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This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.

This book describes the development of novel protein–RNA-binding assays and their applications in a high-throughput manner for the identification of small-molecule modulators of protein–RNA interactions to treat cancer and COVID-19. Modulating protein–RNA interactions with small molecules is expected to provide novel biological insights of the interrelation of diseases with the protein–RNA interactome. The modulations may also be exploited therapeutically. For these reasons, the development of a simple, reliable, and sensitive protein–RNA-binding assay is necessary for high-throughput screening to discover new effective chemical entities capable of acting on diverse protein–RNA interactions. This book discusses the discovery of small-molecule modulators targeting protein–RNA interactions that are potentially valuable to treat cancer and COVID-19 by constructing novel high-throughput screening methods. The results of this dissertation provide valuable insights into the regulation of protein–RNA interactions in chemical biology and drug development.

Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. - Includes comprehensive coverage on molecular biology - Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided - Contains contributions from renowned experts in the field

This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.

The formation of disulphide bonds is probably the most influential modification of proteins. These bonds are unique among post-translational modifications of proteins as they can covalently link cysteine residues far apart in the primary sequence of a protein. This has the potential to convey stability to otherwise marginally stable structures of proteins. However, the reactivity of cysteines comes at a price: the potential to form incorrect disulphide bonds, interfere with folding, or even cause aggregation. An elaborate set of cellular machinery exists to catalyze and guide this process: facilitating bond formation, inhibiting unwanted pairings and scrutinizing the outcomes. Only in recent years has it become clear how intimately connected this cellular machinery is with protein folding helpers, organellar redox balance and cellular homeostasis as a whole. This book comprehensively covers the basic principles of disulphide bond formation in proteins and describes the enzymes involved in the correct oxidative folding of cysteine-containing proteins. The biotechnological and pharmaceutical relevance of proteins, their variants and synthetic replicates is continuously increasing. Consequently this book is an invaluable resource for protein chemists involved in realted research and production.

Early Stage Protein Misfolding and Amyloid Aggregation, Volume 329, the latest in the International Review of Cell and Molecular Biology series presents comprehensive reviews and current advances in cell and molecular biology, including articles that address the structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. The series has a worldwide readership and maintains a high standard by publishing invited articles on important and timely topics as authored by prominent cell and molecular biologists. - Provides comprehensive reviews and current advances - Presents a wide range of perspectives on specific subjects - Includes valuable reference material for advanced undergraduates, graduate students, and professional scientists

This book provides essential information on improving protein folding/stability, which is a result of the balance between the intra-molecular interactions of protein functional groups and their interactions with the solvent environment. The protein folding solvent environment mainly consists of salts, small molecule compounds, metabolites, molecular chaperones and other chemical species. Therefore, subtle change in the composition of the environment will alter the protein folding process. The importance of the solvent environment in protein folding is precisely due to the fact that various disease-causing proteopathies can be reversed by manipulating the solvent environment of the malfolded proteins. Hostile environmental stresses represent one of the basic causes of such challenges in protein folding or misfolding. Since cells commonly encounter extreme environmental fluctuations, it is crucial that they equip themselves with strategies to circumvent the hostile environmental conditions. Nature has developed many strategies to ensure that the complex and challenging protein folding reaction occurs with adequate efficiency and fidelity for the success of the organism. Among the strategies employed in a wide range of species and cell types is the elaboration of small organic molecules called osmolytes. Additionally, recent advances have also revealed that certain specific osmolytes might be key biomarkers of cancer, infectious diseases and vaccine flocculation. In fact, a large pool of data has been generated regarding their potential for the therapeutic intervention of neurodegenerative diseases and other metabolic disorders caused by protein aggregation or proteostasis failure. Reflecting the multiple applications of these small molecules in the health and other industries, this book combines contributions by respected leaders in the field and will help to inspire college students, basic researchers, and clinicians to translate these biological roles of osmolytes into clinical practice. It will also shed light on some important future prospects of osmolytes like their role as drug excipients and provide a deeper understanding of their mechanism of action in the prevention of neuro-degenerative diseases.

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.

This succinct volume addresses the production of inactive, potentially toxic proteins in the absence of correct protein folding and the resultant neurodegenerative diseases. Other topics include intrinsic disorder in protein structure and function and the effects of molten globules on protein toxicity. This concise and yet thorough text also discusses using toxin structure as a model for studying structural and functional aspects of protein chemistry. Protein Toxins in Modeling Biochemistry, a SpringerBrief, is essential reading for advanced researchers, scientists and advanced graduate students interested in protein chemistry and related areas of biochemistry and molecular science.

