This unique volume reviews the beautiful architectures and varying mechanical actions of the set of specialized cellular proteins called molecular chaperones, which provide essential kinetic assistance to processes of protein folding and unfolding in the cell. Ranging from multisubunit ring-shaped chaperonin and Hsp100 machines that use their central cavities to bind and compartmentalize action on proteins, to machines that use other topologies of recognition - binding cellular proteins in an archway or at the surface of a 'clamp' or at the surface of a globular assembly - the structures show us the ways and means the cell has devised to assist its major effectors, proteins, to reach and maintain their unique active forms, as well as, when required, to disrupt protein structure in order to remodel or degrade. Each type of chaperone is beautifully illustrated by X-ray and EM structure determinations at near- atomic level resolution and described by a leader in the study of the respective family. The beauty of what Mother Nature has devised to accomplish essential assisting actions for proteins in vivo is fully appreciable.

First published in 1991, Chemical Reagents for Protein Modification, 2nd Edition provides a unique combination of theoretical and practical considerations for the use of chemical reagents for site-specific modification of proteins. The book is divided into three sections, with the first section describing general techniques, including information on the organic chemistry of the various modification reactions; the separation and characterization of site-specific modified proteins, including applications to proteins separated by electrophoresis followed by blotting; the specific chemical cleavage of peptide bonds in proteins; the separation of peptides by high-performance liquid chromatography and electrophoresis; and the use of chemical reagents to assess conformational change in proteins. The second section provides an encyclopedic description of reagents and reactions for the site-specific modification of individual amino acid residues in proteins. The final section presents descriptions of the use of chemical reagents to label biologically significant sites in proteins, including enzyme active sites and the use of covalent cross-linking to measure protein-protein interactions. Particular emphasis is placed on the use of photoaffinity reagents. The book will be an extremely useful research tool for all investigators interested in the solution chemistry of proteins.

Human cells produce at least 30,000 different proteins. Each has a specific function characterized by a unique sequence and native conformation that allows it to perform that function. While research in this post-genomic era has created a deluge of invaluable information, the field has lacked for an authoritative introductory text needed to inform researchers and students in all of those fields now concerned with protein research. Introduction to Peptides and Proteins brings together some of the most respected researchers in protein science to present a remarkably coherent introduction to modern peptide and protein chemistry. The first sections of the book delve into - Basic peptide and protein science from assembly through degradation Traditional and emerging research methods including those used in bioinformatics and proteomics New computational approaches and algorithms used to find patterns in the vast data collected by sequencing projects After providing a foundation in tools and methods, the authors closely examine six protein families, including representative classes such as enzymes, cell-surface receptors, antibodies, fibrous proteins, and bioactive peptide classes. They concentrate on biochemical mechanisms and where possible indicate therapeutic or biotechnical possibilities. Then focusing on clinical aspects, the authors investigate misfolding as found in prion diseases, miscleavage as found in Alzheimer's, and mis-sequencing as found with some cancers. Drawing from some of their own research, the authors summarize recent achievements and emerging applications. They discuss the use of proteins and peptides as drugs and the solid-phase synthesis required for drug production. They also look at the use of peptides as functional biomolecules and research tools. No longer just th

Experimental protein engineering and computational protein design are broad but complementary strategies for developing proteins with altered or novel structural properties and biological functions. By describing cutting-edge advances in both of these fields, Protein Engineering and Design aims to cultivate a synergistic approach to protein science. Experimental Protein Engineering The first half of the book discusses experimental approaches to protein engineering and starts by describing several high-throughput screening platforms for protein engineering. Key techniques used for diversity generation are also discussed. The next few chapters present examples of therapeutics, enzymes, biomaterials, and other proteins that have been engineered by rational or combinatorial approaches. The section finishes with a chapter on the use of non-natural amino acids in protein engineering. Computational Protein Design The second half of the book introduces computational protein design, beginning with a chapter on computational and informatics algorithms used in protein engineering. Core components of computational protein design are then discussed in detail, and examples of heuristic protein design are provided. Subsequent chapters present examples of how computational design has played a critical role in advancing the field of protein engineering. Concluding with a chapter outlining current challenges in the field, this book makes computational protein design and diversity-oriented protein engineering widely accessible to a broad audience in academia and industry alike.

