The aim of the book is to discuss the application of molecular pathology in cancer research, and its contribution in the classification of different tumors and identification of potential molecular targets, as well as how this knowledge may be translated into clinical practice, and the huge impact this field is likely to have in the next 5 to 10 years.

This second edition of Membrane Protein Purification and Crystallization, A Practical Guide is written for bench scientists working in the fields of biochemistry, biology, and proteomic research. This guide presents isolation and crystallization techniques in a concise form, emphasizing the critical aspects unique to membrane proteins. It explains the principles of the methods and provides protocols of general use, permitting researchers and students new to this area to adapt these techniques to their particular needs. This edition is not only an update but is comprised mainly of new contributions. It is the first monograph compiling the essential approaches for membrane protein crystallization, and emphasizes recent progress in production and purification of recombinant membrane proteins.
Key features
* Provides general guidelines and strategies for isolation and crystallization of membrane proteins
* Gives detailed protocols that have wide application, and low specialized equipment needs
* Emphasizes recent progress in production and purification of recombinant membrane proteins, especially of histidine-tagged and other affinity-epitope-tagged proteins
* Summarizes recent developments of Blue-Native PAGE, a high resolution separation technique, which is independent of the use of recombinant techniques, and is especially suited for proteomic analyses of membrane protein complexes
* Gives detailed protocols for membrane protein crystallization, and describes the production and use of antibody fragments for high resolution crystallization
* Presents a comprehensive guide to 2D-crystallization of membrane proteins

Over the past thirty years, many elegant genetic and biochemical approaches have been combined in order to advance the study of protein secretion and the necessary navigation through cell membranes, yet, despite this progress, less than two hundred membrane protein structures are known, nowhere near the complete inventory that the discovered protein export systems suggest. In Protein Secretion: Methods and Protocols, leading experts in the field provide robust, well-established protocols to elucidate the multiplicity of tools that have been developed to study protein sorting, membrane targeting, transmembrane crossing, and secretion across multiple membranes. With examples involving both prokaryotic and eukaryotic organisms, the volume covers subjects ranging from bioinformatics and proteomics to fundamental enzymology and genetics to cell biology, structural analyses, and biophysics. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the key materials and reagents, step-by-step, readily reproducible protocols, and detailed notes on troubleshooting and avoiding known pitfalls. Comprehensive and dependable, Protein Secretion: Methods and Protocols focuses on well-characterized paradigms so that scientists studying a vast array of subjects from biochemistry and genetics to biotechnology and biopharmaceuticals can benefit and expand upon their vital research.

A wide range of researchers are currently investigating different properties and applications for copper-containing proteins. Biochemists researching metal metabolism in organisms ranging from bacteria to plants to animals are working in a completely different area of discovery than scientists studying the transportation and regulation of minerals and small molecule nutrients. They are both working with copper-containing proteins, but in very different ways and with differing anticipated outcomes.

This new edited volume in the Springer Subcellular Biochemistry Series presents a comprehensive, state-of-the-art overview of the proteomics of peroxisomes derived from mammalian, Drosophila, fungal, and plant origin, and contains contributions from leading experts in the field. The development of sensitive proteomics and mass spectrometry technologies, combined with bioinformatics approaches now allow the identification of low-abundance and transient peroxisomal proteins and permits to identify the complete proteome of peroxisomes, with the consequent increase of our knowledge of the metabolic and regulatory networks of these important cellular organelles. The book lines-up with these developments and is organized in four sections including: (i) mass spectrometry-based organelle proteomics; (ii) prediction of peroxisomal proteomes; (iii) analysis of peroxisome proteome interaction networks; and (iv) peroxisomes in relation to other subcellular compartments. The editor Luis A. del Rio is Professor ad honorem of the Spanish National Research Council (CSIC) in the Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry and Cell & Molecular Biology of Plants, at the Estacion Experimental del Zaidin, Granada, Spain. Del Rio's research group focuses on the metabolism of reactive oxygen species (ROS), reactive nitrogen species (RNS) and antioxidants in plant peroxisomes, and the ROS- and RNS-dependent role of peroxisomes in plant cell signalling. The editor Michael Schrader is Professor of Cell Biology & Cytopathology in the Department of Biosciences at the University of Exeter, UK. Using mammalian peroxisomes as model organelles, Prof. Schrader and his team aim to unravel the molecular machinery and signalling pathways that mediate and regulate the formation, dynamics and abundance of these medically relevant cellular compartments.

