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The MPSA international conference is held in a different country every two years. It is devoted to methods of determining protein structure with emphasis on chemistry and sequence analysis. Until the ninth conference, MPSA was an acronym for Methods in Protein Sequence Analysis. To give the conference more flexibility and breadth, the Scientific Advisory Committee of the lOth MPSA decided to change the name to Methods in Protein Structure Analysis; however, the emphasis remains on'methods'and on'chemistry.'In fact, this is the only major conference that is devoted to methods. The MPSA conference is truly international, a fact clearly reflected by the composi­ tion of its Scientific Advisory Committee. The Scientific Advisory Committee oversees the scientific direction of the MPSA and elects the chairman of the conference. Members of the committee are elected by active members, based on scientific standing and activity. The chairman, subject to approval of the Scientific Advisory Committee, appoints the Organizing Committee. It is this latter committee that puts the conference together. The lectures of the MPSA have traditionally been published in a special proceedings issue. This is different from, and more detailed than, the special MPSA issue of the Journal of Protein Chemistry in which only a brief description of the talks is given in short papers and abstracts. In the I Oth MPSA, about half the talks are by invited speakers and the remainder were selected from submitted short papers and abstracts.

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.

Techniques in Protein Chemistry III compiles papers presented at the Fifth Protein Society Symposium in Baltimore on June 22-26, 1991. This book discusses the protein and peptide recovery from PVDF membranes; high-sensitivity peptide mapping utilizing reversed-phase microbore and microcolumn liquid chromatography; and capillary electrophoresis for preparation of peptides and direct determination of amino acids. The TFMSA/TFA cleavage in t-Boc peptide synthesis; applications of automatic PTC amino acid analysis; and identification of O-glycosylation sites with a gas phase sequencer are also elaborated. This text likewise covers the conformational stability of the molten globule of cytochrome c and role of aqueous solvation in protein folding. This publication is useful to students and researchers interested in methods and research approaches on protein chemistry.

Techniques in Protein Chemistry V highlights current methods in peptide and protein mass spectrometry, sequence and amino acid analysis, fragmentations, separations, protein folding and modeling, peptide and protein NMR, and peptide synthesis. This volume emerged from the manuscripts presented at the Seventh Symposium of the Protein Society, held in San Diego on July 24-28, 1993. This volume is organized into eight parts encompassing 61 chapters. The first part surveys the peptide and protein characterization, detection, and analysis by mass spectrometry. The subsequent parts describe the structural characterization and analysis of posttranslational processing events, as well as the characterization of protein and amino acid sequences using several analytical techniques. Other parts explore other analytical methods for peptide and protein separations; some aspects involved in protein design and functional domain analysis; and the evaluation of protein conformation, folding, and modeling. The last parts contain research papers on NMR analysis of peptide and protein solution structures. These parts also look into topics related to peptide synthesis and peptide libraries. This book is intended primarily for protein and analytical chemists.

Protein Physics: A Course of Lectures covers the most general problems of protein structure, folding and function. It describes key experimental facts and introduces concepts and theories, dealing with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states. The book systematically summarizes and presents the results of several decades of worldwide fundamental research on protein physics, structure, and folding, describing many physical models that help readers make estimates and predictions of physical processes that occur in proteins. New to this revised edition is the inclusion of novel information on amyloid aggregation, natively disordered proteins, protein folding in vivo, protein motors, misfolding, chameleon proteins, advances in protein engineering & design, and advances in the modeling of protein folding. Further, the book provides problems with solutions, many new and updated references, and physical and mathematical appendices. In addition, new figures (including stereo drawings, with a special appendix showing how to use them) are added, making this an ideal resource for graduate and advanced undergraduate students and researchers in academia in the fields of biophysics, physics, biochemistry, biologists, biotechnology, and chemistry. Fully revised and expanded new edition based on the latest research developments in protein physics Written by the world's top expert in the field Deals with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states Summarizes, in a systematic form, the results of several decades of worldwide fundamental research on protein physics and their structure and folding Examines experimental data on protein structure in the post-genome era

The contents of this volume derive loosely from an EMBO worksh9P held at EMBL (Heidelberg) towards the end of 1989. The topic of Patterns in Protein Sequence and Structure attracted a wide range of participants, from biochemists to computer scientists, and that diversity has, to some extent, remained in the contributions to this volume. The problems of interpreting biological sequence data are to an increasing extent forcing molecular biologists to learn the language of computers, including at times, even the abstruse language of the computer scientists themselves. While, on their side, the computer scientists have discovered a veritable honey-pot of real data on which to test their algorithms. This enforced meeting of two otherwise alien fields has resulted in some difficulties in communication and it was an aim of the EMBO workshop to help resolve these. By the end, most biologists at the meeting had, at least, heard the terms Dynamic Programming and Regular Expression while for their part the computer programmers began to realise that protein sequences might be more than simple Markov chains in a 20-letter alphabet. Thanks to the modern facilities at EMBL, the three day meeting was video-taped and from this a transcript was taken and offered to the speakers as the basis for a contribution to this volume.

