This second edition expands on the previous edition with new chapters that are suitable for newcomers, as well as more detailed chapters that cover protein stability and storage, avoiding proteolysis during chromatography, protein quantitation methods including immuno-qPCR, and the challenges that scale-up of production poses to the investigator. Many of the chapters also discuss generation and purification of recombinant proteins, recombinant antibody production, and the tagging of proteins as a means to enhance their solubility and simplify their purification on an individual scale or in high-throughput systems. This book also provides readers with chapters that describe not just the more commonly used methods, but also recently developed approaches such as proteomic/mass spectrometric techniques and Lectin-based affinity chromatography. 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, Protein Chromatography: Methods and Protocols, Second Edition is a valuable resource for anyone who is interested in the field of protein chromatography.

This volume provides a comprehensive guide on the Cyr61 (Cysteine-rich 61) (CCN) family of proteins and genes from basic research to cutting-edge methodologies and state-of-the-art techniques. Chapters details practical tips to overcome any obstacles with experimentation pertaining to chemistry, biology, physiology, pathology, medical and dental sciences and pharmacology of CCN 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, CCN Proteins: Methods and Protocols will be a valuable resource for a wide audience, ranging from the experienced CCN researchers looking for new approaches to junior graduate students just beginning in CCN research.

This detailed collection covers how the biological functions of histone deacetylases (HDACs) and histone acetyltransferases (HATs) can be detected in various experimental settings, both in vivo and in vitro. The book also covers the generation and specificity of deacetylase inhibitors and how such agents can be used to test experimental hypotheses. Written for the popular 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, as well as tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, HDAC/HAT Function Assessment and Inhibitor Development: Methods and Protocols serves as an ideal guide to this vital area of study.

This is the second edition of a very well received book that details how the sumoylation system functions and how it modulates numerous cellular activities. SUMO is a post-translational modifier in the ubiquitin super-family that has gained recognition over the last twenty years as an essential and prevalent regulatory molecule. Individual chapters explore the biochemistry, molecular biology, and cell biology of the sumoylation system and its substrate proteins. The book is divided into three themed parts: Molecular Functions (I), Cell Growth Regulation (II), and Diseases (III). Parts I and II focus on the contribution of sumoylation to cellular activities in both the nuclear and cytoplasmic compartments. The nuclear activities covered include nucleic acid metabolism (both RNA and DNA), chromosome structure and replication, and nucleocytoplasmic transport. Cytoplasmic processes presented include regulation of membrane ion channels, general metabolism, and apoptotic signalling. Topics in Part III include the role of sumoylation in developmental abnormalities (craniofacial and cardiovascular), diabetes, neurodegenerative diseases, cancer, and infections with viruses and bacteria. Each of the corresponding chapter authors is an active researcher who has made significant contributions to understanding sumoylation. This second edition provides updates and revisions to most of the original chapters plus adds six new chapters to address important developing areas of sumoylation research. This volume is intended for a scientific audience from undergraduates to independent researchers. The content will serve as both a solid introduction for the novice reader and an in depth treatment for the advanced scholar.

Focuses on Biology, Pharmacology, and Therapeutic Applications The study and diverse applications of bioactive peptides traverse many sub-disciplines within chemistry, biology, physics, and medicine. Answering a long-standing need, Bioactive Peptides focuses on the biology, pharmacology, and therapeutic applications of endogenous peptide mediators and their analogues. Moving peptide science beyond chemical synthesis strategies and into the realms of peptide biology and therapeutics, it presents the overall contribution that peptide science has made to molecular, cellular, and whole organism biology, while also discussing future targets and therapeutic applications. Beneficial for Experts and Novices Alike Part I provides details of bioactive peptides that interact with common drug targets and analyzes some of the most competitive areas of current research worldwide. While it is widely known that mammalian physiological systems utilize bioactive peptides that have yet to be discovered, other animals provide a rich and valuable source of bioactive peptides. This fascinating area of science is the theme of Part II. Parts III and IV investigate the unique bioactivities of various peptides that are ripe for further exploration. This definitive reference also includes: A detailed description and analysis of a broad range of peptides that interact with G protein-coupled receptors, the quantitatively dominant drug target A discussion of non-ribosomal peptides, which hold promise as sources of endogenous mediators Important examples of common methodologies employed to identify, characterize, and further develop bioactive peptides from a range of natural sources With mounting worldwide interest in their therapeutic potential, bioactive peptides-includ