In Flavins and Flavoproteins: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study flavins and flavoproteins. These include review style methods and protocols to exemplify the variety, the power and the success of modern techniques and methods in application to flavoproteins. Part I of this Volume covers general properties, syntheses and applications of free flavins as well as its analogs and flavoproteins. Part II covers characterizations of flavins and flavoproteins using modern experimental techniques as well as theoretical methods. Written in the highly successful Methods in Molecular Biology 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, Flavins and Flavoproteins: Methods and Protocols aids scientists in continuing to tackle the countless questions that need to be answered to more fully comprehend the vast diversity and specificity of flavin-governed biological processes.

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.

Protein Physics is a lively presentation of the most general problems of protein structure, folding and function from the physics and chemistry perspective, based on lectures given by the authors. It deals with fibrous, membrane and, most of all, with the best studied water-soluble globular proteins, in both their native and denatured states. The major aspects of protein physics are covered systematically, physico-chemical properties of polypeptide chains; their secondary structures; tertiary structures of proteins and their classification; conformational transitions in protein molecules and their folding; intermediates of protein folding; folding nuclei; physical backgrounds of coding the protein structures by their amino acid sequences and protein functions in relation to the protein structure. The book will be of interest to undergraduate and graduate level students and researchers of biophysics, biochemistry, biology and material science.
* Designed for a wide audience of undergraduate and graduate students, as well as being a reference for researchers in academia and industry
* Covers the most general problems of protein structure, folding, and function and introduces the key concepts and theories
* Deals with fibrous, membrane and especially water-soluble globular proteins, in both their native and denatured states
* Summarizes and presents in a systematic form the results of several decades of world wide fundamental research on protein physics, structure and folding
* Examines experimental data on protein structure in the post-genome era

This detailed volume addresses recent developments in phosphoproteomic techniques with a particular focus on the plant system. Over the recent decades, proteomic methods were refined to study the significance and dynamics of protein phosphorylation in various biological contexts. However, working with plant tissue imposes particular challenges to the biologist which are attributed to the rigid cell wall making protein extraction more difficult, the skewed protein abundance with Rubisco as a highly abundant protein and a large central vacuole leading to low protein yield and increased degradative enzyme activity. The methodologies in this book seek to move beyond these issues. 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 authoritative, Plant Phosphoproteomics: Methods and Protocols serves as an ideal reference for researchers investigating this vital area of plant science.

This volume documents this unique family of cell surface proteins. Despite masquerading as intractable and difficult to clone and characterize, ENOX proteins have and continue to offer remarkable opportunities for research, commercial development and outside confirmation of therapeutic, diagnostic and new paradigms to help explain complex biological processes.

A cofactor is a component part of many enzymes and functions by uniting with another molecule in order to become active.
The use of cofactors to supplement the native amino acids of a protein is essential to maintain the chemical capabilities necessary for organisms to survive. This volume focuses on the significant advances of the past decade in identifying and describing new cofactors--either small molecules or those derived posttranslationally.

The subject of this volume is a comprehensive examination of the biochemistry and biology of all classes of known PAS proteins, with the intention that readers will find insight into their own work and ideas from study of the multitude of PAS protein functions. PAS proteins control numerous physiological and developmental events, and span phylogeny from bacteria to man. Bacterial and plant PAS proteins act as sensors of environmental stimuli, including light, oxygen, and energy status.

Not surprising, given these roles, there is intense investigation of the roles of bHLH-PAS proteins in issues of human health including: (1) cancer induction, (2) cancer growth and vascularity, (3) birth defects, including Down syndrome, (4) appetite control and obesity, (5) sleep rhythm disorders, and (6) mental health disorders such as social interactions and learning.

PAS proteins encompass many fields of biology, and scientists who work in these fields (circadian rhythms, oxygen regulation, toxin metabolism, bacterial sensors, and development) are an audience, particularly those who actively work on PAS proteins and researchers interested in transcriptional control, signal transduction, and evolution.

The development of proteomic analyses using advanced mass spectrometry techniques has revolutionized the way proteins are studied, namely, as individual molecules within a complex system. HIV-1 Proteomics: From Discovery to Clinical Application comprehensively covers protein analysis from the early classic experimental days to current state-of-the-art HIV-1 proteomics in a clear informative style that brings expert-level understanding to the novice. Discussion of important clinical applications and future directions for the field also make this an ideal read for the expert. After finishing this book, the reader will have a complete and functional understanding of protein analysis from traditional biochemistry to modern proteomics.

Heat Shock Proteins and Plants provides the most up-to-date and concise reviews and progress on the role of heat shock proteins in plant biology, structure and function and is subdivided into chapters focused on Small Plant HSPs (Part I), Larger Plant HSPs (Part II) and HSPs for Therapeutic Gain (Part III). This book is written by eminent leaders and experts from around the world and is an important reference book and a must-read for undergraduate, postgraduate students and researchers in the fields of Agriculture, Botany, Crop Research, Plant Genetics and Biochemistry, Biotechnology, Drug Development and Pharmaceutical Sciences.