Handbook of Biologically Active Peptides, Second Edition, is the definitive, indispensable reference for peptide researchers, biochemists, cell and molecular biologists, neuroscientists, pharmacologists, and endocrinologists. Its chapters are designed to be a source for workers in the field and enable researchers working in a specific area to examine related areas outside their expertise. Peptides play a crucial role in many physiological processes, including actions as neurotransmitters, hormones, and antibiotics. Research has shown their importance in such fields as neuroscience, immunology, pharmacology, and cell biology. The second edition of Handbook of Biologically Active Peptides presents this tremendous body of knowledge in the field of biologically active peptides in one single reference. The section editors and contributors represent some of the most sophisticated and distinguished scientists working in basic sciences and clinical medicine. Presents all aspects of biologically active peptides in one resource Features more than 20 sections spanning plant, bacterial, fungal, venom, and invertebrate peptides to general peptides Includes immunological, inflammatory, cancer, vaccine, and neurotrophic peptides Discusses peptide precursors, mRNA distribution, processing, and receptors, not just pathophysiological implications

The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

An ultimate goal of modern biology is to understand how the genetic blueprint of cells(genotype)determinesthestructure,function,andbehaviorofalivingorganism (phenotype). At the center of this scienti?c endeavor is characterizing the bioch- ical and cellular roles of proteins, the working molecules of the machinery of life. A key to understanding of functional proteins is the knowledge of their folded str- tures in a cell, as the structures provide the basis for studying proteins'functions and functional mechanisms at the molecular level. Researchers working on structure determination have traditionally selected - dividual proteins due to their functional importance in a biological process or pa- way of particular interest. Major research organizations often have their own protein X-ray crystallographic or/and nuclear magnetic resonance facilities for structure - termination, which have been conducted at a rate of a few to dozens of structures a year. Realizing the widening gap between the rates of protein identi?cation (through DNA sequencing and identi?cation of potential genes through bioinformatics an- ysis) and the determination of protein structures, a number of large scienti?c init- tives have been launched in the past few years by government funding agencies in the United States, Europe, and Japan, with the intention to solve protein structures en masse, an effort called structural genomics. A number of structural genomics centers (factory-like facilities) have been established that promise to produce solved protein structures in a similar fashion to DNA sequencing.

Structure-based drug discovery methods have been transformed in the last 5-10 years and are now having a major impact on the discovery of new drugs. Some of the most exciting developments in the field, such as Fragment-based methods, are described in this book. The book describes the latest developments in technologies that can be used to obtain the 3-D structures including the high profile structural genomics approaches being utilised worldwide. The use of 3-D protein structures in new, Fragment-based, approaches to drug discovery are described in some detail. This book includes experimental approaches using X-ray crystallography and NMR for Fragment-based screening as well as other biophysical methods for studying protein/ligand interactions. In addition, developments in computational chemistry methodology are covered together with an assessment of practical applications.

Peptides play a crucial role in many physiological processes including actions as neurotransmitters, hormones, and antibiotics. Research has shown their importance in such fields as neuroscience, immunology, pharmacology, and cell biology. The Handbook of Biologically Active Peptides presents, for the first time, this tremendous body of knowledge in the field of biologically active peptides in one single reference. The section editors and contributors represent some of the most sophisticated and distinguished scientists working in basic sciences and clinical medicine. The Handbook of Biologically Active Peptides is a definitive, all-encompassing reference that will be indispensable for individuals ranging from peptide researchers, to biochemists, cell and molecular biologists, neuroscientists, pharmacologists, and to endocrinologists. Chapters are designed to be a source for workers in the field and will enable researchers working in a specific area to examine other related areas with which they would not ordinarily be familiar.•Chapters are designed to be a source for workers in the field and will enable researchers working in a specific area to examine other related areas that they would not ordinarily be familiar.•Fascinating relationships described in the book include the presence of some peptides originally found in frog skin that persist in the human human and brain where they can affect food intake and obesity.

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

The application of computational methods to DNA and protein science is a new and exciting development in biology. Bioinformatics: Sequence and Genome Analysis is a comprehensive introduction to this emerging field of study. The book has many unique and valuable features: It is written for any biologist who wants to understand methods of sequence and structure analysis and how the necessary computer programs work; Sequence alignment, structure prediction, phylogenetic and gene prediction, database searching, and genome analysis are clearly explained and amply illustrated; Underlying algorithms and assumptions are clearly explained for the non-specialist; Examples are presented in simple numerical terms rather than complex formulas and notation; Theoretical underpinnings are linked to biological problems and their solutions; Extensive tables provide descriptions and Web sources for a broad range of publicly available software; An associated Website (www.BioinformaticsOnline.org), accessible free of charge by book purchasers, provides links to Internet sources referred to in the text, as well as problem sets for classroom use, and other useful material not included in the text. Based on the author's extensive experience as a molecular geneticist and bioinformaticist at the University of Arizona, this is a uniquely educational book, ideal as a laboratory reference for investigators and also as teaching reference for graduate and undergraduate students studying this fast-changing discipline.

