Proteins are the most diverse group of biologically important substances. With the recent technological advances in the genomics area and the efforts in proteomics research, the rate of discovery for new proteins with unknown structure and function has increased. These proteins generated from genomic approaches present enormous opportunities for research and industrial application. Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods is a compilation of chapters within the exciting area of protein purification designed to give the laboratory worker the information needed to design and implement a successful purification strategy. It presents reliable and robust protocols in a concise form, emphasizing the critical aspects on practical problems and questions encountered at the lab bench. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods will be an ideal source of scientific information to advanced students, junior researchers, and scientists involved in health sciences, cellular and molecular biology, biochemistry, and biotechnology and other related areas in both academia and industry.

This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task - it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.

Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure. In, Homology Modelling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. 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, Homology Modelling: Methods and Protocols guides scientists in the available homology modeling methods.

Cell-cell adhesion is fundamental for the development and homeostasis of animal tissues and organs. Adherens junctions (AJs) are the best understood cell-cell adhesion complexes. In this volume, internationally recognized experts review AJ biology over a wide range of organization; from atoms to molecules, to protein complexes, molecular networks, cells, tissues, and overall animal development. AJs have also been an integral part of animal evolution, and play central roles in cancer development, pathogen infection and other diseases. This book addresses major questions encompassing AJ biology. - How did AJs evolve? - How do cadherins and catenins interact to assemble AJs and mediate adhesion? - How do AJs interface with other cellular machinery to couple adhesion with the whole cell? - How do AJs affect cell behaviour and multicellular development? - How can abnormal AJ activity lead to disease? Valuable for both newcomers and experts in the field, this book offers a comprehensive resource for the research laboratory and a teaching tool for advanced undergraduate and graduate courses in cell and developmental biology.

This second edition expands upon the previous edition with current, detailed developments in the field and brings together a multi-disciplinary team of leading researchers to provide their latest protocols for clinical proteomics 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 Practical, Clinical Proteomics: Methods and Protocols, Second Edition presents approaches that will serve as a reliable guide to researchers, including clinicians, chemists, molecular biologists, bioinformaticians and computational, biologists, and investigators working on biomarker development.

Cancer is one of the leading death cause of human population increasingly seen in recent times. Plants have been used for medicinal purposes since immemorial times. Though, several synthetic medicines are useful in treating cancer, they are inefficient and unsafe. However, plants have proved to be useful in cancer cure. Moreover, natural compounds from plants and their derivatives are safe and effective in treatment and management of several cancer types. The anticancer plants such as Catharanthus roseus, Podophyllum peltatum, Taxus brevifolia, Camptotheca acuminate, Andrographis paniculata, Crateva nurvala, Croton tonkinensis, Oplopanax horridus etc., are important source of chemotherapeutic compounds. These plants have proven their significance in the treatment of cancer and various other infectious diseases. Nowadays, several well-known anticancer compounds such as taxol, podophyllotoxins, camptothecin, vinblastine, vincristine, homoharringtonine etc. have been isolated and purified from these medicinal plants. Many of them are used effectively to combat cancer and other related diseases. The herbal medicine and their products are the most suitable and safe to be used as an alternative medicine. Based on their traditional uses and experimental evidences, the anticancer products or compounds are isolated or extracted from the medicinally important plants. Many of these anticancer plants have become endangered due to ruthless harvesting in nature. Hence, there is a need to conserve these species and to propagate them in large scale using plant tissue culture. Alternatively, plant cell tissue and organ culture biotechnology can be adopted to produce these anticancer compounds without cultivation. The proper knowledge and exploration of these isolated molecules or products could provide an alternative source to reduce cancer risk, anti-tumorigenic properties, and suppression of carcinogen activities. Anticancer plants: Volume 1, Properties and Application is a very timely effort in this direction. Discussing the various types of anticancer plants as a source of curative agent, their pharmacological and neutraceutical properties, cryo-preservations and recent trends to understand the basic cause and consequences involved in the diseases diagnosis. We acknowledge the publisher, Springer for their continuous inspiration and valuable suggestions to improvise the content of this book. We further extend our heartfelt gratitude to all our book contributors for their support, and assistance to complete this assignment. I am sure that these books will benefit the scientific communities including academics, pharmaceuticals, nutraceuticals and medical practitioners.