This book describes hydration structures of proteins by combining experimental results with theoretical considerations. It is designed to introduce graduate students and researchers to microscopic views of the interactions between water and biological macromolecules and to provide them with an overview of the field. Topics on protein hydration from the past 25 years are examined, most of which involve crystallography, fluorescence measurements, and molecular dynamics simulations. In X-ray crystallography and molecular dynamics simulations, recent advances have accelerated the study of hydration structures over the entire surface of proteins. Experimentally, crystal structure analysis at cryogenic temperatures is advantageous in terms of visualizing the positions of hydration water molecules on the surfaces of proteins in their frozen-hydrated crystals. A set of massive data regarding hydration sites on protein surfaces provides an appropriate basis, enabling us to identify statistically significant trends in geometrical characteristics. Trajectories obtained from molecular dynamics simulations illustrate the motion of water molecules in the vicinity of protein surfaces at sufficiently high spatial and temporal resolution to study the influences of hydration on protein motion. Together with the results and implications of these studies, the physical principles of the measurement and simulation of protein hydration are briefly summarized at an undergraduate level. Further, the author presents recent results from statistical approaches to characterizing hydrogen-bond geometry in local hydration structures of proteins. The book equips readers to better understand the structures and modes of interaction at the interface between water and proteins. Referred to as "hydration structures", they are the subject of much discussion, as they may help to answer the question of why water is indispensable for life at the molecular and atomic level.

Regulated turnover of extracellular matrix (ECM) is an important component of tissue homeostasis. In recent years, the enzymes that participate in, and control ECM turnover have been the focus of research that touches on development, tissue remodeling, inflammation and disease. This volume in the Biology of Extracellular Matrix series provides a review of the known classes of proteases that degrade ECM both outside and inside the cell. The specific EMC proteases that are discussed include cathepsins, bacterial collagenases, matrix metalloproteinases, meprins, serine proteases, and elastases. The volume also discusses the domains responsible for specific biochemical characteristics of the proteases and the physical interactions that occur when the protease interacts with substrate. The topics covered in this volume provide an important context for understanding the role that matrix-degrading proteases play in normal tissue remodeling and in diseases such as cancer and lung disease. The series Biology of Extracellular Matrix is published in collaboration with the American Society for Matrix Biology.

Blurb for Volume 2
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant class proteins, and provide a comprehensive collection of proven experimental techniques for studying it both in vitro and in vivo. This second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells. The first companion volume, Reviews and Case Histories sets the stage for this volume by introducing the various classes of intra- and extra-cellular calcium-binding proteins and their mode of action.
Single Blurb for Both Volumes
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. The first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in dairy proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins andtheir modes of action. The second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells.

Since the first edition of Protein Nanotechnology Protocols Instruments and Applications the intersection of protein science and nanotechnology has become an exciting frontier in interdisciplinary sciences. The second edition of Protein Nanotechnology Protocols Instruments and Applications expands upon the previous editions with current, detailed chapters that provide examples of proteins which are now being harnessed for a wide range of applications, some more developed than others. This book also delves into engineering proteins and an overview of the sorts of tools that are now readily available to manipulate the structure and function of proteins, both rationally and using methods inspired by evolution. 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 Nanotechnology Protocols Instruments and Applications, Second Edition seeks to provide an overview of this multi-faceted field and a useful guide to those who wish to contribute to it.

This is the first compilation of protein lipidation enzymes. This volume summarizes recent dramatic developments regarding enzymes responsible for protein lipidation, a process critical for a number of physiological functions, including cell proliferation and morphology. Inhibitors of protein lipidation have recently been shown to be useful as anticancer drugs. Enzymatic mechanisms, mutational analysis, and structural studies are presented.
Key Features
* The enzymatic mechanisms of protein lipidation
* Three-dimensional structures of protein farnesytransferase, protein geranylgeranytransferase II, and n-myristoryltransferase