The activity of many biopharmaceutical polymers is dependent on conformation, and the next several years will see increased interest in the conformational analysis of these polymers resulting from the development of biosimilar or "follow-on" biological products. While a wide variety of approaches to analysis exists, finding the most viable ones would be much easier with a consolidated reference that details the benefits and cost of each approach, with an emphasis on real results and real products.

Explores the Growing Role of Conformational Analysis in Comparing Generic Biopharmaceuticals

Approaches to the Conformational Analysis of Biopharmaceuticals gathers the most useful techniques and methods into a single volume, putting the greatest emphasis on those approaches that have proven the most fruitful. Rather than cover specific uses of techniques in detail, this book provides commercial biotechnologists and researchers with the information and references they need to make good choices about the technology they choose to use. With a large number of references that direct readers to primary source material, it includes studies drawn from the gamut of current literature, covering physical methods, such as differential scanning calorimetry, light scanning, and analytical ultracentrifugation. It also addresses chemical methods, such as hydrogen deuterium exchange and trace labeling, along with infrared, ultraviolet, and Raman spectroscopy.

Written by Roger Lundblad, a true pioneer in protein science, this volume supplies the necessary information researchers need to access when deciding on the most cost-effective approach, including:

• Comparability of biopharmaceuticals
• Characterization of follow-on biologics
• Quality attributes of protein biopharmaceuticals
• Confrontational analysis of biopharmaceutical products

With a clear focus on relevant commercial biotechnology, this book belongs on the shelves of those serious researchers who are paving the way for the next generation of biopharmaceutical polymers.

The Protein Reviews series serves as a publication vehicle for reviews that focus on crucial contemporary and vital aspects of protein structure, function, evolution and genetics. Volumes are published online first, prior to publication in a printed book. Chapters are selected according to their importance to the understanding of biological systems, relevance to the unravelling of issues associated with health and disease, or impact on scientific or technological advances and developments. Volume 22 presents six review chapters authored by experts in related fields. The first chapter covers carotenoid-protein interactions. Chapter two addresses the non-continuum of eukaryotic transcriptional regulation. The third chapter reviews the structure of the regulatory and catalytic domains of the photoreceptor phosphodiesterase (PDE6) holoenzyme. Chapter four reviews the current knowledge on small molecule compounds that have been evaluated as rhodopsin modulators to be considered as leads for the development of novel therapies for retinitis pigmentosa. Chapter five deals with Plasticity-associated functionality and inhibition of the HIV protease. Finally, chapter six covers single-run catalysis and kinetic control of human telomerase holoenzyme. This volume is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

Often considered the workhorse of the cellular machinery, proteins are responsible for functions ranging from molecular motors to signaling. The broad recognition of their involvement in all cellular processes has led to focused efforts to predict their functions from sequences, and if available, from their structures. An overview of current research directions, Computational Protein-Protein Interactions examines topics in the prediction of protein-protein interactions, including interference with protein-protein interactions and their design. Explores Computational Approaches to Understanding Protein-Protein Interactions Outlining fundamental and applied aspects of the usefulness of computations when approaching protein-protein interactions, this book incorporates different views of the same biochemical problem from sequence to structure to energetics. It covers protein-protein interaction prediction and dynamics, design, drug design for inhibition, and uses for the prediction of function. The text provides general chapters that overview the topic and also includes advanced material. The chapters detail the complexity of protein interaction studies and discuss potential caveats. Addresses the Next Big Problem in Molecular Biology While it is important to predict protein associations, this is a daunting task. Edited by two experts in the field and containing contributions from those at the forefront of research, the book provides a basic outline of major directions in computational protein-protein interactions research at the heart of functional genomics and crucial for drug discovery. It addresses the next big problem in molecular biology: how to create links between all the pieces of the cell jigsaw puzzle.