This book is a neurochemistry-based companion for Protein Misfolding and Neurodegenerative Diseases: Molecular Targets, an Elsevier title by the same author publishing in December 2014. While the first book focuses on biology and molecular targets, this companion book describes how these targets are regulated by small molecules and disease-modifying compounds. The book begins with a brief introduction to how key proteins become dysfunctional, and each subsequent chapter describes major disease mechanisms in Alzheimer's and other tauopathies. Properties and development status of these molecular targets and disease mechanisms are thoroughly described, as are small molecule effectors of autophagy and dis-aggregating agents. - Written to provide comprehensive coverage of neurodegenerative disease-modifying compounds - Provides discipline-specific chapters that cover medicinal chemistry and clinical applications - Provides an overview of more than 200 chemical classes and lead compounds, acting on selected molecular targets that are of relevance to any neurodegenerative disorder - Coverage of misfolding diseases, chaperone proteins, ubiquitination and autophagy/oncology makes this book suitable for structural neurochemists, chemists, biologists, non-CNS scientists, and scientists interested in drug discovery

The book will discuss classes of proteins and their folding, as well as the involvement of bioinformatics in solving the protein folding problem. In vivo and in vitro folding mechanisms are examined, as well as the failures of in vitro folding, a mechanism helpful in understanding disease caused by misfolding. The role of energy landscapes is also discussed and the computational approaches to these landscapes.

Molecular chaperones are a fundamental group of proteins that have been identified only relatively recently. They are key components of a protein quality machinery in the cell which insures that the folding process of any newly-synthesized polypeptide chain results in the formation of a properly folded protein and that the folded protein is maintained in an active conformation throughout its functional lifetime. Molecular chaperones have been shown to play essential roles in cell viability under both normal and stress conditions. Chaperones can also assist in the unfolding and degradation of misfolded proteins and in disaggregating preformed protein aggregates. Chaperones are also involved in other cellular functions including protein translocation across membranes, vesicle fusion events, and protein secretion. In recent years, tremendous advances have been made in our understanding of the biology, biochemistry, and biophysics of function of molecular chaperones. In addition, recent technical developments in the fields of proteomics and genomics allowed us to obtain a global view of chaperone interaction networks. Finally, there is now a growing interest in the role of molecular chaperones in diseases. This book will provide a comprehensive analysis of the structure and function of the diverse systems of molecular chaperones and their role in cell stress responses and in diseases from a global network perspective. ​

Sheds new light on intrinsically disordered proteins and peptides, including their role in neurodegenerative diseases With the discovery of intrinsically disordered proteins and peptides (IDPs), researchers realized that proteins do not necessarily adopt a well defined secondary and tertiary structure in order to perform biological functions. In fact, IDPs play biologically relevant roles, acting as inhibitors, scavengers, and even facilitating DNA/RNA-protein interactions. Due to their propensity for self-aggregation and fibril formation, some IDPs are involved in neurodegenerative diseases such as Parkinson's and Alzheimer's. With contributions from leading researchers, this text reviews the most recent studies, encapsulating our understanding of IDPs. The authors explain how the growing body of IDP research is building our knowledge of the folding process, the binding of ligands to receptor molecules, and peptide self-aggregation. Readers will discover a variety of experimental, theoretical, and computational approaches used to better understand the properties and function of IDPs. Moreover, they'll discover the role of IDPs in human disease and as drug targets. Protein and Peptide Folding, Misfolding, and Non-Folding begins with an introduction that explains why research on IDPs has significantly expanded in the past few years. Next, the book is divided into three sections: Conformational Analysis of Unfolded States Disordered Peptides and Molecular Recognition Aggregation of Disordered Peptides Throughout the book, detailed figures help readers understand the structure, properties, and function of IDPs. References at the end of each chapter serve as a gateway to the growing body of literature in the field. With the publication of Protein and Peptide Folding, Misfolding, and Non-Folding, researchers now have a single place to discover IDPs, their diverse biological functions, and the many disciplines that have contributed to our evolving understanding of them.

A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy­ sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold­ ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap­ proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen­ tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam­ pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.

