Protein analysis is increasingly becoming a cornerstone in deciphering the molecular mechanisms of life. Proteomics, the large-scale and high-sensitivity analysis of proteins, is already pivotal to the new life sciences such as Systems Biology and Systems Medicine. Proteomics, however, relies heavily on the past and future advances of protein purification and analysis methods. DIGE, being able to quantify proteins in their intact form, is one of a few methods that can facilitate this type of analysis and still provide the protein isoforms in an MS-compatible state for further identification and characterization with high analytical sensitivity. Differential Gel Electrophoresis: Methods and Protocols introduces the concept of DIGE and its advantages in quantitative protein analysis. It provides detailed protocols and important notes on the practical aspects of DIGE with both generic and specific applications in the various areas of Quantitative Proteomics. Divided into four concise sections, this detailed volume opens with the basics of DIGE, the technique and its practical details with a focus on the planning of a DIGE experiment and its data analysis. The next section introduces various DIGE methods from those employed by scientists world-wide to more novel methods, providing a glance at what is on the horizon in the DIGE world. The volume closes with an overview of the wide range of DIGE applications from Clinical Proteomics to Animal, Plant, and Microbial Proteomics applications. Written in the highly successful Methods in Molecular Biology (TM) 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, Differential Gel Electrophoresis: Methods and Protocols can be used by novices with some background in biochemistry or molecular biology as well as by experts in Proteomics who would like to deepen their understanding of DIGE and its employment in many hyphenations and application areas. With its many protocols, applications, and methodological variants, it is also a unique reference for all who seek fundamental details on the working principle of DIGE and ideas for possible future uses of DIGE in novel analytical approaches.

The liver is responsible for a wide range of critical functions essential to life, and is composed of several different cell types. In Liver Proteomics: Methods and Protocols, expert researchers in the field detail many of the methods that are used to study the live. These methods include the most up-to-date strategies being used to characterize the liver proteome at the global, cellular, subcellular, post translational and functional level.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, Liver Proteomics: Methods and Protocols seeks to aid scientists in the further study of this crucially important organ.

Poly (ADP-ribose) Polymerases (PARPs) are abundant and ubiquitous proteins that regulate crucial processes of the cell cycle, DNA repair, genomic stability, and transcriptional regulation. Being involved in basic cell functions, PARPs mediate rapid responses to such environmental factors as stress, infection, nutrition and hormonal signals. Whereas PARP inhibitors can suppress tumor growth and proliferation in certain breast, ovarian, and prostate cancers, understanding how PARP controls cellular functions is essential for the development of novel cancer treatments strategies. Divided into three convenient sections, Poly(ADP-Ribose) Polymerase: Methods and Protocols aims to explain how PARP proteins act within the normal development of an organism as well as in pathogenic conditions, seeks to advance the knowledge of developmental pathways regulation, and endeavors to facilitate the development of new therapeutic drugs and methods to target PARP-dependent processes. Written in the highly successful Methods in Molecular Biology (TM) 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, Poly(ADP-Ribose) Polymerase: Methods and Protocols serves as an ideal guide to scientists who wish to continue exploring this exciting and progressive research field.

Chemical genomics technology has been steadily improving, delivering new biological probes and drugs, and the explicit use of the term 'chemical proteomics' has increased with it, as proteins have always been at the heart of this technology. In Chemical Genomics and Proteomics: Reviews and Protocols, experts in the field present updated reviews of the chemistry of small molecules and their interaction with protein targets as well as detailed protocols that cover different types of ligands, carbohydrates, and lipids. For example, the generation of their protein targets and methods for measuring their interactions is covered. Written in the highly successful Methods in Molecular Biology (TM) series format, methodology 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 up to date, Chemical Genomics and Proteomics: Reviews and Protocols aims to provide inspiration to those who wish to use chemical genomics and proteomics in their work and develop this young field into full maturity through the incorporation of the new biological and chemical technologies beginning to emerge here.

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 1 includes sections on assessing IDPs in the living cell,NMR based techniques, vibrational spectroscopy, and other spectroscopic techniques. 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.

Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and signaling events that lead to a multitude of biological effects. Membrane proteins have also been implicated in many critical diseases such as atherosclerosis, hypertension, diabetes and cancer. In Membrane Protein Structure Predictions Methods: Methods and Protocols, expert researcher in the field detail the advances in both experimental and computational approaches of the structure, dynamics and interactions of membrane proteins dividing the volume into two sections. The first section details the procedures used for measurements of structure and dynamics of membrane proteins. While the second section contains a survey of the computational methods that have played a critical role in membrane protein structure prediction as well as in providing atomic level insight into the mechanism of the dynamics of membrane receptors. 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, Membrane Protein Structure Predicitons: Methods and Protocols seeks to aid scientists in the further study of membrane protein structure and function.

