Application of NMR and Molecular Docking in Structure-Based Drug Discovery, by Jaime L. Stark and Robert Powers NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions, by Olga Vinogradova and Jun Qin The Use of Residual Dipolar Coupling in Studying Proteins by NMR, by Kang Chen und Nico Tjandra NMR Studies of Metalloproteins, by Hongyan Li and Hongzhe Sun Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics, by Rieko Ishima Contemporary Methods in Structure Determination of Membrane Proteins by Solution NMR, by Tabussom Qureshi and Natalie K. Goto Protein Structure Determination by Solid-State NMR, by Xin Zhao Dynamic Nuclear Polarization: New Methodology and Applications, by Kong Hung Sze, Qinglin Wu, Ho Sum Tse and Guang Zhu

Protein Folding Protocols presents protocols for studying and characterizing protein folding from the unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process.
Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. These approaches have tremendous implications, ranging from drug design, functional assignment, comprehension of the nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular pathways and their dynamics.

"Theoretically, one should obtain essentially the same clinical picture from failure of an end-organ to respond to a hormone as from a decreased production or absence of said hormone. " With these words, Fuller Albright began his now classic paper describing a novel disease, pseudo hypoparathyroidism (PHP), and a novel concept, hormone resis- tance as a cause of disease. Soon, other hormone resistance disorders such as nephrogenic diabetes insipidus (NDI) were recognized, and the concept was extended to resistance to other substances such as calcium ions in familial hypocalciuric hypercalcemia (FHH). Later, diseases characterized by excess rather than deficient hormone action such as McCune-Albright syndrome (MAS) and familial male precocious puberty (FMPP) were recognized to be caused by autonomous endocrine hyperfunction. Although many i!!vestigators provided careful and detailed descriptions of the clinical features of these and other related endocrine disorders, an understanding of pathogenesis proved elusive for many years. In just the past few years, we have gone from clinical description to a molecular understanding of these interesting disorders. This remarkable progress reflects a synthe- sis of three distinct, but now overlapping, areas of biomedical research: the aforemen- tioned recognition and careful clinical description of specific diseases, the elucidation of the basic mechanisms of signal transduction, and the application of the powerful tools of molecular biology and genetics. Fundamental studies on the mechanisms of hormone action by Rodbell and colleagues at NIH culminated in the discovery of a major signal transduction pathway involving heterotrimeric G proteins.

SELDI is distinct from other TOF-MS technologies in that it couples features of chromatography and mass spectrometry, facilitating analyte enrichment and sample cleanup on an array surface. In the growing field of proteomics, SELDI technology has been widely used for biomarker discovery and characterization in diverse applications including diagnostics, drug development, and basic research. SELDI-based biomarker studies can typically be divided into four phases: discovery, validation, purification and identification, and assay development. SELDI-TOF Mass Spectrometry: Methods and Protocols provides an overview of the current applications of SELDI-TOF MS (surface enhanced laser desorption/ionization time-of-flight mass spectrometry), with an emphasis on study and experimental design, data analysis and interpretation, and assay development. 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, SELDI-TOF Mass Spectrometry: Methods and Protocols will provide information on optimizing study design, experimental protocols, and data analysis and interpretation to yield robust biomarkers and biomarker assays, using examples from different disease areas.

This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.

In this fast moving field the main goal of this volume is to provide up-to-date information on the molecular and functional properties and pharmacology of mammalian TRP channels. Leading experts in the field will describe properties of a single TRP protein/channel or portray more general principles of TRP function and important pathological situations linked to mutations of TRP genes or their altered expression. Thereby this volume on Transient Receptor Potential (TRP) Channels provides valuable information for readers with different expectations and backgrounds, for those who are approaching this field of research as well as for those wanting to make a trip to TRPs.

This volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods of 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. Authoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.

Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.

