immense research power has been dedicated to experiments to solve the biological implications of each and every protein acetylation. Two particular sites of protein acetylation have been described intensively: the N-terminal methionine residue of a nascent protein and lysine residues within a protein. In Protein Acetylation: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study protein acetylation. These include methods and techniques for identification of protein acetylation, column- and gel electrophoresis-based approaches, computationally prediction, and the biological response to protein acetylation. Written in the highly 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 laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Acetylation: Methods and Protocols seeks to aid scientists in the further study of the technical aspects involved in understanding protein acetylation.

This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology. This broad, unified approach is made possible, in large part, by the very wide scope of Dr. Xia's own research experience. The integration of genomics, proteomics and transcriptomics into a single volume makes this book required reading for anyone entering the new and emerging fields of Systems Biology and Evolutionary Bioinformatics.

G-Protein-Coupled Receptors, Part B, 2nd Edition, Volume 149, the latest release in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers Optical Approaches for Visualization of Arrestin Binding to Muscarinic Receptors, Luciferase Reporter Assay for Unlocking Ligand-mediated Signaling of GPCRs, Assays to Measure GPCR Dependent Cellular Migration, Characterization of the Frizzled GPCRs, Binding Assays for Bradykinin and Angiotensin Receptors, Detection of Misfolded Rhodopsin Aggregates in Cells, Measuring GPCR Ubiquitination and Trafficking, Culture of Primary Neurons and its Use in Studying GPCR Trafficking, and much more.

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.

Animal cells present an extreme variability in their shapes in relation to their physiological properties. For instance, fibroblastic cells are tightly attached to the extra-cellular matrix and display a flattened, spindle-shaped morphology. Neuronal cells self-organize as a network through a complex branching of dendrites and a long axonal extension. Resting peripheral blood lymphocytes are poorly adhesive and maintain a spherical, smooth shape, while macroph- ages produce many pseudopodal extensions involved in the recognition of foreign molecules. In addition to the variability of the morphology of the cells that constitute different organs, many cell types also modify dynamically their morphology in response to environmental changes, leading to differential cell motility, migration, adhesion, polarity or intercellular contacts. This wide plasticity of cell morphology is promoted and maintained by the cytoskeleton, which is composed of the three interconnected actin micro filaments, tubulin microtubules and intermediate filaments networks, all capable of assembly and disassembly. Over the past few years, the Rho family of Ras-like GTPases emerged as key proteins that mediate extracellular signalling pathways leading to the forma- tion of polymerized actin-containing structures such as ruffles, lamellipodia and filopodia. Since the discovery of the first member RhoA in 1985, 13 mem- bers have so far been characterized in human cells. Most of Rho proteins are highly conserved between species as distant as yeast, slime mold, insects and mammals, which points to their fundamental role in cellular physiology.

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.

Fibroblast Growth Factors presents research and results from the leading global research group on FGF, providing up-to-date and comprehensive coverage of the field. The book describes the history, basic research and growth engineering technology involved with FGFs, while also introducing detailed research methods. It comprises eight chapters that detail successes and problems in relation to wound healing of engineered growth factors and considers injury repair and regeneration, non-mitogenic mutants, structure modification, pathology, physiology, pharmacology, development, FGF/FGFR inhibitors, bioengineering, and new drug development. It will serve as a key reference book for researchers working on FGFs.

As this book. Antibacterial Peptide Protocols, will attest, my enthusi asm for the field of antibacterial peptides is based on a conviction (and I am unashamed to say, prejudice) that these substances are in essence antibiotics produced by the host that then participate in host defense against infectious agents. Because of their capacity to exert antibiotic-like action against patho genic microorganisms (bacteria, fungi, parasites, and viruses), there is reason to believe that these agents will soon be used clinically to treat infectious diseases. In fact, in recent years, biotechnology companies have been formed for the sole purpose of developing antibacterial peptides for clinical use. It should be emphasized that antibacterial peptides will likely play a major role in the treatment of infectious diseases, particularly with the increasing prob lem of multidrug-resistant microbes and the relative dearth of new antibiotics being provided by pharmaceutical companies. The topic of this volume of Methods in Molecular Biology, the diverse methods used in research on antibacterial peptides, is thus quite timely. As the subject of antibacterial peptides develops into its own discipline (something strongly suggested by the explosion in the number of papers published over the past decade), it is essential that reliable techniques and strategies be made available not only to those of us in the field, but also to the newcomers and researchers in complementary disciplines."