This detailed book expands upon the previous edition with a collection of methods for those performing experimental work on small GTPases of the Rho family. Split into four sections, the volume explores computational modeling and imaging procedures, biochemical methods related to post-translational modifications of Rho GTPases as well as some high throughput methods, functional assays that allow for monitoring the consequences of manipulating Rho GTPases in a variety of cell types and cell biology processes, and techniques specifically designed for studies in selected non-mammalian model organisms (zebrafish, social ameba, plants and algae). 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 laboratory protocols, and tips on trouble shooting and avoiding known pitfalls. Authoritative and up-to-date, Rho GTPases: Methods and Protocols, Second Edition constitutes an invaluable tool for all those with an interest in this remarkable family of signaling proteins.

This book presents a new approach to the Protein Folding Problem. It starts with a clear description of what the protein folding problem involves. Then, it suggests non-conventional answers to some of the questions posed. In particular, it emphasizes the importance of hydrophilic interactions and hydrophilic forces, rather than the hydrophobic effects, for the stability of the native structure of proteins, as well for the speed of the folding process.

The Coronin Family of Proteins Christoph S. Clemen, * Vasily Rybakin and Ludwig Eichinger he coronins, first described in Dictyostelium discoideum in 1991, have meanwhile been detected in all eukaryotes except plants. They belong to the superfamily of WD40-repeat Tproteins and represent a large family of proteins, which are often involved in cytoskeletal functions. Phylogenetic studies clearly distinguish 12 subfamilies of which six exclusively occur in vertebrates. In the present book we have made a sincere attempt to provide a comprehensive overview on all aspects of coronin proteins including history, structure, subcellular localization and function in different organisms. In addition, we also included a general overview on the WD40 family of proteins and the structurally related Kelch family. The book should be of interest for scientists outside the field, but is more importantly intended as a fast and competent guide for newcomers as well as doctoral and postdoctoral scientists to coronin research in all its facets. The book is divided into four major sections. It provides in the first part an introduction into two superfamilies of proteins with p-propellers, the WD40- and the Kelch-family. Lynn Cooley and Andrew M. Hudson provide evidence that the WD40- and Kelch-repeat families most likely did Figure 1. Condensed phylogenetic tree of the coronin protein family. The tree constitutes the basis of a new nomenclature and shows the evolutionary relationship of the twelve coronin subfamilies {CRN1-CRN12). See also chapter 11-2 by Reginald O. Morgan and M. Pilar Fernandez

This book is unique; the factual content and ideas it expounds are only just beginning to be touched upon in standard texts. Protein Electron Transfer is a major collaborative effort by leading experts and explores the molecular basis of the rapidly expan

This book presents a new approach to the Protein Folding Problem. It starts with a clear description of what the protein folding problem involves. Then, it suggests non-conventional answers to some of the questions posed. In particular, it emphasizes the importance of hydrophilic interactions and hydrophilic forces, rather than the hydrophobic effects, for the stability of the native structure of proteins, as well for the speed of the folding process.

This volume explores current technologies used to investigate the formation, insertion, and function of metalloclusters associated with proteins. Chapters describe relevant topics about Fe-S cluster metabolism are explored through genetic, biochemical, spectroscopic methods. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Fe-S Proteins: Methods and Protocols aims to be a useful practical guide to researchers to help further their study in this field.