This book presents multiple new and classical methods for studying the vital poly-ADP-ribose (pADPr) pathway. Beginning with techniques for the detection and quantification of the product of poly(ADP-ribose) polymerase (PARP) enzymatic activity and detection of variation in pADPr production during the cell cycle, the volume continues with sections on the identification of pADPr protein acceptors, methods focusing on studying molecular mechanisms of PARP functions in eukaryotic cells, particularly those involved in control of DNA repair and oxidative stress, as well as in expression regulation, approaches to the in vitro reconstitution of PARP-1 interaction with chromatin, the development and testing of small molecule PARP inhibitors, and the functions of understudied members of PARP family. 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, Poly(ADP-Ribose) Polymerase: Methods and Protocols, Second Edition serves as an ideal companion to the first edition for scientists whose investigations involve this important pathway. The chapter 'Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach' is published open access under a CC BY 4.0 license.

This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. 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: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Addressing the increased use of protein and peptide candidates as treatments for previously untreatable diseases, this comprehensive and progressive source provides the reader with a roadmap to an increased understanding of issues critical for successfully developing a protein or peptide therapeutic candidate. Proteins and Peptides is an invaluable source for drug discovery and development scientists in the biopharmaceutical industry who frequently navigate the maze of protein and peptide pharmacokinetics, pharmacodynamics, and metabolism. Key features include: issues related to delivery of protein and peptide therapeutics in elderly populations and pharmacogenomics lessons learned on the major marketed areas of proteins and peptides, including interleukins, interferons, growth factors, and peptide hormones innovations for protein and peptide delivery such as needle-less delivery strategies for delivery of these molecules to locations such as the eye and brain generic issues of proteins and peptides

This book is a practical review which focuses on computational analysis and on in silico approaches towards the systematic discovery of various key functional gene expression elements in microalgae as a model. So far, in this regard very little information is available. Efficient stepwise procedures for analysing the matrix attachment regions (MARs) are outlined, as well as for translation initiation sites (TIS), signal peptide (SP) sequences, gene optimization and transformation systems. These outlines can be efficiently deployed as practical models for the systematic discovery of key expression elements and for the optimization of cis/transgenes in other micro/organisms. The first chapter is an introduction on the key gene expression elements analysed in this book, including scaffold/matrix attachment regions, translation initiation sites, signal peptides as well as gene optimization. Chapter 2 focuses on systematic strategies and computational approaches toward in silico analysis of each factor. The analyses outcomes is assessed individually in chapter 3 followed by developing the specific conceptual models for each element in Chapter 4. The concluding remarks are discussed in Chapter 5. This work is of interest to computational and experimental biologists interested in transcriptional regulation analysis as well as to researchers and scientists who wish to consider the use of bioinformatics and computational biology in design, analysis, or regulatory reviews of key gene expression elements for the production of recombinant proteins experiments.

This book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.

The role of vitamin A in living organisms has been known throughout human history. In the last 100 years, the biochemical nature of vitamin A and its active derivative, retinoic acid, its physiological impact on growth processes, and the essential details of its mechanism of action have been revealed by investigations carried out by researchers using vertebrate and more recently invertebrate models to study a multiplicity of processes and conditions, encompassing embryogenesis, postnatal development to old age. A wealth of intercellular interactions, intracellular signaling systems, and molecular mechanisms have been described and the overall conclusion is that retinoic acid is essential for life. This book series, with chapters authored by experts in every aspect of this complex field, unifies the knowledge base and mechanisms currently known in detailed, engaging, well-illustrated, focused chapters that synthesize information for each specific area. In view of the recent information explosion in this field, it is timely to publish a contemporary, comprehensive, book series recapitulating the most exciting developments in the field and covering fundamental research in molecular mechanisms of vitamin A action, its role in physiology, development, and continued well-being, and the potential of vitamin A derivatives and synthetic mimetics to serve as therapeutic treatments for cancers and other debilitating human diseases. Volume II is divided into nine chapters contributed by prominent experts in their respective fields. Each chapter starts with the history of the area of research. Then, the key findings that contributed to development of the field are described, followed by a detailed look at key findings and progress that are being made in current, ongoing research. Each chapter is concluded with a discussion of the relevance of the research and a perspective on missing pieces and lingering gaps that the author recommends will be important in defining future directions in vitamin A research.