This volume provides comprehensive and detailed protocols that discuss proteomic techniques, plant endosomes, and isolation of organelles and subcellular fractions. The chapters in this book explore numerous plant species and cover topics, such as isolation and purity assessment of membranes from Norway spruce; proteomic analysis of nuclei; analyzing the vacuolar membrane (tonoplast) proteome; isoforms of a thylakoid-bound protein; assay of plasma membrane H+-ATPase in plant tissue under abiotic stresses; and identification and characterization of plant membrane proteins using ARAMEMNON. 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. Practical and thorough, Plant Membrane Proteomics: Methods and Protocols is a valuable resource that promotes the use of plant membrane proteomics to develop the future of the field.

Offers discussions on the chemical and physicochemical modification of proteins for the enhancement of surface activity and functional properties in a variety of systems. The volume provides examples of specific applications of modified proteins in gelation, emulsification, foaming, adsorption and surface tension reduction for use in the food, cosmetics, pharmaceutical, and surfactant manufacturing industries.

This text is aimed at a student readership but will also be useful to life science researchers faced with the task of isolating a protein.

The logic of the overall approach to protein isolation is explained and the physical principles of each separation method are made clear by the use of simple models and analogies drawn from everyday experiences. The author's aim has been to deepen the readers' insight into protein isolation methods, so that they may tackle new problems and perhaps devise new approaches to old problems. Many of the methods described are drawn from the author's own research and are thus uniquely described here; examples are three-phase partitioning, non-linear electrophoresis and a simple approach to buffer making. In this 2nd edition, the treatment of the basic physical principles has been expanded and clarified, the importance of ionic strength in measuring enzyme pH optima is emphasised and a computer program for the calculation of buffers of defined ionic strength is provided. The section on three-phase partitioning has been expanded to include the latest research findings on the use of t-butanol to inhibit enzymes and minimise homogenisation artefacts, the treatment of HPLC has been expanded and the most common practical methods are explained in detail in a new chapter. Additional study questions are provided, as are the answers to all study questions.

This is a fully up-dated and expanded practical guide to protein structure-function relationships. This important area of research is brought up-to-date by the leading scientists in the field. The compilation of detailed protocols focuses on protein function, proteome research and characterization of pharmaceutical proteins, while following the successful format of the Methods in Molecular Biology series. Comprehensive and cutting edge, the book serves as practical guide for researchers working in the field of protein structure-function relationships and the rapidly growing field of proteomics, as well as scientists in the pharmaceutical industries.

Methods in Protein Sequence Analysis contains an intensely prac tical account of all the new methodology available to scientists carrying out protein and peptide sequencing studies. Many of the striking advances in fields as diverse as immunology, cell motility, and neurochemistry have in fact been fueled by our ever more powerful ability to determine the sequences and structures of key proteins and peptides. It is our hope that the rich array of tech niques and methods for sequencing proteins discussed in this volume-methods that generate much of the information crucial to progress in modern biology-will now become accessible to all who can benefit from them. The papers of the present volume constitute the Proceedings of the IVth International Conference on Methods in Protein Se quence Analysis, which was held at Brookhaven National Labo ratory, Upton, NY, September 21-25, 1981. It was the most recent in a series of biennial conferences, the previous one having been held in Heidelberg, GFR, in 1979. The series was originated by Richard Laursen, and initially dealt with one aspect of the field, solid-phase sequencing. The scope of the meeting was very broad and among the many aspects of protein sequencing discussed were: instrumentation, strategy, chemicals, mass spectrometry, cleavage of proteins and separation of peptides, and solid, liquid, manual, and even "gas phase" sequencing."

Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, Methods in Proteome and Protein Analysis presents the most interesting papers from the 14th MPSA meeting.

Major topics include: protein and peptide sample preparation and separation; new reagent for protein sequence analysis; mass spectrometry in protein research; analysis of posttranslational modification; protein-protein interaction using MALDI-MS; manipulation of genome or functional compositon trap; structure-function correlation study using optical biosensors of microcolorimetrical techniques; structural proteomics as NMR or fluorescence polarization study; the classification and prediction of structure or functional sites; in silico analysis of proteins and proteomes; increasing throughput and data quality for proteomics.