Proteins are the functional units of the cellular machinery and they provide significant information regarding the molecular basis of health and disease. Therefore, techniques to separate and isolate the various proteins are critical to studying and understanding their functional characteristics. One of the widely used techniques for this purpose is electrophoresis. In Protein Electrophoresis: Methods and Protocols, contributions from experts in the field have been collected in order to provide practical guidelines to this complex study. Each chapter outlines a specific electrophoretic variant in detail so that laboratory scientists may perform a technique new to their lab without difficulty. 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 accessible, Protein Electrophoresis: Methods and Protocols seeks to serve laboratory scientists with well-honed, detailed methodologies in an effort to further our knowledge of this essential field.

The genomes of cellular organisms are organized as double-stranded DNA, a structure that must be unwound to provide DNA replication, recombination, and repair machinery access to genomic information. However, DNA unwinding comes with inherent risks to genome stability. To help mediate these risks, bacterial, archael, and eukaryotic cells have evolved protective ssDNA-binding proteins (SSBs) that bind ssDNA with high affinity and specificity. SSBs also aid genome metabolic processes through direct interactions with key proteins in genome maintenance enzymes. Single-Stranded DNA Binding Proteins: Methods and Protocols assembles methods developed for examining the fundamental properties of SSBs and for exploiting the biochemical functions of SSBs for their use as in vitro and in vivo reagents. Clearly and concisely organized, the volume opens with an introduction to the structures and functions of SSBs, followed protocols for studying SSB/DNA complexes, methods for studying SSB/heterologous protein complexes, protocols for interrogating post-translational modifications of SSBs, and concludes with uses of fluorescently-labeled SSBs for in vitro and in vivo studies of genome maintenance processes. 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, Single-Stranded DNA Binding Proteins: Methods and Protocols provides a rich introduction for investigators who are interested in this fascinating family of DNA-binding proteins.

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.

Recent findings have implied a distinct therapeutic potential for drugs targeting Transient Receptor Potential (TRP) channels in a wide variety of diseases, many with no existing satisfactory treatment options. Thus, the TRP superfamily of ion channels has attracted a great deal of well-deserved attention. TRP Channels in Drug Discovery provides a thorough collection of the most up-to-date reviews and protocols on the subject, coming from top experts in the field. Volume I presents a series of state-of-the-art minireviews on the most interesting TRP channels (from TRPA1 to TRPV4), as well as TRP-related protocols involving airways and the genitourinary tract. Written for the Methods in Pharmacology and Toxicology (TM) series, this work includes the kind of detailed description and key implementation advice that ensures successful results in the lab. Comprehensive and cutting-edge, TRP Channels in Drug Discovery serves as an ideal reference for graduate students in academic laboratories as well as for pharmaceutical scientists developing new drugs and clinicians interested in novel drugs in the pipeline.

This excellent book covers wide-ranging topics in interdisciplinary microbiology, addressing various research aspects and highlighting advanced discoveries and innovations. It presents the fascinating topic of modern biotechnology, including agricultural microbiology, microalgae biotechnology, bio-energy, bioinformatics and metagenomics, environmental microbiology, enzyme technology and marine biology. It presents the most up-to-date areas of microbiology with an emphasis on shedding light on biotechnological advancements and integrating these interdisciplinary microbiology research topics into other biotechnology sub-disciplines. The book raises awareness of the industrial relevance of microbiology, which is key component of this unique collection. The topics include production of antioxidant-glutathione, enzyme-engineering methods, probiotic microbiology and features of microbial xylanases. It also covers some other remarkable aspects of microbiology, like potential health hazards in recreational water and fullerene nanocomposites, which are vital for biotechnological interventions. This book will be valuable resource for senior undergraduate and graduate students, researchers and other interested professionals or groups working in the interdisciplinary areas of microbiology and biotechnology.

Proteostasis is central to the development of various human diseases caused due to excessive protein misfolding and the disregulation of the protein quality control system. In this book, respected researchers from many leading institutions contribute their insights on proteostasis maintenance. The coverage mainly focuses on the basics of maintaining proteostasis, the consequences of proteostatic system failure, and how chaperone systems constantly maintain proteostasis. In addition, the book presents in detail different treatment strategies for diseases caused by proteostatic system failure, as well as the inhibition of proteostatic failure using small molecule compounds. It examines advances in the modulation of proteopathies, providing a comprehensive source of key mechanistic insights on these diseases. As such, the book offers a valuable resource for beginners and more experienced investigators alike who are looking for detailed and reliable information on protein homeostasis, the diseases that can develop due to related imbalances and the essential role of molecular and chemical chaperones.