This book describes applications of acridines for the treatment of various neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and various prion diseases, and discusses the potential of acridines in neuro-regenerative medicine. Using modern data-mining software, it presents structures of acridines with nucleic acids and proteins and compares them with the native structures. Furthermore, the book presents modern methods of acridine synthesis, comparing them with the most useful conventional methods. Acridines interact with both nucleic acids and proteins, and due to their direct interactions with various enzymes, they can be suitable for the treatment of neurodegenerative diseases, inflammation, immunological disorders, and protozoal diseases. The characteristic spectral properties of acridines can be employed in labeling proteins, nucleic acids, lipids, and even cells and their compartments. Moreover, they can be applied in photodynamic therapy.

Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the "hot" topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. 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, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.

This book is the first to be entirely devoted to the challenging art of handling membrane proteins out of their natural environment, a key process in biological and pharmaceutical research, but one plagued with difficulties and pitfalls. Written by one of the foremost experts in the field, Membrane Proteins in Aqueous Solutions is accessible to any member of a membrane biology laboratory. After presenting the structure, functions, dynamics, synthesis, natural environment and lipid interactions of membrane proteins, the author discusses the principles of extracting them with detergents, the mechanisms of detergent-induced destabilization, countermeasures, and recent progress in developing detergents with weaker denaturing properties. Non-conventional alternatives to detergents, including bicelles, nanodiscs, amphipathic peptides, fluorinated surfactants and amphipols, are described, and their relative advantages and drawbacks are compared. The synthesis and solution properties of the various types of amphipols are presented, as well as the formation and properties of membrane protein/amphipol complexes and the transfer of amphipol-trapped proteins to detergents, nanodiscs, lipidic mesophases, or living cells. The final chapters of the book deal with applications: membrane protein in vitro folding and cell-free expression, solution studies, NMR, crystallography, electron microscopy, mass spectrometry, amphipol-mediated immobilization of membrane proteins, and biomedical applications. Important features of the book include introductory sections describing foundations as well as the state-of-the-art for each of the biophysical techniques discussed, and topical tables which organize a widely dispersed literature. Boxes and annexes throughout the book explain technical aspects, and twelve detailed experimental protocols, ranging from in vitro folding of membrane proteins to single-particle electron cryomicroscopy, have been contributed by and commented on by experienced users. Membrane Proteins in Aqueous Solutions offers a concise, accessible introduction to membrane protein biochemistry and biophysics, as well as comprehensive coverage of the properties and uses of conventional and non-conventional surfactants. It will be useful both in basic and applied research laboratories and as a teaching aid for students, instructors, researchers, and professionals within the field.

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.

Recent work has begun to elucidate at the molecular level how albumin is handled by the kidney and how albuminuria develops in various proteinuric diseases including minimal change disease and focal segmental glomerulosclerosis. This volume provides a comprehensive overview of the renal handling of albumin - from basic mechanisms to the pathophysiology of proteinuric diseases. In describing the basic mechanisms of albuminuria, a particular highlight will be the focus on advanced imaging techniques such as intravital microscopy that have allowed a detailed "window" into albumin transit through the kidney. The volume will cover the epidemiological studies which show that albuminuria is a strong and independent marker of kidney disease progression and cardiovascular events, the molecular details of albumin handling in the kidney at the level of the glomerulus and the proximal tubule and the pathophysiology of proteinuric diseases including minimal change disease, membranous nephropathy, focal segmental glomerulosclerosis and diabetic nephropathy.

This volume explores the latest methods used to study and define serpin molecular structure, basic protease inhibition, serpin targets, and the roles of serpin in biology and disease using animal models. The chapters in this book cover topics such as crystallography and phage display, peptide design, phospholipid binding, and thrombus formation to microbiome analysis and 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. Cutting edge and authoritative, Serpins: Methods and Protocols is a valuable resource for researchers and scientists interested in learning more about this evolving field.

