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.

The Physics of Protein Structure and Dynamics

The Physics of Protein Structure and Dynamics
Author: Reinhard Schweitzer-Stenner
Publisher: Elsevier
Total Pages: 328
Release: 2024-09-23
Genre: Science
ISBN: 0443159653

The Physics of Protein Structure and Dynamics looks at various aspects of protein structure and dynamics from a physico-chemical point of view. It goes into some depth regarding the description of non-covalent forces that determine the relative stability of folded and unfolded proteins. Anharmonic protein dynamics involving motions between different minima of a rugged Gibbs energy landscape is described in great detail. The book combines various aspects of the protein folding/unfolding processes with an overview of intrinsically disordered proteins, which have attracted considerable interest of the protein community over the last 25 years but are thus far underrepresented in classroom-oriented textbooks. The book looks at protein folding and intrinsically disordered proteins as heavily interrelated topics that need to be viewed together. Furthermore, it presents some basic physico-chemical aspects of protein/peptide self-assembly into nanoscale fibrils. Intrinsically disordered peptides and proteins play a major role particularly in aggregation and self-assembly processes that lead to various diseases (Alzheimer, Parkinson, Huntington, Mad-Cow). Therefore, the relevance of protein disorder for protein self-assembly deserves a closer look. Protein self-assembly cannot be separated from protein folding since it is frequently the product of misfolding. With regard to modern theories, the folding processes are linked to insights on protein dynamics and the discovered relationship between proteins and spin glasses. - The readers will benefit from being provided with an in-depth overview of the physical concepts that govern different aspects of protein folding, disorder and self-assembly. By emphasizing the relationship between these issues, the approach adds a holistic character to the book - The book is to a major extent mathematically based. Mathematics is part of the language of physicists and physical chemists which cannot be properly substituted by words - For instructors, the book will offer a unique source for her/his teaching of current protein physics issues - The way how the book will be constructed (multiple references to primary literature with DOI links, literature-based problem sets and topics for discussion) will facilitate a learning process suitable for research-oriented students - Problem solving frequently requires the writing of short computer programs, something that is underemphasized in chemistry and biochemistry education (with the exception of computationally trained students, of course)

Fuzziness

Fuzziness
Author: Monika Fuxreiter
Publisher: Springer Science & Business Media
Total Pages: 210
Release: 2012-03-07
Genre: Medical
ISBN: 1461406595

Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.

Protein Folding, Misfolding and Aggregation

Protein Folding, Misfolding and Aggregation
Author: Victor Muñoz
Publisher: Royal Society of Chemistry
Total Pages: 289
Release: 2008-06-24
Genre: Science
ISBN: 1847558283

Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods have evolved to permit resolving fast processes of folding reactions and visualizing single molecules during folding. The findings from these novel experiments and detailed computer simulations have confirmed the main predictions of analytical theory of protein folding. In summary, protein folding research has finally acquired the status of a truly quantitative science, paving the way for more exciting developments in the near future. This unique book covers all the modern approaches and the many advances experienced in the field during the last 10 years. There is also much emphasis on computational methods and studies of protein aggregation which have really flourished in the last decade. It includes chapters in the areas that have witnessed major developments and are written by top experts including:computer simulations of folding, fast folding, single molecule spectroscopy, protein design, aggregation studies (both computational and experimental). Readers will obtain a unique perspective of the problems faced in the biophysical study of protein conformational behaviour in aqueous solution and how these problems are being solved with a multidisciplinary approach that combines theory, experiment and computer simulations. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches is essential reading for graduate students actively involved in protein folding research, other scientists interested in the recent progress of the field and instructors revamping the protein folding section of their biochemistry and biophysics courses.

Protein Physics

Protein Physics
Author: Alexei V. Finkelstein
Publisher: Elsevier
Total Pages: 530
Release: 2016-06-22
Genre: Science
ISBN: 0081012365

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

Protein Oxidation and Aging

Protein Oxidation and Aging
Author: Tilman Grune
Publisher: John Wiley & Sons
Total Pages: 494
Release: 2012-11-07
Genre: Science
ISBN: 111849301X

Reviews our current understanding of the role of protein oxidation in aging and age-related diseases Protein oxidation is at the core of the aging process. Setting forth a variety of new methods and approaches, this book helps researchers conveniently by exploring the aging process and developing more effective therapies to prevent or treat age-related diseases. There have been many studies dedicated to the relationship between protein oxidation and age-related pathology; now it is possible for researchers and readers to learn new techniques as utilizing protein oxidation products as biomarkers for aging. Protein Oxidation and Aging begins with a description of the tremendous variety of protein oxidation products. Furthermore, it covers: Major aspects of the protein oxidation process Cellular mechanisms for managing oxidized proteins Role of protein oxidation in aging Influence of genetic and environmental factors on protein oxidation Measuring protein oxidation in the aging process Protein oxidation in age-related diseases References at the end of each chapter serve as a gateway to the growing body of original research studies and reviews in the field.

Protein Families

Protein Families
Author: Christine A. Orengo
Publisher: John Wiley & Sons
Total Pages: 566
Release: 2014-02-03
Genre: Science
ISBN: 0470624221

New insights into the evolution and nature of proteins Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family. Edited and authored by leading international experts, Protein Families offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families. Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives. Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton. All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field. Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.

Protein Aggregation in Bacteria

Protein Aggregation in Bacteria
Author: Silvia Maria Doglia
Publisher: John Wiley & Sons
Total Pages: 300
Release: 2014-04-03
Genre: Science
ISBN: 1118855035

Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies—and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria Physiological importance and consequences of aggregation for the bacterial cell Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.

Amino Acids, Peptides and Proteins

Amino Acids, Peptides and Proteins
Author: Maxim Ryadnov
Publisher: Royal Society of Chemistry
Total Pages: 252
Release: 2014-12-09
Genre: Science
ISBN: 184973982X

Amino Acids, Peptides and Proteins comprises a comprehensive and critical review of significant developments at this biology/chemistry interface. Each volume of this Specialist Periodical Report opens with an overview of amino acids and their applications. Each chapter incorporates current trends of the reviewed topic and the author's outlook of future perspectives. This is to facilitate the monitoring of the covered area and their potential expansion with the inclusion of other specialist reports in subsequent volumes. All chapters are compiled by leading researchers in their subject areas, which presents this series as an appealing source of information for the research community in both academia and industry.