The book recognizes that throughout the scientific, medical, and economic communities, new tests incorporating biomarkers are needed to improve the diagnosis of patients suffering from metabolic disorders. The early identification of those at risk of developing obesity will help to place these individuals on the best treatment course as early as possible for improved treatment outcomes. This will also help to cut costs incurred by the healthcare services. For all of this to occur, new research efforts are needed to identify novel biomarkers that can be used to predict the disease in the presymptomatic stage, for disease monitoring and for prediction of treatment response. It is also possible that new drug targets can be identified using these approaches which, in turn, can lead to the development of new treatment approaches. This volume also includes a series of reviews on biomarker discovery and usage in the study of diseases marked by perturbations in metabolism. It will describe the pros and cons of the various approaches and cover the successes and failures in this important research field.

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

Today, activation endoproteolysis of secretory proteins is recognized as a fundamental biological mechanism of spatial and temporal regulation of protein activity as well as of diversification of protein functions. In Proprotein Convertases, experts in the field examine detailed methods involving proprotein convertases, the enzymes mediating this endoproteolysis, which reside within or cycle between the various compartments of the secretory pathway. Providing a timely assessment of impact of activation/inactivation endoproteolysis in the secretory pathway, the volume offers a broader perspective on the biochemistry of the PCSKs (proprotein convertases, subtilisin/kexin-type) by exploring structural and functional analogies with bacterial subtilisin and on the enzymology of endoproteolysis itself by describing the involvement in the process of non-PCSK-type such as cathepsin L. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their specific topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Meticulous and up-to-date, Proprotein Convertases represents an instructive and useful reference book for all scientists interested in endoproteolytic activation and/or inactivation of secretory proproteins through limited proteolysis, for experts in the field and newcomers to it as well.

The topic of this book, Collectins, is a family of proteins whose major function is in innate immunity, where Collectins act as pattern recognition receptors (PRRs). In general they recognize targets such as microbial surfaces and apoptotic cells, and once bound to a target, Collectins promote the clearance of microorganisms and damaged host tissue. New cell-surface proteins and glycoproteins, which act as Collectin receptors, are currently being identified. Some Collectins, particularly MBL, activate the complement system, which enhances the ability of antibodies to fight pathogens, via three MBL-associated proteases, the MASPs. Additionally, recent research has begun to show wider-ranging activities of Collectins, such as: * Their role in metabolism, and therefore their involvement in lifestyle diseases such as obesity and cardiovascular disease. * Their ability to modulate the adaptive immune response, as well as to recognize and trigger apoptosis of cancer cells, which makes them effective in the annihilation of cancer cells with multiple mutations. * The regulation of their expression by gonadal steroid hormones implicates them with critical roles in both male and female fertility. * Altered levels of Collectins have been associated with various autoimmune diseases. This book brings together current knowledge of the structure, functions and biological activities of Collectins, to describe their integral role in human health.

In this book, renowned scientists describe how cholesterol interacts with various proteins. Recent progress made in the high-resolution visualization of cholesterol-protein interactions using crystallography and cryogenic electron microscopy has substantially advanced the knowledge of critical features. These features enable specific recognition of the cholesterol molecule by proteins, a process that was built on earlier studies using binding assays, computational modeling and site-directed mutagenesis. Direct Mechanisms in Cholesterol Modulation of Protein Function offers comprehensive insights into the current understanding of cholesterol-driven modulation of protein function via direct sensing. Its nine chapters are organized into two distinct parts. In the first part, the chapters introduce the reader to the general characteristics of cholesterol binding sites in proteins. This part starts with a tour into common cholesterol recognition motifs, followed by an overview of the major classes of steroid-binding proteins. It then continues with two chapters that present a comprehensive analysis of molecular and structural characteristics of cholesterol binding sites in transmembrane and soluble protein domains. In the second part of the book, examples of cholesterol binding sites and consequences of specific cholesterol recognition for protein function are presented for G protein-coupled receptors, ion channels and cholesterol-transporting proteins. The book is valuable for undergraduate and graduate students in biochemistry and nutrition, as well as basic science and medical researchers with a keen interest in the biophysical properties of cholesterol and physiological consequences of cholesterol presence in biological systems.