Protein tyrosine phosphatases remove phosphates from the phosphotyrosine residues of target proteins and reverse the action of various protein tyrosine kinases. This essential interplay between the opposing actions of protein tyrosine phosphatases and protein tyrosine kinases forms the basis of signaling networks that underlie the cellular workings of human physiology. Initially passed-off as housekeeping genes; these proteins were only acknowledged to maintain a steady background of phosphotyrosine levels in the cell. However, recent progress in studying their role in embryonic development and human disease has established their importance as regulators of signal regulation. Convincing evidence shows the role of mutations in these proteins to cause and/or intensify the severity of various diseases including metabolic and neurological disorders and also cancer. Protein tyrosine phosphatases have slowly, yet convincingly become crucial targets for therapeutic intervention of various human pathophysiologies. This book describes these signaling enzymes using the molecular details of their structure and mechanistic function. Various subtypes of cysteine-based Class I, II, III and the Haloacid dehalogenase related Class IV protein tyrosine phosphatases have been illustrated and explained. The superfamily of proteins is also described vis-a-vis its complimentary protein phosphoserine/phosphoserine phosphatases. Membrane bound receptor forms and the cytosolic non-receptor protein tyrosine phosphatases have been described for their biological function. This book serves as a reference for any reader looking to understand the sequence features, structural elements, molecular mechanism and cellular function of this superfamily of signaling enzymes.

This volume expands upon the collection of techniques published in Protein Electrophoresis: Methods and Protocols (2012) with more practical and reproducible methods to study protein gel detection and imaging. The chapters in this book cover topics such as coomassie-brilliant blue staining of polyacrylamide gels; silver staining techniques; microwave assisted protein staining, de-staining, and in-solution digestion of proteins; curumin and turmeric as an environment-friendly protein gel stain; in-gel protein phosphotase assay using fluorogenic substrates; destaining with fungal laccase; and radiolabeling and analysis of labeled 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. Comprehensive and practical, Protein Gel Detection and Imaging: Methods and Protocols is a valuable resource for expert and novice scientists and researchers who are interested in learning and experimenting with this field.

Progress in functional proteomics has been limited for a long time, partially caused by limitations in assay sensitivity and sample capacity; however, protein microarrays have the ability to overcome these limitations so that a highly parallel analysis of hundreds of proteins in thousands of samples is attainable. In Protein Microarrays: Methods and Protocols, expert researchers in the field present an up-to-date collection of robust strategies in the field of protein microarrays and summarize recent advantages in the field of printing technologies, the development of suitable surface materials, as well as detection and quantification technologies. 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 notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Protein Microarrays: Methods and Protocols aims to stimulate the application and further advancement of this powerful technology in labs worldwide.

Volume 6 of Biomembranes covers transmembrane receptors and channels. A particularly important role for the membrane is that of passing messages between a cell and its environment. Part I of this volume covers receptors for hormones and growth factors. Here, as in so many other areas of cell biology, the application of the methods of molecular biology have led to the recognition of a number of families of receptors. Typically, such receptors contain an extracellular ligand binding domain, a transmembrane domain, and an intracellular catalytic domain whose activation, as a result of ligand binding, leads to generation of second messengers within the cell and stimulation of a range of cytosolic enzymes. An alternative signaling strategy, exploited in particular in the nervous system, is to use ion channels to allow controlled movement of monovalent (Na+, K+) or divalent (Ca2+) cations in or out of the cell, resulting in changes in membrane potential or alterations in the intracellular concentration of Ca2+. Part II of this volume is concerned with these ion channels and with other, often simpler, ion channel systems whose study can throw light on channel mechanism.

