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

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.

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 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.

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.

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.

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 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.

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.

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."

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.

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.

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."

This book covers the latest findings of a wide variety of viral, prokaryotic and eukaryotic macromolecular protein complexes and builds upon the solid macromolecular foundations established by previous volumes of the Subcellular Biochemistry series. Thus, an almost encyclopaedic coverage of the broad field of protein complex structure and function has been established. The 17 interesting chapters included in this book have been organised into four sections: Soluble Protein Complexes, Membrane Protein Complexes, Fibrous Protein Complexes and Viral Protein Complexes. Significant topics present here are: Fatty Acid Synthase, the Fork Protection Complex, Ribonucleotide Reductase, the Kinetochore, G proteins, the FtsEX Complex, the Kainate Receptor, the Photosystem I-antenna, the Mycobacterial Arabinofuranosyltransferases, the the Bacterial Flagellum, the Actomyosin Complex, Motile Cilia, SLS Collagen Polymorphic Structures, and the Reovirus Capsid and Polymerase. Up-dates/expansion of chapter topics present in earlier volumes are now included in chapters here, e.g., those on Ferritin-like proteins and the Multi-tRNA Synthetase. The book is richly illustrated throughout, the result of an impressive integration of structural data from X-ray crystallography and cryo-electron microscopy. The functional aspects of protein-protein interactions are also given a high priority.

This fully updated edition provides a series of methods for how best to assess functions of histone deacetylases and acetyltransferases. The disease-relevance of dysregulated protein deacetylation by overexpressed or aberrantly activated histone deacetylases has spurred an intense search for novel and improved inhibitors of these enzymes, as reflected in this collection. Expert contributors explore the generation and evaluation of novel histone deacetylase inhibitors and new and improved techniques to assess acetylation-dependent molecular mechanisms in vitro and in vivo. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, HDAC/HAT Function Assessment and Inhibitor Development: Methods and Protocols, Second Edition serves as an ideal guide for researchers seeking to further elucidate this vital area of study.

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 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.

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.

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.

Leading researchers and innovators describe in step-by-step detail the latest techniques that promise to significantly impact the practice of proteomics, as well as its success in developing novel clinical agents. The methods span the entire spectrum of top-down and bottom-up approaches, including microarrays, gels, chromatography, and affinity separations, and address every aspect of the human proteome, both quantitatively and qualitatively. The techniques of protein detection utilized are diverse and range from fluorescence and resonance light scattering to surface plasmon resonance and mass spectrometry. The protocols follow the successful Methods in Molecular Biology (TM) series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

This book consists of a series of 82 precise, easy-to-read articles by internationally renowned scientists and emphasizes the practical approach to HPLC with minimal theory, although the underlying principles for peptide and protein separations are clearly expressed. All of the major modes of microbore, ultrafast and analytical HPLC are discussed, including size-exclusion, ion-exchange, reversed-phase, hydrophobic interaction, and affinity and immunoaffinity chromatography. A section on preparative HPLC, including displacement techniques, is also presented. Problem-solving approaches to the separation of various classes of biologically active peptides and proteins are thoroughly explored, while the importance of peptide standards for monitoring column performance and for optimizing separation conditions is emphasized. Several articles focus on the choice of the correct detection method (electrochemical, UV, fluorescence), as well as the need for a proper knowledge of approaches to column and instrument maintenance and trouble-shooting. A section on predictive approaches deals with both computer simulation of peptide separations and peptide structure. The book also includes complementary techniques to HPLC, as well as other useful applications of HPLC. It enables both novice and experienced chromatographers to realize the full potential of this extremely powerful technique, in the process making an important contribution to scientific literature.

With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics-the study of the expressed part of the genome-has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry-especially in the fields of molecular biology, biochemistry, microbiology, and cell biology-should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Non-vesicular intracellular cholesterol transport is an important mechanism for maintaining membrane cholesterol homeostasis. Recent reports of studies directed at soluble cholesterol transport proteins indicate that aberrant expression of the START proteins may contribute to disease states associated with disorders in cholesterol homeostasis. This is an exciting new direction in the field and the purpose of this book will be to highlight the current research directed at potential roles for the START family in diabetes, cancer, and atherogenesis. This book also provides a personal and historical perspective of the discovery-to-publication journey that the authors had for their particular START domain family member. The goal will be to provide perspectives to graduate students, post-doctoral fellows, and endocrinology fellows on the research discovery process.

The breadth of modern biology is characterized by a comprehension of phenomena at many levels of organization. Such levels of understanding range from the organismal to the molecular. It is when all these levels can be discussed together that a sense of true achievement begins to be felt. The topical area of fatty acid transport and metabolism was the focus of the Third International Conference on Lipid-Binding Proteins held at the University of Minnesota in May 1997. This volume contains a sampling of the proceedings of this meeting.