Plant signalling has emerged as an integrated field which has become indispensable in recent times to study any biological process. Over the last decade, an enormous amount of information has been generated in this field and the advances in information technology gave birth to bioinformatics which has helped greatly in managing the galaxy of information. It is now possible to view the different information's in a systems biology approach which has unravelled the association/ new processes and thus helped us enormously in understanding of the biological processes. The present book is an attempt at understanding the plant signalling processes with different perspectives. Even though the plants are sessile but there exists a tremendous interconnected network of perception at morphological, physiological and molecular levels. The impact of the surrounding environment in terms of abiotic and biotic stresses is significant in terms of its survival, adaptation and productivity for the human welfare. The plants possess a wide array of processes at the organ, tissue and cellular levels which are governed by a plethora of molecules. The molecules govern individual processes and these exists a cross talk between them to form a complex network of processes. The book tries to envision how different processes are operating at different points in the life cycle of the plant.

This second of two volumes discusses subfamily proteins which function in molecular and vesicular transport mechanisms inside the cell. In this volume the focus lies on the Rab, Ran and Arf subfamily members. As in Volume 1, the book is written by international renowned scientists in the field of small G-proteins. In elaborate reviews, biochemistry, structure, function and G-protein - effector interactions are described. Together with Volume 1 this book provides an comprehensive state-of-the-art work on small G-proteins (GTPases). It is written for Graduates and Professors in Biochemistry and Cell Biology interested in the mechanism and function of small G-proteins but are extremely valuable for those who want to move into the field.

Super secondary structure(SSS) helps to understand the relationship between primary and tertiary structure of proteins. In Protein Supersecondary Structure: Methods and Protocols expert researchers in the field detail the usefulness of the study of super secondary structure in different areas of protein research. This is done through four main studies SSS representation, SSS prediction, SSS and protein folding, and other application of SSS concept to protein biology. 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 Supersecondary Structure: Methods and Protocols highlight some of the major advances in the many fast-growing areas of supersecondary structure research.

Through all of the recent progress provided by high throughput DNA sequencing technologies, it has become clearer and clearer that the study of proteins and protein organelles will be the key to unlocking our ability to manipulate cells and intervene in human disease. In Protein Expression in Mammalian Cells: Methods and Protocols, expert researchers in the field present a compendium of vital techniques to further our knowledge of mammalian protein expression. 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 tips for troubleshooting and avoiding known pitfalls. Authoritative and concise, Protein Expression in Mammalian Cells: Methods and Protocols will aid scientists seeking to delve deeper into our own biology through the medium of other mammalian cells and proteins.

Proteins act as macromolecular machinery that mediate many diverse biological processes - the molecular mechanisms of this machinery has fascinated biologists for decades. Analysis of the kinetic and thermodynamic features of these mechanisms could reveal unprecedented aspects of how the machinery function and will eventually lead to a novel understanding of various biological processes. This dissertation comprehensively demonstrates how two universally conserved guanosine triphosphatases in the signal recognition particle and its membrane receptor maintain the efficiency and fidelity of the co-translational protein targeting process essential to all cells. A series of quantitative experiments reveal that the highly ordered and coordinated conformational states of the machinery are the key to their regulatory function. This dissertation also offers a mechanistic view of another fascinating system in which multistate protein machinery closely control critical biological processes. Written while completing graduate work at California Institute of Technology.

'Antibacterial Surfaces' covers the advances being made in the design of antibacterial surfaces, which have the ability to either prevent the initial attachment of bacterial cells, or kill any cells that come into contact with these surfaces. This book discusses the mechanisms associated with the attachment of bacteria to surfaces and the main strategies currently being employed to control the initial attachment processes. These strategies are expanded upon in the subsequent chapters, where the definition and description of antibacterial surfaces are clarified, as are the mechanisms that come into play when determining the effectiveness of an antibacterial surface. Subsequent chapters discuss a number of naturally occurring antibacterial surfaces, the methods currently being used for producing synthetic antibacterial surfaces, and the current and potential applications of such materials. This book will be of great interest to people who work with materials that need to remain free of bacterial films, from designing safer biomedical implants to the production of self-cleaning materials where the prevention of biofilm formation has significant economic advantages.

The proteome consists of a complex mixture of proteins each of which need to be folded correctly in order to function for the health of the organism, and many of these proteins require molecular chaperones to reach the correct conformation and, in some cases, to remain in a folded form. In Molecular Chaperones: Methods and Protocols, expert researchers address a wide variety of approaches to the study these mechanisms, featuring the workings of heat shock proteins and heat shock transcription factors, in vitro and in vivo. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters features 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, Molecular Chaperones: Methods and Protocols serves as an ideal guide for all scientists who wish to pursue this vital biological action and its impact on human health and disease.

