The Unfolded Protein Response

The Unfolded Protein Response
Author: Roberto Pérez Torrado
Publisher:
Total Pages: 332
Release: 2022
Genre: Electronic books
ISBN: 9781071617328

This volume is divided in six section covering the most experimental approaches involved in the study of the unfolded protein response (UPR) pathway. Chapters detail determination of unfolded protein levels, methods to study UPR signal transmission, analysing the outcomes of the UPR pathway activation, UPR studies in mammalian models, UPR in alternative models, and UPR and disease. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, The Unfolded Protein Response: Methods and Protocols aims to describe key methods and approaches used in the study of the UPR pathway and its complex cellular implications. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Unfolded Proteins

Unfolded Proteins
Author:
Publisher: Elsevier
Total Pages: 422
Release: 2002-11-04
Genre: Science
ISBN: 0080524524

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

Unfolded Proteins

Unfolded Proteins
Author: Trevor P. Creamer
Publisher: Nova Publishers
Total Pages: 330
Release: 2008
Genre: Science
ISBN: 9781604561074

The word revolution has a number of definitions (The American Heritage Dictionary, 2006). The one most pertinent to this series and volume is 'a sudden or momentous change in a situation'. Recent years have seen an unprecedented explosion of interest in unfolded proteins in all of their various forms. Coupled with this increase in interest we have seen momentous changes in the way unfolded proteins are viewed. Two particular paradigms have come under close scrutiny: unfolded proteins are disordered random coils devoid of persistent structure, and protein function first requires protein structure. The first of these is currently a hotly debated subject. The second paradigm we can safely claim has been overturned. There is a second definition of revolution that is quite relevant to a significant portion of the work reviewed herein, in particular those chapters dealing with local and persistent structure in unfolded proteins. That definition is 'a turning or rotational motion about an axis' (The American Heritage Dictionary, 2006). About four decades ago, Charles Tanford (1968) demonstrated that highly denatured proteins possess hydrodynamic properties consistent with Paul Flory's random coil (Flory, 1969). Given that the Flory random coil definition included the stipulation that conformers making up the denatured state ensemble would differ in energy by just a few kT, there has been the assumption that denatured states must therefore be completely random in nature with no persistent structure or biases towards particular conformers. Notably however, Tanford did note the random coil-like hydrodynamic data he obtained did not necessarily rule out the presence of structure in denatured proteins (Tanford, 1968). Around the same time, Sam Krimm and M. Lois Tiffany noted that the CD spectra they obtained for proteins in the presence of high concentration of chemical denaturants had similarities to spectra obtained for homopolymers of proline, lysine, and glutamic acid in water (Tiffany and Krimm, 1968a, 1968b, 1973, 1974). Homopolymers of these residues were known to adopt the left-handed polyproline II conformation, leading Tiffany and Krimm to hypothesise that highly denatured proteins possess significant polyproline II helix content. Of these two views, that espousing the lack of structure in denatured proteins became more widely adopted and was, over time, adopted as a central paradigm in protein folding. As several of the chapters in this volume note, a Tiffany and Krimm-like view appears to be, to some extent, the more correct one. The level to which it is correct is still unknown, although it is clear that the polyproline II helical conformation is not the only, perhaps not even the most common, persistent conformation present in unfolded proteins. Thus we have come through a full circle or revolution. (from the preface)

Proteins

Proteins
Author: Thomas E. Creighton
Publisher: Macmillan
Total Pages: 534
Release: 1993
Genre: Medical
ISBN: 9780716770305

Organized on a combined basis of chronology and of structural and functional hierarchy, This comprehensive text describes all aspects of proteins--biosynthesis, evolution, dynamics, ligand binding, catalysis, and energy transduction--not just their structures. This edition (first was 1984) is thoroughly updated--especially in the area of protein biosynthesis--and features end-of-chapter exercises and problems, many of which require the student to consult the cited literature in order to obtain the answer. Annotation copyright by Book News, Inc., Portland, OR

Protein Misfolding, Aggregation and Conformational Diseases

Protein Misfolding, Aggregation and Conformational Diseases
Author: Vladimir N. Uversky
Publisher: Springer Science & Business Media
Total Pages: 538
Release: 2007-05-26
Genre: Medical
ISBN: 0387365346

The second volume continues to fill the gap in protein review and protocol literature. It does this while summarizing recent achievements in the understanding of the relationships between protein misfoldings, aggregation, and development of protein deposition disorders. The focus of Part B is the molecular basis of differential disorders.

Instrumental Analysis of Intrinsically Disordered Proteins

Instrumental Analysis of Intrinsically Disordered Proteins
Author: Vladimir Uversky
Publisher: John Wiley & Sons
Total Pages: 792
Release: 2011-01-31
Genre: Science
ISBN: 0470602600

Instrumental techniques for analyzing intrinsically disordered proteins The recently recognized phenomenon of protein intrinsic disorder is gaining significant interest among researchers, especially as the number of proteins and protein domains that have been shown to be intrinsically disordered rapidly grows. The first reference to tackle this little-documented area, Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation provides researchers with a much-needed, comprehensive summary of recent achievements in the methods for structural characterization of intrinsically disordered proteins (IDPs). Chapters discuss: Assessment of IDPs in the living cell Spectroscopic techniques for the analysis of IDPs, including NMR and EPR spectroscopies, FTIR, circular dichroism, fluorescence spectroscopy, vibrational methods, and single-molecule analysis Single-molecule techniques applied to the study of IDPs Assessment of IDP size and shape Tools for the analysis of IDP conformational stability Mass spectrometry Approaches for expression and purification of IDPs With contributions from an international selection of leading researchers, Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation fills an important need in a rapidly growing field. It is required reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, physiologists, and specialists in drug design and development, proteomics, and molecular medicine with an interest in proteins and peptides.

Protein Folding and Misfolding

Protein Folding and Misfolding
Author: Heinz Fabian
Publisher: Springer Science & Business Media
Total Pages: 257
Release: 2011-09-18
Genre: Science
ISBN: 3642222307

Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field. The chapters are not intended to give exhaustive reviews of the literature but, instead to illustrate examples demonstrating the sort of information, which infrared techniques can provide and how this information can be extracted from the experimental data. By discussing the strengths and limitations of the infrared approaches for the investigation of folding and misfolding mechanisms this book helps the reader to evaluate whether a particular system is appropriate for studies by infrared spectroscopy and which specific advantages the techniques offer to solve specific problems.

Protein and Peptide Folding, Misfolding, and Non-Folding

Protein and Peptide Folding, Misfolding, and Non-Folding
Author: Reinhard Schweitzer-Stenner
Publisher: John Wiley & Sons
Total Pages: 484
Release: 2012-02-08
Genre: Science
ISBN: 1118183355

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.