Assisting Oxidative Protein Folding: How Do Protein Disulphide-Isomerases Couple Conformational and Chemical Processes in Protein Folding?, by A. Katrine Wallis and Robert B. Freedman Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins, by Cordelia Schiene-Fischer, Tobias Aumüller and Gunter Fischer Small Heat-Shock Proteins: Paramedics of the Cell, by Gillian R. Hilton, Hadi Lioe, Florian Stengel, Andrew J. Baldwin und Justin L. P. Benesch Allostery in the Hsp70 Chaperone Proteins, by Erik R. P. Zuiderweg, Eric B. Bertelsen, Aikaterini Rousaki, Matthias P. Mayer, Jason E. Gestwicki and Atta Ahmad Hsp90: Structure and Function, by Sophie E. Jackson Extracellular Chaperones, by Rebecca A. Dabbs, Amy R. Wyatt, Justin J. Yerbury, Heath Ecroyd and Mark R. Wilson

The role of metal ions in protein folding and structure is a critical topic to a range of scientists in numerous fields, particularly those working in structural biology and bioinorganic chemistry, those studying protein folding and disease, and those involved in the molecular and cellular aspects of metals in biological systems. Protein Folding an

The use of thermodynamics in biological research can be equated to an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. - Elucidates the relationships between structure and energetics and their applications to molecular design, aiding researchers in the design of medically important molecules - Provides a'must-have'methods volume that keeps MIE buyers and online subscribers up-to-date with the latest research - Offers step-by-step lab instructions, including necessary equipment, from a global research community

In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. The use of thermodynamics in biological research is used as an'energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well.

Misfoldedaggregatedproteinoncewasconsideredasinterestingasyesterday'strash—a bothersome by-product of important and productive activities, to be disposed of and forgotten as quickly as possible. Yesterday's trash has become today's focus of cons- erable scienti?c interest for at least two reasons: (1) protein aggregates are at the core of a number of chronic degenerative diseases such as Alzheimer's disease, and (2) - gregation poses signi?cant obstacles to the manufacture of safe, ef?cacious, and stable protein products. As interest in protein misfolding, aggregation, and stability has soared beyond the core group of traditional protein-folding scientists, and as substantial scienti?c progress in understanding and controlling protein misfolding has been achieved, the need to summarize the state of the art became manifest. Although there are many excellent texts and edited collections on protein structure and folding, these volumes tend to relegate protein misfolding and aggregation to a minor role. Review articles and books focused on the biological role of protein aggregates in diseases have been published recently. Misbehaving Proteins: Protein (Mis)folding, Aggregation, and Stability differs from theseotherrecenteffortsinitsemphasisonfundamentalcomputationalandexperimental studies and in its linkage of disparate consequences of protein misfolding (e.g., from clinical manifestations to manufacturing headaches) to their common causes.

Protein Folding Kinetics - Biophysical Methods (2nd Edition) gives a deep insight into the principles and concepts of the kinetic and structural resolution of fast chemical and biophysical reactions of proteins with emphasis on protein-folding reactions. The study of fast protein-folding reactions and the understanding of the folding paradox have significantly advanced due to the recent development of new biophysical methods which allow not only kinetic resolution in the sub-millisecond time scale but also structural resolution with unprecedented precision. Pathways and structures of early and late folding events and the transition state structures of fast- and ultrafast-folding proteins can now be studied in far more detail. Important techniques include biophysical, chemical, molecular biological and mathematical methods, in particular protein engineering, Phi-value analysis, time-resolved circular dichroism, optical triggers and pulsed infrared LASER methods, pressure and temperature jump, ultrafast mixing, stopped flow and quenched flow, dielectric relaxation and electric-field-jump, acoustic relaxation, fluorescence- and isotope-labeling, H/D exchange methods, NMR line broadening and stopped-flow NMR, transition state theory, solutions of rate equations, and evolutionary computer programming. Protein Folding Kinetics - Biophysical Methods is written for students and researchers in biochemistry, biophysics, and related fields. Special features in the second edition: -Includes detailed information and 12 color figures on the high resolution of folding transition states. -Discusses structural determinants of the rate of protein folding on a timescale from microseconds to seconds. -Provides information on self-evolving computer programs for protein-folding simulations and protein-structure predictions.

Energetics of Biological Macromolecules, Part E focuses on methods related to allosteric enzymes and receptors, including fluorescent proves, spectroscopic methods and quantitative analysis as well as on cooperativity in protein folding. NMR and mass spectrometry methods are discussed. - Allosteric Enzymes and Receptors - Cooperativity in Protein Folding and Assembly

A variety of complementary techniques and approaches have been used to characterize peptide and protein unfolding induced by temperature, pressure, and solvent. Volume 62, Unfolded Proteins, assembles these complementary views to develop a more complete picture of denatured peptides and proteins. The unifying observation common to all chapters is the detection of preferred backbone confirmations in experimentally accessible unfolded states. - Peptide and protein unfolding induced by temperature, pressure, and solvent - Denatured peptides and proteins - Detection of preferred backbone confirmations in experimentally accessible unfolded states

One of the most intriguing discoveries in molecular biology in the last decade is the existence of an evolutionary conserved and essential system, consisting of molecular chaperones and folding catalysts, which promotes the folding of the proteins in the cell. This text summarizes our current knowledge of the cellular roles, the regulation and the