This expert volume provides insights into the technological fundamentals together with a comprehensive overview of the potentialities of peptide microarray technology in basic research and clinical assays. Advancements made in recent years in peptide library synthesis, immobilization chemistry and array production have created a foundation from which different new applications are derived, extending the ways in which peptide microarray technology is applied every day. Divided into three sections, the book covers cutting-edge methods and technology, chemoselective strategies for peptide immobilization, and peptide microarrays for medical applications. Written for the high 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 protocols and tips on troubleshooting and avoiding known pitfalls. Fully updated and authoritative, Peptide Microarrays: Methods and Protocols, Second Edition seeks to encourage scientists to apply current peptide array protocols to the study of interesting new biochemical and medical questions and to assist researchers aiming at developing new methods to further develop peptide microarray technology.

Transcriptomics and proteomics, studying the profile of the expression of nucleic acids and proteins respectively, are increasingly applied to gain a mechanistic insight into a wide spectrum of investigation, and the use of expression profiling studies for the central nervous system and brain function aids in the understanding of neurodegenerative disorders and tumor development mechanisms. In Expression Profiling in Neuroscience, expert researchers provide a survey of the most commonly used approaches in the field and scan the different ways of studying the central nervous system/brain environment through expression profiling. The first part addresses the gene expression profiling of the brain at a large scale or to a specific cell type such as blood-brain barrier endothelium. Then, the second part describes the protein expression studies and the different technologies applied. Written for the popular Neuromethods series, chapters include corresponding background information, tested laboratory protocols, and step-by-step methods for reproducible laboratory experiments. Detailed and authoritative, Expression Profiling in Neuroscience presents the state-of-the-art techniques necessary to expand research further into this vital area of study.

After the identification of a potential protein drug, the next critical step is the production of sufficient authentic material for testing, characterization, and clinical trials, which, when successful, leads to the need for robust methodologies for large-scale production, purification, characterization, viral inactivation, and continued testing of the final protein product. Building on the valuable first edition, Therapeutic Proteins: Methods and Protocols, Second Edition aims to cover each of these key aspects of protein drug production through the contributions of authors from highly esteemed industrial and academic institutions around the world. Emphasizing the newest developments in the field, this second edition also includes additional emphasis on discovery, including new display and screening methods as well as the design and engineering of new types of therapeutic proteins. There is also discussion of computational and bioinformatics methods, and chapters on safety aspects of therapeutic protein development. Written in the highly successful Methods in Molecular Biology (TM) format, protocol 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. Fully updated and practical, Therapeutic Proteins: Methods and Protocols, Second Edition provides an essential resource to all scientists working in the field of therapeutic proteins.

Tryptophan metabolism via kynurenine pathway plays a critical role in both health and a variety of human diseases. This book highlights the known associations between kynurenine pathway and various disease states, as well as examines the current status of drug development and clinical trials of compounds known to alter tryptophan metabolism. The research plays a critical role in molecular targeted therapies directed at altering the kynurenine pathway of tryptophan metabolism. The initial and rate-limiting step of tryptophan metabolism is mediated by one of two enzymes, tryptophan-2,3-dioxygenase (TDO; predominantly in the liver, but also in the brain) and indoleamine-2,3-dioxygenase (IDO; in a host of tissues in response to immune activation). Targeting the enzymes IDO and TDO, as well as other downstream effectors would therefore be likely to generate novel treatment options that would be helpful in a wide variety of clinical settings. This book provides a unique bridge between basic mechanistic understanding of the role of the kynurenine pathway with translational applications and clinical relevance. It will explore the indications that tryptophan metabolism is a potential biomarker of disease activity, can contribute to local and possibly systemic immune suppression in cancer, and is an attractive target for which a variety of inhibitors are readily available.

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.

As two relatively new fields of study, proteomics and nanotechnology have developed in parallel with each other to allow an increased precision in the identification of post-translational protein modifications as well as to provide a more automated isolation and detection of rare proteins in both serum and tissues. The Nanoproteomics: Methods and Protocols volume organizes and collects technical advances from leaders in the field to make laboratory protocols more readily available and understandable to those who are attempting to incorporate nanotechnologic techniques into their proteomic research. Conveniently divided into five sections, this detailed volume covers preliminary sample preparation, nanoscale fluidic devices and methods, nanostructured surfaces and nanomaterials, and nanoproteomic techniques to detect and understand protein and proteomic alterations specific to human pathology. Written in the highly successful series entitled Methods in Molecular Biology (TM), these chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols that are readily reproducible, and tips on troubleshooting and avoiding known pitfalls. Convenient and authoritative, Nanoproteomics: Methods and Protocols offers key procedures that are culled from the laboratories of leaders in the field of nanoproteomics with the aim of helping researchers in their standardization and proliferation of protocols that will lead to a more wide scale adoption and smoother progress in this vital field.