Amino acid sequence analysis is useful for the study of problems ranging from modifications of single molecules to complex networks and interactions of species. Many available amino acid sequences are providing the basis for various studies at the proteome level.The dynamics of protein expression and the simulation of complex biological systems in which proteins interact with certain kinetics and in their respective compartments are just about to be tackled. Amino acid sequences will be crucial reference points for such studies.Key Features• Mass spectrometric analysis of proteins• Protein sequence databases• Amino acid substitution matrices• Amino acid-based phylogeny and alignment• Individual variation in protein-coding sequences of the human genome• Identifying nature's protein Lego(r) set

New types of mass spectrometric instrumentation and new ionization techniques have dramatically extended the applicability of mass spectrometry to the analysis of proteins and peptides. In Mass Spectrometry of Proteins and Peptides, John R. Chapman recreates the success of his earlier acclaimed book (Protein and Peptide Analysis by Mass Spectrometry, 1996) with a major new collection of cutting-edge methods in this area. Contributed by well-established investigators, each chapter provides background information before guiding the researcher step-by-step through the experimental process, with detailed instructions to help assure experimental success. The applications covered range widely and include protein sequencing, higher-order structure determination, epitope mapping, kinetics, quantitation, glycosylation analysis, and bacterial typing. Authoritative and eminently practical, Mass Spectrometry of Proteins and Peptides demonstrates the full scope of this versatile analytical technique. All protein chemists and biochemists, as well as bioanalytical scientists, who want to exploit these powerful methods in their work, will find this book indispensable.

The deeper understanding of protein structure now emerging from cutting-edge research is not only illuminating evolutionary and biochemical mechanisms, but also promises enormous ramifications for molecular medicine, as well as for biotechnology, biophysics, biology, genetics, and other molecular sciences. In Protein Structure Prediction: Methods and Protocols, world-class investigators detail their most successful methods-and the theory behind them-for delineating the shape, form, and function of proteins. The protocols range from basic to advanced and include sequence alignment, the prediction of transmembrane protein structure, and the development of suitable folding potentials. There are also techniques for receptor site prediction, the identification of motifs and domains, the comparative modeling of proteins, the docking of peptides and ligands, and ab initio approaches to protein loop and side-chain prediction. To ensure robust and successful experimental results, each protocol contains step-by-step instructions, as well as tips on pitfalls to avoid and how procedures may be optimized for different systems. Comprehensive, accessible, and highly practical, Protein Structure Prediction: Methods and Protocols offers protein researchers, structural biologists, and other investigators a critical synthesis of the latest research results, as well as the vital guidance needed to understand the structure and interaction of proteins and peptides.

Since the publication of Nonistopic DNA Probe Techniques in 1992, the move away from radioactive materials for research and diagnostics has continued. This is due in part to public awareness of the hazards of radioactive waste and laws making radioactive disposal more difficult and costly and to improvement in both the sensitivity and convenience of nonisotopic techniques. Several new nonisotopic techniques have been developed and substantial improvements made to existing nonisotopic methods since 1992, and these are now included in Nonisotopic Probing, Blotting, and Sequencing. Nonisotopic Probing, Blotting, and Sequencing is an updated, expanded edition of the bestseller, Nonisotopic DNA Probe Techniques. It has been thoroughly revised to include the latest improvements in nonisotopic tagging techniques for macromolecules. Like its predecessor, it enables researchers to select the best nonisotopic method for their needs and maximize success by following its straightforward protocols. Provides strategies and detailed procedures for labeling, blotting, and probing specific nucleic acid sequences and, with this edition, protein molecules Gives protocols for nonisotopic DNA sequencing - new in this edition Gives extensive, practical information Presents background information for each method Provides expert accounts from the inventor or developer of each method Contains seven entirely new chapters Covers all major types of nonisotopic procedures for labeling and detection

Why a Second Edition?The Second Edition provides practical answers to the general question,'How can I obtain useful sequence information from my protein or peptide?'rather than the more specific question asked in the first edition,'How can I obtain the N-terminal sequence?'Important new methods include ways of dealing with blocked N termini, computer analysis of protein sequences, and the recent revolution in mass spectrometry. Mass spectrophotometric characterization of proteins and peptides N-terminal sequencing of proteins with blocked N termini Internal amino acid sequence analysis after protease digestion in-gel and on-blot Improved microscale peptide purification methods Computer analysis of protein sequences New protocols tested and refined through everyday use in authors'laboratories Updated reference chapter covering all aspects of protein microsequencing

