Structural genomics is the systematic determination of 3-D 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

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.

Over the past decade, there has been an increase in powerful proteomics technologies that allow greater fundamental insights into the blood proteome. Further developments in informatic analyses, software developments, and computational tools are providing insights into large data sets, open-source data along with large-scale application of bioinformatics. Serum/Plasma Proteomics: Methods and Protocols, Second Edition is a comprehensive resource of protocols for areas, pre-analytical through to analytical, of plasma and serum proteomics. Divided into five convenient sections, covering fractionation strategies for in-depth blood proteome analysis, defined procedures for blood collection, handling and storage, detailed protocols for performing both antibody-based and non-antibody based quantitative assays, proteome analysis of blood cell compartments, circulating nanomebraneous vesicles and blood-related fluids, data management, statistical design, and bioinformatic challenges. 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, Serum/Plasma Proteomics: Methods and Protocols, Second Edition delivers a valuable foundation for the development and application of blood-based proteomics, and further incorporates blood cell components, including platelets, red blood cells, circulating extracellular vesicles/exosomes, and related biofluids.

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.

One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field.

Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions

Teaches readers how to analyze their own datasets using available online databases, software tools, and web servers, which are listed and updated on the book s web companion page.

Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students."

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.

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.

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.

The 2eof this classic Guide to Protein Purification provides a complete update to existing methods in the field, reflecting the enormous advances made in the last two decades. In particular, proteomics, mass spectrometry, and DNA technology have revolutionized the field since the first edition s publication but through all of the advancements, the purification of proteins is still an indispensable first step in understanding their function. This volume examines the most reliable, robust methods for researchers in biochemistry, molecular and cell biology, genetics, pharmacology, biotechnology and sets a standard for best practices in the field. It relates how these traditional and new cutting-edge methods connect to the explosive advancements in the field. This "Guide to" gives imminently practical advice in order to avoid costly mistakes in choosing a method and brings in perspective from the premier researchers while it presents a comprehensive overview of the field today.
Gathers top global authors from industry, medicine, and research fields across a wide variety of disciplines including biochemistry, genetics, oncology, pharmacology, dermatology and immunologyAssembles chapters on both common and less-common relevant techniquesProvides robust methods as well as an analysis of the advancements in the field that, for an individual investigator, can be a demanding and time-consuming process"

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

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.

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.

Published continuously since 1944, the" Advances in Protein Chemistry and Structural Biology" serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This eclectic volume features articles on a variety of topical subjects.

Includes new information about protocols and analysis of proteins Eclectic volume presents chapters by a wide range ofleading experts Presents new, cutting-edge information that will serve as an essential addition to any bookshelf or laboratory "

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.

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

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.

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.

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.

"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.

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.

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

"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.