This second edition expands on the previous edition with new chapters that are suitable for newcomers, as well as more detailed chapters that cover protein stability and storage, avoiding proteolysis during chromatography, protein quantitation methods including immuno-qPCR, and the challenges that scale-up of production poses to the investigator. Many of the chapters also discuss generation and purification of recombinant proteins, recombinant antibody production, and the tagging of proteins as a means to enhance their solubility and simplify their purification on an individual scale or in high-throughput systems. This book also provides readers with chapters that describe not just the more commonly used methods, but also recently developed approaches such as proteomic/mass spectrometric techniques and Lectin-based affinity chromatography. 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 thorough, Protein Chromatography: Methods and Protocols, Second Edition is a valuable resource for anyone who is interested in the field of protein chromatography.

In recent years remarkable progress has been accomplished with respect to our knowledge about bacterial protein toxins. This refers especially to structural aspects of protein toxins but also holds true for genetics, molecular biology and biochemical mechanisms underlying the action of toxins. This volume covers the very current and exciting aspects of up-to-date bacterial toxicology and comprehensively reviews the most important bacterial protein toxins such as the intracellular acting toxins which exhibit enzyme activity, as well as those toxins that interact with cell plasma membranes by damaging the membranes (pore formation) or stimulating cell receptors (superantigens). This is the most current reference work on these important bacterial protein toxins, which are presented from the point of view of different disciplines such as pharmacology, microbiology, cell biology and protein chemistry.

This edited book provides the first comprehensive overview on conventional and emerging processing technologies for the extraction and purification of proteins and/or peptides from plant sources with a special focus on subsequent product development. The book opens with an introduction to the most conventional processing technologies used in industry today: the alkaline extraction followed by isoelectric precipitation, and air classification. The book also focusses on novel extraction and purification technologies, covering the most recent green emerging technologies based on enzymatic processes, solvents, high-pressure processing, barometric membrane technologies, and microwave-assisted extraction, among others. The final chapters bridge the gap between the presented methods and product development and highlight how these technologies can alter protein functionality and nutritional quality of the extracted protein, and thereby, impact human health. In the context of rising consumer interest in foods from plant-protein ingredients and the United Nations targets for Sustainable Development Goal 12 on 'Responsible Consumption and Production', this book will provide an indispensable resource for students, engineers and researchers in academia and industry, working in the area of food science, food technology and plant-based product development.

Following the two meetings on Lactoferrin Structure and Function that were held in Honolulu, Hawaii, in 1993 and 1995, the Third International Conference on Lactoferrin Structure and Function was held in Le Touquet, France, and has successfully reinforced and diversified the previously created bridges between biochemists, clinicians, and companies. In fact, scientists, physicians, and people of industry from different domains have brought a wealth of recent information concerning biochemistry and technical advances in the identification of lactoferrin-derived compounds as well as cell biology, molecular biol ogy, pathology, and medical applications of lactoferrin and lactoferrin-derived com pounds. We were so delighted with the rapid growth of knowledge concerning many biologi cal and immunological functions of lactoferrins and the relationships between their struc ture and function, we wanted to share our pleasure with the readers interested in this field. The present book. which represents a review of some of the most exciting contributions, is intended to reflect the status of our knowledge and transmit our hopes for the future devel opment of in vivo applications of natural and recombinant lactoferrins. We would like to express our gratitude to the sponsors who contributed to the or ganization of the meeting in such a pleasant place and allowed the participation of several young researchers. We would also like to thank all the participants who have answered with enthusiasm our invitation and to every one of the Laboratoire de Chimie Biologique for the constant and efficient help."

Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.

This detailed volume explores newly-developed methods in PIWI-interacting RNAs (piRNAs) research, methods currently applied to other ncRNAs involved in nuclear regulation which can be used to study piRNAs, and piRNA methods applied in non-classical organisms. It also includes several bioinformatic and biophysical methods related to piRNA studies, consistent with the increasing importance of high-throughput sequencing and computational methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, piRNA: Methods and Protocols serves as an ideal guide for researchers seeking to elucidate the numerous mysteries of this area of multicellular biology.