How does the chemical description of a protein relate to its three-dimensional structure? How does the three-dimensional structure relate to the machinery that brings about a chemical reaction? How does the sequence of a gene encode not only the sequence of a protein but, more importantly, the architecture and function of that protein? Protein Structure and Function provides a clear and critical survey of our current understanding of the structure and function of proteins to answer questions such as these. Opening with a consideration of the link between protein sequence and structure, it goes on to explore the structural basis of protein function and how this function is controlled. Finally, it examines a range of case studies that illuminate the range of roles performed by proteins, and the diverse structures these proteins exhibit. Protein Structure and Function combines articulate prose with striking full colour illustrations, while the unique Primers in Biology modular structure integrates text, illustrations, definitions, and literature references for each topic into one double-page spread, bringing to the student's fingertips all the tools that they need to master that topic. Online Resource Centre The Online Resource Centre features figures from the book available to download, for registered adopters of the book.

This book summarizes the early successes, drawbacks and accomplishments in cell biology and cell biotechnology achieved by the latest projects performed on the International Space Station ISS. It also depicts outcomes of experiments in tissue engineering, cancer research and drug design and reveals the chances that research in Space offers for medical application on Earth. This SpringerBriefs volume provides an overview on the latest international activities in Space and gives an outlook on the potential of biotechnological research in Space in future. This volume is written for students and researchers in Biomedicine, Biotechnology and Pharmacology and may specifically be of interest to scientists with focus on protein sciences, crystallization, tissue engineering, drug design and cancer research.

Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redistribution, signaling, and heat transport in proteins and other molecular machines. The first of four sections of the book address the transport of energy in molecular motors, which function through a combination of chemically driven large-scale conformational changes and charge transport. Focusing on vibrational energy flow in proteins and nanostructures, the next two sections discuss approaches based on molecular dynamics simulations and harmonic analysis. By exploring the flow of free energy in proteins, the last section examines the conformational changes involved in allosteric transitions and the role of coupled protein-solvent dynamics in conformational changes. It also presents computational approaches developed to locate pathways between protein structures. The integrated presentation of this comprehensive, up-to-date volume emphasizes the interrelations between disparate computational approaches that have contributed to our understanding of energy flow in proteins and its role in protein function. By defining the forefront of research in this area, the book delineates the current challenges and opportunities in developing novel methods and applications for the evolving study of energy flow in molecular machines and nanomaterials.

Summing up almost a decade of biomedical research, this topical and eagerly awaited handbook is the first reference on the topic to incorporate recent breakthroughs in amyloid research.
The first part covers the structural biology of amyloid fibrils and pre-fibrillar assemblies, including a description of current models for amyloid formation. The second part looks at the diagnosis and biomedical study of amyloid in humans and in animal models, while the final section discusses pharmacological approaches to manipulating amyloid and also looks at its physiological roles in lower and higher organisms. For Biochemists, Molecular Biologists, Neurobiologists, Neurophysiologists and those working in the Pharmaceutical Industry.

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.

This Brief explores the use of proteomics as a tool for biomarker discovery in human reproduction and summarizes current findings and trends of proteomic studies in both male and female infertility. This simplifies this important but complex topic and equips the novice reader with sufficient background information on the use of proteomics in human reproduction. The up-to-date scenario on proteomic investigations will also appeal to researchers and post graduate students looking to keep abreast with the latest developments in reproductive research. This review summarizes current findings of contemporary proteomic studies on infertility in both males and females with various reproductive pathologies, and its use in predicting the outcome of assisted reproduction. In human reproduction, the search for biomarkers via proteomics is a fast-evolving approach that involves the analysis of proteins in the reproductive tissues and fluids, such as the male gametes, seminal plasma, ovarian and endometrial tissue, and follicular and uterine fluid. By comparing the protein profile of a healthy, fertile individual against that of an infertile individual, the differentially expressed proteins may give an indication to certain proteins that could serve as useful biomarkers that are related to infertility. As proteomic studies continue to unravel the dynamic proteome behind various infertility conditions, there is potential for the discovery of prognostic markers that could ultimately help in both natural and assisted human reproduction.