Current Research in Protein Chemistry: Techniques, Structure, and Function reviews new techniques and methods for determining the structure and function of proteins. Topics covered include protein folding and stability, chimeric proteins, amino acid and peptide analysis, mass spectrometric methods, and protein sequencing techniques. This book is divided into six sections comprised of 55 chapters. The discussion begins with a description of microwave irradiation that uses Teflon-Pyrex tubes for protein hydrolysis, followed by the application of high performance capillary electrophoresis to the analysis of amino acids. The sections that follow explore mass spectrometry, protein sequencing, and capillary electrophoresis as well as protein stability, chimeric proteins and enzyme modifications, and protein structure prediction. Chapters focus on the crystal structure of human interleukin-1a, the acid-denatured states of proteins, solubility of recombinant proteins expressed in Escherichia coli, and catalysis by chimeric proteins. This book will be of value to students and researchers interested in protein chemistry.

The Peptides: Analysis, Synthesis, Biology: Volume 4: Modern Techniques of Conformational, Structural, and Configurational Analysis is an open-ended treatise that provides comprehensive and critical reviews of important developments in all areas of peptide research including analysis, synthesis, and biology. X-ray structure studies, amino acid analysis, and chiroptical analysis of configuration are discussed, along with solid-phase sequencing and ultramicroanalysis with the aid of fluorescence. This volume is comprised of six chapters and begins with an account of crystal structure analysis on molecules containing 2-12 peptide units, focusing on the variety of intramolecular hydrogen bonds, cis peptide units, and multiple conformation. Conformational changes upon complexation with metal ions are considered, together with the inclusion of solvents as integral parts of a molecular structure. The following chapters explore the conformations of insulin, glucagon, pancreatic polypeptide and related molecules, as well as the molecular biology of these hormones based on crystal structures; the usefulness of chiroptical techniques for determining the absolute configuration of amino acids and small peptides; and ultramicroanalysis of peptides and proteins by high performance liquid chromatography and fluorescence detection. The final chapter looks at the status and future potential of solid-phase sequencing. This book is intended as a reference for specialists, a guide for the novice, and a forum for investigators concerned with research on peptides and proteins.

Sequencing of Proteins and Peptides

Techniques in Protein Chemistry VI, an invaluable bench-top reference source for protein chemists, highlights current methods in the following areas: Protein sequencing and amino acid analysis Mass spectral analysis of peptides and proteins Posttranslational processing High-sensitivity protein and peptide separations Protein folding and NMR Analysis of protein interactions Protein design and engineeringTechniques in Protein Chemistry VI, an invaluable bench-top reference source for protein chemists, highlights current methods in the following areas: Protein sequencing and amino acid analysis Mass spectral analysis of peptides and proteins Posttranslational processing High-sensitivity protein and peptide separations Protein folding and NMR Analysis of protein interactions Protein design and engineering

Current Research in Protein Chemistry: Techniques, Structure, and Function focuses on the techniques and methods used for determining the structure and function of proteins. Topics covered range from protein folding and stability to catalysis by chimeric proteins, amino acid and peptide analysis, applications of mass spectrometry to peptide and protein analysis, and protein sequencing. This book is divided into six sections encompassing 55 chapters. The first chapter describes a novel method for protein hydrolysis by means of microwave irradiation that uses Teflon-Pyrex tubes. This is followed by a discussion of the application of high performance capillary electrophoresis to the analysis of amino acids. The sections that follow focus on mass spectrometric methods, protein sequencing, and capillary electrophoresis as well as protein stability, chimeric proteins and enzyme modifications, and protein structure prediction. The crystal structure of human interleukin-1alpha, the acid-denatured states of proteins, solubility of recombinant proteins expressed in Escherichia coli, and catalysis by chimeric proteins are considered. The reader is also introduced to peptide mapping and internal sequencing of proteins from acrylamide gels, new approaches to covalent sequence analysis, alkaline denaturation of hemoglobin, and measurements of disulfide bond stabilities in protein folding intermediates. Students and researchers interested in protein chemistry will find this book extremely helpful.

The first of its kind, Introduction to Biophysical Methods for Protein and Nucleic Acid Research serves as a text for the experienced researcher and student requiring an introduction to the field. Each chapter presents a description of the physical basis of the method, the type of information that may be obtained with the method, how data should be analyzed and interpreted and, where appropriate, practical tips about procedures and equipment.Key Features• Modern Use of Mass Spectroscopy• NMR Spectroscopy• Molecular Modeling and Graphics• Macintosh and DOS/Windows 3.x disks