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.

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.

This volume of Current Topics in Membranes focuses on Membrane Protein Crystallization, beginning with a review of past successes and general trends, then further discussing challenges of mebranes protein crystallization, cell free production of membrane proteins and novel lipids for membrane protein crystallization.
This publication also includes tools to enchance membrane protein crystallization, technique advancements, and crystallization strategies used for photosystem I and its complexes, establishing Membrane Protein Crystallization as a needed, practical reference for researchers.

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.

By combining the tools of organic chemistry with those of physical biochemistry and cell biology, "Non-Natural Amino" "Acids" aims to provide fundamental insights into how proteins work within the context of complex biological systems of biomedical interest.
The critically acclaimed laboratory standard for 40 years, "Methods in Enzymology" is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. With more than 400 volumes published, each "Methods in Enzymology" volume presents material that is relevant in today's labs -- truly an essential publication for researchers in all fields of life sciences.
Demonstrates how the tools and principles of chemistry combined with the molecules and processes of living cells can be combined to create molecules with new properties and functions found neither in nature nor in the test tube
Presents new insights into the molecular mechanisms of complex biological and chemical systems that can be gained by studying the structure and function of non-natural molecules
Provides a "one-stop shop" for tried and tested essential techniques, eliminating the need to wade through untested or unreliable methods

"Molecular Biology of RGS Proteins," a volume of "Progress in Molecular Biology and Translational Science," will include historical discussion of RGS proteins, the role of RGS proteins in addiction, depression and Parkinson's disease and the biology and functional regulation of RGS9 isoforms. This publication further discusses RGS proteins in cellular signaling, protein control in lymphocyte function, and alternative splicing of RGS transcripts and nuclear RGS proteins, offering the latest in research of RGS proteins.

Volume 4 of Biomembranes covers endocytosis, exocytosis and related processes. A major role of the plasma membrane is as a permeability barrier, keeping the inside of the cell inside and the outside, outside. Mechanisms must then exist to allow movement of material between the cell and its environment. One mechanism for export from the cell is by exocytosis, a process in which the membranes of secretory vesicles fuse with the plasma membrane releasing the contents of the vesicle into the extracellular medium. The process has been studied in particular depth for the release of neurotransmitters at the synapse. Import into the cell is possible by the process of receptor-mediated endocytosis in which selected plasma membrane proteins are internalizes; when these proteins are receptors for macromolecules, the result is uptake of the macromolecule. Transferring, the low-density lipoprotein, and asialoglycoproteins are all taken up into cells in this way. Phagocytosis, the ingestion of cells and cell fragments by neutrophils and macrophages, also involves receptors - on the phagocytic membrane - of which the best studied are those for the Fc domain of IgG, for the third component of complement, and for the mannose/fructose carbohydrates. Protection of a host against infection can also be achieved by damaging the integrity of the plasma membrane of the invading organism. This is the strategy evolved by the cytotoxic T lymphocytes, which produce a pore-forming toxin, perforin. Volume 4 of Biomembranes explores the structures and mechanisms involved in these biologically and medically important processes.

This book includes a series of reviews on general aspects of biomarker use in the study of psychiatric and neurodegenerative diseases and the development of medications involved in their treatment. It describes the pros and cons of the various approaches and covers the successes and failures in this research field. It is only by a thorough understanding of the shortcomings that progress can be made. The overall goal is to facilitate the understanding and treatment of these disorders, by providing a viable mechanism of catching up with other areas of modern medicine, such as diabetes and heart disease. Finally, it is anticipated that the development and application of valid biomarker tests and the leveraging of novel drug targets will help the fields of psychiatry on neurodegenerative disorders move into the area of personalized medicine where the right patients can receive the right medication at the right time for the best possible outcome.

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.

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.

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.

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.

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.

The basic principle of electron crystallography is to calculate a 3D density map by combining the amplitudes obtained from electron diffraction patterns with the experimental phases calculated from images of two-dimensional crystals of membrane or soluble proteins. This technology is very well developed and has produced a number of atomic models of membrane proteins in a lipid environment. Focused on comprehensive experimental protocols, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols covers the entire range of techniques used in electron crystallography, including protein sample preparation, 2D crystallization, and screening in negative stain over electron cryo-microscopy (cryo-EM) and data processing, as well as modeling of conformational changes. Additional chapters provide perspective on past, present, and future challenges as well as complementary methods. Written for the popular Methods in Molecular Biology (TM) series, the work contains the kind of detailed descriptions and implementation advice necessary to ensure successful results. Comprehensive and cutting-edge, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols serves laboratories new to the methods as well as state-of-the-art facilities pursuing this exciting area of protein science.