Given the immense progress achieved in elucidating protein protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein protein interactions from the analysis of protein protein complex structures and interfaces. What are the driving forces for protein protein association? How can we extract the mechanism of specific recognition from studying protein protein interfaces? How can this knowledge be used to predict and design protein protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein protein interactions, and how can we influence protein protein interactions by mutagenesis and small-molecule drugs or peptide mimetics? The book consists of about 15 review chapters, written by experts, on the characterization of protein protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein protein complex structures (docking and homology modeling of complexes, etc.) and design of protein protein interactions. It serves as a bridge between studying/analyzing protein protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins. The Ten Most Wanted Solutions in Protein Bioinformatics considers the ten most significant problems occupying those looking to identify the biological properties and functional roles of proteins. -Problem One considers the challenge involved with detecting the existence of an evolutionary relationship between proteins. -Two and Three studies the detection of local similarities between protein sequences and analysis in order to determine functional assignment. -Four, Five, and Six look at how the knowledge of the three-dimensional structures of proteins can be experimentally determined or inferred, and then exploited to understand the role of a protein. -Seven and Eight explore how proteins interact with each other and with ligands, both physically and logically. -Nine moves us out of the realm of observation to discuss the possibility of designing completely new proteins tailored to specific tasks. -And lastly, Problem Ten considers ways to modify the functional properties of proteins. After summarizing each problem, the author looks at and evaluates the current approaches being utilized, before going on to consider some potential approaches. introbul Features

Given the immense progress achieved in elucidating protein protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein protein interactions from the analysis of protein protein complex structures and interfaces. What are the driving forces for protein protein association? How can we extract the mechanism of specific recognition from studying protein protein interfaces? How can this knowledge be used to predict and design protein protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein protein interactions, and how can we influence protein protein interactions by mutagenesis and small-molecule drugs or peptide mimetics? The book consists of about 15 review chapters, written by experts, on the characterization of protein protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein protein complex structures (docking and homology modeling of complexes, etc.) and design of protein protein interactions. It serves as a bridge between studying/analyzing protein protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure. The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

The broad range of G protein-coupled receptors (GPCRs) encompasses all areas of modern medicine and have an enormous impact on the process of drug development. Using disease-oriented methods to cover everything from screening to expression and crystallization, G Protein-Coupled Receptors in Drug Discovery describes the physiological roles of GPCRs and their involvement in various human diseases. The book presents current approaches in drug discovery that include target selection, establishment of screening and functional assays. It also covers recombinant GPCR expression for drug screening and structural biology, different methods for structural characterization of GPCRs, and the importance of bioinformatics. The book has been carefully edited to avoid overlapping information, some duplication has been intentionally permitted so that each chapter can function as an independent unit. Providing in-depth discussions on structure and dynamics of GPCRs, this book outlines the importance of the GPCRs to drug discovery in general and drug targets specifically. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.

Omics is an emerging and exciting area in the field of science and medicine. Numerous promising developments have been elucidated using omics (including genomics, transcriptomics, epigenomics, proteomics, metabolomics, interactomics, cytomics and bioinformatics) in cancer research. The development of high-throughput technologies that permit the solution of deciphering cancer from higher dimensionality will provide a knowledge base which changes the face of cancer understanding and therapeutics.

This is the first book to provide such a comprehensive coverage of a rapidly evolving area written by leading experts in the field of omics. It complies and details cutting-edge cancer research that covers the broad advances in the field and its application from cancer-associated gene discovery to drug target validation. It also highlights the potential of using integration approach for cancer research.

This unique and timely book provides a thorough overview of developing omics, which will appeal to anyone involved in cancer research. It will be a useful reference book for graduate students of different subjects (medicine, biology, engineering, etc) and senior scientists interested in the fascinating area of advanced technologies in cancer research.

Readership: This is a precious book for all types of readers cancer researchers, oncologists, pathologists, biologists, clinical chemists, pharmacologists, pharmaceutical specialists, biostatisticians, and bioinformaticists who want to expand their knowledge in cancer research."

First published in 1991, Chemical Reagents for Protein Modification, 2nd Edition provides a unique combination of theoretical and practical considerations for the use of chemical reagents for site-specific modification of proteins. The book is divided into three sections, with the first section describing general techniques, including information on the organic chemistry of the various modification reactions; the separation and characterization of site-specific modified proteins, including applications to proteins separated by electrophoresis followed by blotting; the specific chemical cleavage of peptide bonds in proteins; the separation of peptides by high-performance liquid chromatography and electrophoresis; and the use of chemical reagents to assess conformational change in proteins. The second section provides an encyclopedic description of reagents and reactions for the site-specific modification of individual amino acid residues in proteins. The final section presents descriptions of the use of chemical reagents to label biologically significant sites in proteins, including enzyme active sites and the use of covalent cross-linking to measure protein-protein interactions. Particular emphasis is placed on the use of photoaffinity reagents. The book will be an extremely useful research tool for all investigators interested in the solution chemistry of proteins.