This book covers structure, function, and important roles of the SH domains, structure-function relationships, the versatile nature of their action, mechanisms of aggregation, specificity of interactions, impact of mutations on protein functional dysregulation, and cell signaling. Their involvement in various cellular processes such as migration, invasiveness, actin reorganization, shaping spines, determination of the morphology assembly of fibrils, and mechanotransduction makes these molecules attractive drug targets. Substrates, inhibitors and activators of PTKs present a wide variety of therapeutic agents in the context of delivering treatments for numerous pathologies. The new emerging field of stem cell therapies and design of biomaterials for treatments relies on the directed regulation of stem cell growth, differentiation and morphology, as well as the production of biomimetic scaffolds that respond to programmed signals. Advances in deciphering the mechanisms of action of these important molecules will lead to the implementation and success of their vital applications.

This book comprehensively reviews the state-of-the-art strategies developed for protein-protein interaction (PPI) inhibitors, and highlights the success stories in new drug discovery and development. Consisting of two parts with twelve chapters, it demonstrates the design strategies and case studies of small molecule PPI inhibitors. The first part discusses various discovery strategies for small molecule PPI inhibitors, such as high throughput screening, hot spot-based design, computational approaches, and fragment-based design. The second part presents recent advances in small molecule inhibitors, focusing on clinical candidates and new PPI targets. This book has broad appeal and is of significant interest to the pharmaceutical science and medicinal chemistry communities.

This volume presents modern and enhanced methods that detail techniques to perform proteomics analyses dedicated to biomarker discovery for human health. Chapters guide readers through pre/post analytical factors, protocols for the preparation of extracellular vesicles and exosomes, and various analytical pipelines including Data Independent Acquisition (DIA), discovery, as well as targeted and top-down proteomics analysis workflows. Bioinformatics tools and workflows to select and evaluate candidate biomarkers or combinations of biomarkers are also presented. 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, Proteomics for Biomarker Discovery: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Over the past decade, there has been an explosive development of research of intrinsically disordered proteins (IDPs), which are also known as unfolded proteins. Structural biologists now recognize that the functional diversity provided by disordered regions complements the functional repertoire of ordered protein regions. In Intrinsically Disordered Protein Analysis: Methods and Experimental Tools, expert researchers explore the high abundance of IDPs in various organisms, their unique structural features, numerous functions, and crucial associations with different diseases. Volume 2 includes sections on single molecule techniques, methods to assess protein size and shape, analyzing conformational behavior, mass-spectrometry, expression and purification of IDP's. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Intrinsically Disordered Protein Analysis: Methods and Experimental Tools helps scientists further their investigations of these fascinating and dynamic molecules.

Due to continuous technical developments and new insights into the high complexity of neurological diseases, there is an increasing need for the application of proteomic technologies which can yield potential biomarker readouts for improved clinical management as well as for the development of new drugs by struggling pharmaceutical companies. This book describes the step-by-step use of proteomic methods such as two-dimensional gel electrophoresis, multiplex immunoassay, liquid chromatography mass spectrometry (LC-MS) and selective reaction monitoring MS, to increase our understanding of these diseases, with the ultimate aim of improving patient care. The volume will be of high interest to clinical scientists, physicians and pharmaceutical company scientists as it gives insights into the latest technologies enabling the revolution of personalized medicine. It is of direct interest to both technical and bench biomarker scientists as it gives step by step instructions on how to carry out each of the protocols. It is also of interest to researchers as each technique will be presented in the context of a specific neurological disorder, including Alzheimer's disease, multiple sclerosis, autism spectrum disorders, schizophrenia, major depressive disorder and bipolar disorder. Finally, it will also highlight the future research efforts in this field, which are endeavoring to convert proteomic platforms to the form of hand held devices which can be used in a point of care setting and return diagnostic results within the timeframe of a visit to the general practitioner.