In the last two decades, our knowledge on regulatory peptides and their cognate receptors, most of which are members of the seven transmembrane receptor families, has increased enormously. Regulatory peptides are small proteins which, besides their hormonal functions in regulating cellular metabolism in various tissues, may also act as neurotransmitters, and thus they often carry the prefix "neuro." Many of the cognate receptors involved in transducing the peptidergic signal across the cell membrane via a family of G proteins exist in multiple forms, the number of which frequently exceeds that of the corresponding peptide ligands. In this book, various peptide-receptor systems are discussed, e.g. CRF, somatostatin, TRH, opioid peptides, vasopressin, and oxytocin. It also discusses new strategies such as "reverse physiology" to uncover new peptides and orphan receptors.

This detailed volume explores a wide variety of applications of yeast surface display, an extensively used protein engineering technology. Beginning with detailed protocols for the construction and efficient selection/screening of yeast surface display libraries, as well as for the analysis of individual yeast-displayed protein variants, the book continues with protocols describing the selection of yeast surface display libraries for binding to mammalian cells or to extracellular matrix as well as protocols for a broad spectrum of specialized yeast surface display applications, demonstrating the versatility of this display platform. Written for the highly 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 methodologies, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Yeast Surface Display serves as a comprehensive resource that enables the implementation of this powerful and versatile technique in virtually any molecular biology laboratory, even in the absence of any prior yeast surface display experience.

The book Heat Shock Protein-Based Therapies provides the most up-to-date review on new heat shock protein-based mechanisms used in the therapy and treatment of various human disorders and diseases, including cancer, muscular atrophy, neurodegenerative disorders (Alzheimer's Disease, Multiple Sclerosis) and infectious diseases (HIV, periodontal disease). Written by leaders in the field of heat shock protein research, the chapters systematically and in a step wise fashion takes the reader through the fascinating sequence of events by which mechanisms dependent on heat shock proteins are targeted. The chapters also provide answers as to HSP biological significance to the host. This book is a must read for graduate and postgraduates in the field of Drug Development, Biotechnology, Pharmaceutical Industry, Phytomedicine, Biology (plant and mammal), Biochemistry (pro- and eukaryotic), Oncology, Immunology, Microbiology, Exercise Medicine, Physiology, Inflammatory diseases, Autoimmunity, Pharmacology and Pathology.

This book provides an overview of the biology and biochemistry of peroxisomes, and discusses the contribution of these organelles to peroxisomal and neurodegenerative diseases. It begins with a detailed introduction to the biogenesis and metabolic functions of peroxisomes, and highlights their role in oxidative stress and in lipid metabolism such as fatty acid oxidation. The following chapters focus on the molecular and clinical aspects of peroxisomal disorders caused by defects in peroxisomal function. In particular, the biological aspects of peroxisomal biogenesis disorders such as Zellweger syndrome and Heimler syndrome are discussed. This includes their underlying genetic causes as well as the biochemical and metabolic defects associated with the disorders. In addition, several chapters cover recent observations suggesting an association between peroxisomal dysfunction and neurodegenerative diseases such as Alzheimer's, Multiple Sclerosis and other degenerative cerebellar pathologies. The final section of the book discusses important cell and animal models for studying the role of peroxisomes in human diseases and presents current therapeutic strategies for their treatment. This book deals with a highly topical subject that is at the heart of current research, and represents a valuable contribution for all students and researchers who want to understand the complex biology of peroxisomes and their role in human diseases.

Transmissible spongiform encephalopathies (TSE), known as prion diseases, have been recognized for nearly 300 years in animals and almost 100 years in humans. Modern studies, including the protein-misfolding cyclic amplification (PMCA), have greatly advanced our understanding of the pathogenesis of prion diseases and facilitated the identification of new prion diseases in animals and humans. In the second edition of Prions and Diseases, more than 60 leading researchers and clinicians worldwide provide an up-to-date discussion of these unique infectious pathogens and their associated diseases. The book provides up-to-date knowledge about the etiology, pathogenesis, classification, histopathological, and clinical aspects of the full range of animal and human prion diseases. As a result, the book contains by far the most authoritative views about the past, present, and future of prions and prion diseases. The new second edition covers such important emerging topics such as inherited human prion disease, stem-cell models in prion research, human prion disease surveillance, and gene therapy strategies.