Based upon a workshop entitled "The Small HSP World" held in Quebec 2-5 October 2014. Twenty-five scientists provided chapters for the book. The chapters are from the best scientists currently working in this field. These colleagues include Arrigo, Benesch, Benjamin, Buchner-Haslbeck-Weinkauf, Benndorf, Boelens, Carra, Chang, Currie, Ecroyd, Emanuelsson, Fu, Garrido, Golenhofen, Gusev, Hightower, Kampinga, Lavoie, MacRae, Quinlan, Tanguay, Vierling, Vigh, Weeks and Wu. Briefly, the book starts with the structure of small heat shock proteins, moving to their functions and finishing with their involvement in diseases. Although this is quite broad, the structural aspect will be the unifying theme of the book.

This book presents a compilation of methods that detail improved protein and peptide sample preparation and identification. Chapters guide readers through methods for depletion of myofibril-associated proteins, peptide sample preparation in urinary proteomics, purification of targeted proteins from native tissues, fractionation strategies for protein analysis, and GeLC-MS as a sample preparation method for sample preparation for proteomics using minimal amount of tissue. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Tissue Proteomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This detailed collection explores techniques involved in the main strategies of nanopore sensing, such as translocation, analyte trapping, and interactions with external binding sites. Opening with a section on nanopore design and nanopore production, the book continues with parts devoted to various biological nanopores, nanopore engineering, and their uses in single molecule sensing, computational methods to study intrinsic nanopore behavior, characterizing the specific translocation activity of a vesicle particle through a nanopore, as well as the use of the technique droplet interface bilayer (DIB) in nanopore and membrane biophysical studies. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Nanopore Technology: Methods and Protocols, with its focus on nanopore technology and biomolecule characterization, will hold the interest of the biophysicists, biochemists, bioengineers, and molecular biologists who are working toward further understanding this key field of research.

A common approach to understanding the functional repertoire of a genome is through functional genomics. With systems biology burgeoning, bioinformatics has grown to a larger extent for plant genomes where several applications in the form of protein-protein interactions (PPI) are used to predict the function of proteins. With plant genes evolutionarily conserved, the science of bioinformatics in agriculture has caught interest with myriad of applications taken from bench side to in silico studies. A multitude of technologies in the form of gene analysis, biochemical pathways and molecular techniques have been exploited to an extent that they consume less time and have been cost-effective to use. As genomes are being sequenced, there is an increased amount of expression data being generated from time to time matching the need to link the expression profiles and phenotypic variation to the underlying genomic variation. This would allow us to identify candidate genes and understand the molecular basis/phenotypic variation of traits. While many bioinformatics methods like expression and whole genome sequence data of organisms in biological databases have been used in plants, we felt a common reference showcasing the reviews for such analysis is wanting. We envisage that this dearth would be facilitated in the form of this Springer book on Agricultural Bioinformatics. We thank all the authors and the publishers Springer, Germany for providing us an opportunity to review the bioinformatics works that the authors have carried in the recent past and hope the readers would find this book attention grabbing.

This detailed collection gathers both established and recent technical procedures to study the Endosomal Sorting Complex Required for Transport (ESCRT) complexes in a wide range of biological systems: Archaea, A. thaliana, U. maydis, S. cerevisiae, S. pombe, C. elegans, D. melanogaster, and mammalian cells. Opening with a section on imaging techniques, the book continues with chapters covering biochemical approaches presenting strategies for production and characterization of recombinant ESCRT proteins, or of specific ESCRT protein domains, as well as genetic and proteomic experimental approaches. Written for the highly successful Methods in Molecular Biology series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, The ESCRT Complexes: Methods and Protocols serves as a compact guide for researchers interested in establishing an integrated approach to investigate the ESCRT machinery functions in cell biology.