This volume explores various methodologies to study biochemical, molecular, and cellular biology aspects of some processes regulated by protein SUMOylation. SUMO: Methods and Protocols is organized into four parts, and starts with an historical overview on protein SUMOylation and a presentation of the methods included in the book. The first part also includes a review on chromatin regulation by dynamic SUMO modifications. The second part focuses on in vitro techniques, including biochemical methods to study mechanistic aspects of protein SUMOylation. The third part includes protocols to be used with cell cultures, which often are the first approaches used in most laboratories. The final part includes methodologies adapted for the analysis in vivo using distinct model organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include a brief introduction to the subject, a list of necessary materials and reagents, a step-by-step reproducible laboratory protocol ending with a Notes section on troubleshooting tips, and tips and strategies to avoid known pitfalls. Unique and cutting-edge, SUMO: Methods and Protocols provides a comprehensive source of protocols for specialists and researchers not familiar with this vital system.

The entire range of the developmental processes in plants is regulated by a shift in the hormonal concentration, tissue sensitivity and their interaction with the factors operating around them. Out of the recognized hormones, attention has largely been focused on five - Auxins, Gibberellins, Cytokinin, Abscisic acid and Ethylene. However, the information about the most recent group of phytohormone (Brassinosteroids) has been incorporated in this book. This volume includes a selection of newly written, integrated, illustrated reviews describing our knowledge of Brassinosteroids and aims to describe them at the present time. Various chapters incorporate both theoretical and practical aspects and may serve as baseline information for future researches through which significant developments are possible. This book will be useful to the students, teachers and researchers, both in universities and research institutes, especially in relation to biological and agricultural sciences.

This thesis examines the evidence for regulatory ubiquitination by focusing on A20. It provides an insightful and in-depth evaluation of the current literature by critically examining the evidence of K63-linked regulatory ubiquitination in regulating cell-signalling. It is also the first thesis to directly test the role of regulatory ubiquitination in NF-kB signaling in vivo. The case for regulatory ubiquitination has been to a large extent predicated upon the presumed deubiquitinase activity of A20, long considered a key regulator of inflammatory responses as mice lacking A20 die from multi-organ inflammation and cachexia. The theses reports the creation and characterization of a knock-in mouse that expresses a mutated form of A20 which selectively lacks the deubiquitinase activity. The knock-in mice surprisingly display completely normal NF- B activation with no accompanying inflammatory phenotype. Given that the presumed role of A20 as a deubiquitinase has been used to support the importance of regulatory K63-linked ubiquitination in NF-kB signaling, this study will help focus future research efforts into alternative target pathways that do not depend on K63 ubiquitination. In fact, the work suggests that it might be important to revisit the role of K63-linked polyubiquitination in cell-signalling. Ubiquitin Chains: Degradation and Beyond is essential reading for anyone conducting research in cell-signalling and immunology. Dr. Arnab De received his PhD from the Department of Microbiology & Immunology at Columbia University. During his PhD, he developed transgenic mice to study the mechanism of action of a critical tumor-suppressor called A20. He is also well known for having developed peptide-based prodrugs as therapeutics for diabetes. His work has been reported by the media, and has resulted in multiple patents and publications in peer reviewed journals. He presented his findings at the American Peptide Symposium and was awarded the Young Investigator's Award. He is the author of the book entitled Application of Peptide-Based Prodrug Chemistry in Drug Development, with a foreword written by Professor Jean Martinez (Former President, European Peptide Society) and published in the series SpringerBriefs in Pharmaceutical Science & Drug Development. His research interests lie at the intersection of chemistry and medicine. Besides biomedical research, he is also generally interested in public health policy and general scientific outreach.

Photoswitching Proteins: Methods and Protocols, focuses on proven applications of photoswitching proteins in cell and neurobiology. Optical approaches have been mostly embraced by the neurosciences to allow fast, high-resolution characterization and manipulation of single cells in complex neuronal tissue. These tools, including photoswitching of proteins, are now successfully used in almost all fields of biological research. 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 key tips on troubleshooting and avoiding known pitfalls.Comprehensive and practical, Photoswitching Proteins: Methods and Protocols highlights many of the possibilities for research based on light-inducible, high-resolution manipulation of biological systems.