This book discusses the paradigm-shifting phenomenon of intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and functional IDP regions (IDPRs). The properties of IDPs and IDPRs are highly complementary to those deriving from the presence of a unique and well-defined three-dimensional fold. Ignored for a long time in high-resolution studies of proteins, intrinsic protein disorder is now recognized as one of the key features for a large variety of cellular functions, where structural flexibility presents a functional advantage in terms of binding plasticity and promiscuity and this volume explores this exciting new research. Recent progress in the field has radically changed our perspective to study IDPs through NMR: increasingly complex IDPs can now be characterized, a wide range of observables can be determined reporting on the structural and dynamic properties, computational methods to describe the structure and dynamics are in continuous development and IDPs can be studied in environments as complex as whole cells. This volume communicates the new exciting possibilities offered by NMR and presents open questions to foster further developments. Intrinsically Disordered Proteins Studied by NMR Spectroscopy provides a snapshot to researchers entering the field as well as providing a current overview for more experienced scientists in related areas.

This succinct volume addresses the production of inactive, potentially toxic proteins in the absence of correct protein folding and the resultant neurodegenerative diseases. Other topics include intrinsic disorder in protein structure and function and the effects of molten globules on protein toxicity. This concise and yet thorough text also discusses using toxin structure as a model for studying structural and functional aspects of protein chemistry. Protein Toxins in Modeling Biochemistry, a SpringerBrief, is essential reading for advanced researchers, scientists and advanced graduate students interested in protein chemistry and related areas of biochemistry and molecular science.

This brief introduces the structural and functional characterization of this important group of proteins. The content of each chapter is aimed at the non-specialist so that key concepts, methodologies and applications can be presented in a "snapshot" style volume. Multiheme cytochromes are ever more important now that it is possible to obtain genome sequences of microorganisms which have major biotechnological and environmental implications. There is a tremendous profusion of multiheme cytochromes which have great potential as targets for bioremediation and bioenergy applications. This brief gives a glimpse of an intriguing and fast-moving field.

Medicinal chemistry is both science and art. The science of medicinal chemistry offers mankind one of its best hopes for improving the quality of life. The art of medicinal chemistry continues to challenge its practitioners with the need for both intuition and experience to discover new drugs. Hence sharing the experience of drug research is uniquely beneficial to the field of medicinal chemistry. Drug research requires interdisciplinary team-work at the interface between chemistry, biology and medicine. Therefore, the topic-related series Topics in Medicinal Chemistry covers all relevant aspects of drug research, e.g. pathobiochemistry of diseases, identification and validation of (emerging) drug targets, structural biology, drugability of targets, drug design approaches, chemogenomics, synthetic chemistry including combinatorial methods, bioorganic chemistry, natural compounds, high-throughput screening, pharmacological in vitro and in vivo investigations, drug-receptor interactions on the molecular level, structure-activity relationships, drug absorption, distribution, metabolism, elimination, toxicology and pharmacogenomics. In general, special volumes are edited by well known guest editors.

This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.

This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

Based upon a workshop entitled “The Small HSP World� held in Québec 2-5 October 2014. Twenty-five scientists provided chapters for the book. The chapters are from the best scientists currently working in this field.  These colleagues include Arrigo, Benesch, Benjamin, Buchner-Haslbeck-Weinkauf, Benndorf, Boelens, Carra, Chang, Currie, Ecroyd, Emanuelsson, Fu, Garrido, Golenhofen, Gusev, Hightower, Kampinga, Lavoie, MacRae, Quinlan, Tanguay, Vierling, Vigh, Weeks and Wu. Briefly, the book starts with the structure of small heat shock proteins, moving to their functions and finishing with their involvement in diseases. Although this is quite broad, the structural aspect will be the unifying theme of the book.

Proteins are the cell's workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions - whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.