Quantitation of Amino Acids and Amines by Chromatography: Methods and Protocols is intended to serve as a ready-to-use guide for the identification and quantification of amino acids and amines in various matrices, providing an overview on the theory and protocol of available methods. It presents chromatograms with exact elution programs enabling visual analysis and compares the advantages-disadvantages of various chromatographic techniques. In accordance with the chronological order of the development of chromatographic methods, different techniques are discussed: The possibilities of gas chromatography (GC), followed by those of the high performance liquid chromatography (HPLC) and the most recent techniques capillary electrophoresis (CE), capillary, electrochromatography (CEC).
The characteristics of the given chromatographic procedure, relating to the topic in question, are classified according to the preliminary preparation/derivatization process(es), which means the simple methods, suitable for the analysis of the selected compound(s) in natural form, are followed by various derivatization proposals. Detailed protocols provide the reader with guidance in beginning tasks and on how to improve current methods. This book appeals to a wide audience and is recommended for those looking towards the wider reaches of identification and quantification of amino acids and amines.
* Provides a systematic, and comprehensive summary of chromatographic techniques and derivatization processes
* Compares advantages/disadvantages of various chromatographic techniques
* Readers can undertake practical tasks using detailed protocols given in the book

This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

This volume highlights the role of proteostasis in human health and associated disease model systems, reflecting its rising importance which has led to the development of new technologies to obtain insight into underling protein mechanistic events. 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, Proteostasis: Methods and Protocols aims to become a reference book on proteostasis in human health.

The field of protein NMR spectroscopy has rapidly expanded into new areas of biochemistry, molecular biology and cell biology research that were impossible to study as recently as ten years ago. This third edition of Protein NMR Techniques, expands upon the previous editions with current, detailed authoritative but down-to-earth descriptions of new methodologies. These include techniques for NMR sample preparation, solution and solid state NMR methodologies and data processing. 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 NMR Techniques,Third Edition, seeks to aid scientists in understanding the latest innovations in the field of protein NMR.

Structural genomics is the systematic determination of 3-dimensional structures of proteins representative of the range of protein structure and function found in nature. The goal is to build a body of structural information that will predict the structure and potential function for almost any protein from knowledge of its coding sequence. This is essential information for understanding the functioning of the human proteome, the ensemble of tens of thousands of proteins specified by the human genome.
While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large-scale cloning, expression and purification. One main advantage of this approach is economy of scale.
Key Features
*Examines the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography and NMR spectroscopy
* Looks at structural genomics as a foundation of drug discovery as discovering new medicines is becoming more challenging and the pharmaceutical industry is looking to new technologies to help in this mission

The importance of protein folding has been recognized for many years. It is the underlying etiology in a large number of human diseases and it appears to be a novel method for cellular regulation of the expression of newly translated proteins. These volumes (Parts A & B) address this important topic. As a volume in Progress in Nucleic Acid Research and Molecular Biology, this book provides the latest information on the expanding research being conducted on protein folding.
*Follow the new editor-in-chief, P. Michael Conn, as he introduces this first thematic volume in the series an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding
*Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer s and diabetes
*Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science"

"Molecular Modeling of Proteins, Second Edition" provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful "Methods in Molecular Biology" series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls.

Update-to-date and authoritative, "Molecular Modeling of Proteins, Second Edition" aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume.
*Follow the new editor-in-chief, P. Michael Conn, as he introduces this second thematic volume in the series an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding
*Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer s and diabetes
*Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science"

Display technologies have become a very powerful way of generating therapeutic lead molecules and specific reagents for increasing our understanding of biology; however, despite being first described shortly after phage display, the use of ribosome display and related methods have been much less widespread. Since this is in part due to the complexity of the methods, "Ribosome Display and Related Technologies: Methods and Protocols" seeks to extend their use by collecting expert contributions describing these detailed protocols. The protocols described range from well-established methods that have been used for a decade to generate high affinity antibodies, which are already in the clinic, to methods that are in their early stages of application such as display of peptides incorporating non-canonical amino acids. 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.

Invaluable and easy to use, "Ribosome Display and Related Technologies: Methods and Protocols" will be of great benefit to those with general molecular biology or protein engineering experience who wish to select peptides or proteins by display, those with phage display experience who would benefit from the application of ribosome display, as well as those with some ribosome display experience who would like to expand the range of applications to which they are applying the technology."

This new edition provides updated and novel protocols of neuroproteomics methods that encompass both global-scale as well as targeted and specialized topics, which are timely additions for the molecular and phenotypic analysis of the central nervous system and CNS-related disorders. The detailed contents of this book include the exploration of several exciting areas of advanced methods used for neuroproteomics research including relative and absolute protein quantitation by mass spectrometry, characterization of post-translational modifications, as well as bioinformatics and computational approaches. Written for the highly successful Methods in Molecular Biology series, methodology 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. Updated and accessible, Neuroproteomics: Methods and Protocols, Second Edition serves researchers and clinical scientists involved in the area of biomarker research and protein biochemistry, as well as molecular biologists and biochemists who have been involved in proteomics research already or even for those new to the field.

ABPP Methodology: Introduction and Overview, by Matthew B. Nodwell und Stephan A. Sieber Activity-Based Protein Profiling for Natural Product Target Discovery, by Joanna Krysiak und Rolf Breinbauer Photoaffinity Labeling in Activity-Based Protein Profiling, by Paul P. Geurink, Laurette M. Prely, Gijs A. van der Marel, Rainer Bischoff und Herman S. Overkleeft Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis, by William P. Heal und Edward W. Tate Functional Analysis of Protein Targets by Metabolomic Approaches, by Yun-Gon Kim und Alan Saghatelian