One ofthe major drivers in biological research is the establishment ofstructures and functions of the 50,000 or so proteins in our bodies. Each has a characteristic- dimensional structure, highly "ordered" yet "disordered"! This structure is essential for a protein's function and, significantly, it must be sustained in the competitive and complex environment of the living cell. It is now being recognised that when a cell loses control, proteins can se- assemble into more complex supermolecular structures such as the amyloid fibres and plaques associated with the pathogenesis of prion (CJD) or age-related (Alzheimer's) diseases. This is a pointer to the wider significance of the self-assembling properties of polypeptides. It has been long known that, in silk, polypeptides are assembled into- sheet structures which impart on the material its highly exploitable properties of flexibility combined with high tensile strength. But only now emerging is the recognition that peptides can Self-assemble into a wide variety of non-protein-like structures, including fibrils, fibres, tubules, sheets and monolayers. These are exciting observations and, more so, the potential for materials and medical exploitations is so wide ranging that over 80 scientists from Europe, USA, Japan and Israel. met 1-6 July 1999 in Crete, to discuss the wide-ranging implications of these novel developments. There was a spirit of excitement about the workshop indicative of an important new endeavor. The emerging perception is that of a new class of materials set to become commercially viable early in the 21st century.

This thorough book covers the most recent proteomics techniques, databases, bioinformatics tools, and computational approaches that are used for the identification and functional annotation of proteins and their structure. The most recent proteomic resources widely used in the biomedical scientific community for storage and dissemination of data are discussed. In addition, specific MS/MS spectrum similarity scoring functions and their application in the field of proteomics, statistical evaluation of labeled comparative proteomics using permutation testing, and methods of phylogenetic analysis using MS data are also described in detail. Written for the highly successful Methods in Molecular Biology series, chapters contain the kind of detail and key implementation advice to ensure successful results. Authoritative and cutting-edge, Proteome Bioinformatics serves as a useful resource for researchers who are beginners as well as advanced investigators in the field of proteomics.

Membrane proteins, representing nearly 40% of all proteins, are key components of cells involved in many cellular processes, yet only a small number of their structures have been determined. Membrane Protein Structure Determination: Methods and Protocols presents many detailed techniques for membrane protein structure determination used today by bringing together contributions from top experts in the field. Divided into five convenient sections, the book covers various strategies to purify membrane proteins, approaches to get three dimensional crystals and solve the structure by x-ray diffraction, possibilities to gain structural information for a membrane protein using electron microscopy observations, recent advances in nuclear magnetic resonance (NMR), and molecular modelling strategies that can be used either to get membrane protein structures or to move from atomic structure to a dynamic understanding of a molecular functioning mechanism. 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 on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Membrane Protein Structure Determination: Methods and Protocols serves as an ideal reference for scientists seeking to further our knowledge of these vital and versatile proteins as well as our overall understanding of the complicated world of cell biology.

Blurb for Volume 1
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. This first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in diary proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins and their modes of action. The second companion volume focuses on cutting-edge experimental methods for studying solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding proteins in general.
Single Blurb for Both Volumes:
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. The first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in dairy proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins and their modes of action. The second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells.

Protein Folding Kinetics - Biophysical Methods (2nd Edition) gives a deep insight into the principles and concepts of the kinetic and structural resolution of fast chemical and biophysical reactions of proteins with emphasis on protein-folding reactions. The study of fast protein-folding reactions and the understanding of the folding paradox have significantly advanced due to the recent development of new biophysical methods which allow not only kinetic resolution in the sub-millisecond time scale but also structural resolution with unprecedented precision. Pathways and structures of early and late folding events and the transition state structures of fast- and ultrafast-folding proteins can now be studied in far more detail. Important techniques include biophysical, chemical, molecular biological and mathematical methods, in particular protein engineering, Phi-value analysis, time-resolved circular dichroism, optical triggers and pulsed infrared LASER methods, pressure and temperature jump, ultrafast mixing, stopped flow and quenched flow, dielectric relaxation and electric-field-jump, acoustic relaxation, fluorescence- and isotope-labeling, H/D exchange methods, NMR line broadening and stopped-flow NMR, transition state theory, solutions of rate equations, and evolutionary computer programming. Protein Folding Kinetics - Biophysical Methods is written for students and researchers in biochemistry, biophysics, and related fields.

Special features in the second edition:

-Includes detailed information and 12 color figures on the high resolution of folding transition states.

-Discusses structural determinants of the rate of protein folding on a timescale from microseconds to seconds.

-Provides information on self-evolving computer programs for protein-folding simulations and protein-structure predictions.

This thesis offers readers a comprehensive introduction to amyloid proteins and the computational methods used with them. Katrine Skeby critically assesses and compares both the literature and the experiments performed by other researchers, which further elevates the quality and relevance of her own work. Amyloid proteins are highly complex, and this research provides unparalleled insights, especially with regard to the origin of cytotoxicity and to developing technologies for early detection, revealing in detail the molecular mechanisms behind hIAPP behavior. Several studies within the thesis answer difficult questions which promote future research into the properties of amyloid proteins.