Cell surface molecules are critically important in regulating cell structure and function. Recent advances on the functional role of cell surface molecules, particularly glycoconjugates are presented in this book. Comprising of 22 chapters from the 2011 International Symposium on Biochemical Roles of Eukaryotic Cell Surface Macromolecules, it covers topics on the analysis of glycome, biophysical approaches to study cell surface molecules, glycoconjugate metabolism and its dysregulation, and molecular mechanisms involved in cell-cell and cell-matrix interaction.

Volume 5 of Biomembranes covers an important group of membrane proteins, the ATPases. The P-type ATPases couple the hydrolysis of ATP to the movement of ions across a membrane and are characterized by the formation of a phosphoyrlated intermediate. Included are the plasma membrane and muscle sarcoplasmic reticulum Ca2+ -ATPases, the (Na+ -K+) -ATPase, the gastric (H+ -K+) -ATPase, the plasma membrane H+ -ATPase of fungi and plants, the Mg2+ - transport ATPase, the Salmonella typhimurium, and the K+ -ATPase of Escherichia coli, KdpB. The other important classes of ATPase in eukaryotic systems are the vacuolar H+ -ATPases and the F0F1 ATP synthase, and, in bacteria, the anion-translocating ATPases, responsible for resistance to arsenicals and antimonials, and the (Na+ -Mg2+) -ATPase of Acholeplasma. Finally, eukaryotic systems contain a variety of ectonucleotidases important, for example, in hydrolysis of extracellular ATP released as a cotransmitter from cholinergic and adrenergic nerve terminals. Volume 5 of Biomembranes explores structure-function relationships for these mebrane-bound ATPases.

Exploring these type II trans-membrane proteins, The TNF Superfamily: Methods and Protocols focuses on various techniques to investigate aspects of the TNF Superfamily members in health and disease. Opening with protocols to understand the signaling process of TNF family members, this detailed volume continues with technical examples of investigating the role of TNF family members in physiopathologies, protocols on modulation of TNF signaling by pathogens, experimental applications of TNF-reporter mice, as well as methodologies for various assays of TNF family members and the production of recombinant molecules. Written for the 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. Practical and ready to use, The TNF Superfamily: Methods and Protocols will aid researchers investigating this key family of proteins, involved in vital processes such as providing signals for activation, differentiation, survival and death of cells, modulation of immune response and inflammation, hematopoiesis and osteoclastogenesis.

Through the rapid development of proteomics methods and technologies, an enormous amount of data was created, leading to a wide-spread rethinking of strategy design and data interpretation. In Data Mining in Proteomics: From Standards to Applications, experts in the field present these new insights within the proteomics community, taking the historical evolution as well as the most important international standardization projects into account. Along with basic and sophisticated overviews of proteomics technologies, standard data formats, and databases, the volume features chapters on data interpretation strategies including statistics, spectra interpretation, and analysis environments as well as specialized tasks such as data annotation, peak picking, phosphoproteomics, spectrum libraries, LC/MS imaging, and splice isoforms. As a part of the highly successful Methods in Molecular Biology(TM) series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and cutting-edge, Data Mining in Proteomics: From Standards to Applications is a well-balanced compendium for beginners and experts, offering a broad scope of data mining topics but always focusing on the current state-of-the-art and beyond.

Biological membranes are the essential structuring elements of all living cells. Many enzymatic reactions take place at the membrane-water interface. To gain detailed insight into membrane properties, it is therefore of great importance to understand the complex nature of the interactions of membrane proteins with lipids. Lipid-Protein Interactions: Methods and Protocols provides a selection of protocols to examine protein-lipid interactions, membrane and membrane protein structure, how membrane proteins affect lipids and how they are in turn affected by the lipid bilayer and lipid properties. The methods described here are all actively used, complementary, and necessary to obtain comprehensive information about membrane structure and function. They include label-free approaches, imaging techniques and spectroscopic methodologies. 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, Lipid-Protein Interactions: Methods and Protocols seeks to serve both professional and novices with its wide range of the methods frequently used in this area of research.