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Author : David Edward Wildes
Publisher :
ISBN 13 :
Total Pages : 402 pages
Book Rating : 4.:/5 (35 download)
Download or read book High Energy Conformations in Protein Folding and Binding written by David Edward Wildes and published by . This book was released on 2006 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Barry T. Nall
Publisher :
ISBN 13 :
Total Pages : 236 pages
Book Rating : 4.:/5 (319 download)
Download or read book Conformations and Forces in Protein Folding written by Barry T. Nall and published by . This book was released on 1991 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Richard A. Friesner
Publisher : John Wiley & Sons
ISBN 13 : 0471465232
Total Pages : 544 pages
Book Rating : 4.4/5 (714 download)
Download or read book Computational Methods for Protein Folding, Volume 120 written by Richard A. Friesner and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.
Author : Kenneth P. Murphy
Publisher : Springer Science & Business Media
ISBN 13 : 1592591930
Total Pages : 258 pages
Book Rating : 4.5/5 (925 download)
Download or read book Protein Structure, Stability, and Folding written by Kenneth P. Murphy and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.
Author : Monika Fuxreiter
Publisher : Springer Science & Business Media
ISBN 13 : 1461406595
Total Pages : 210 pages
Book Rating : 4.4/5 (614 download)
Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Thinh Luong
Publisher :
ISBN 13 :
Total Pages : 204 pages
Book Rating : 4.:/5 (127 download)
Download or read book Protein Folding Upon Binding and Conformational Rheostats written by Thinh Luong and published by . This book was released on 2021 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the work horses of the cell that perform the vast majority of functions essential for life. The mechanism by which proteins fold to their functional native state has been a subject of extensive research for more than 50 years now. Downhill folders are the class of proteins whose folding reaction is heterogeneous, non-cooperative, and happens without encountering a significant free energy barrier, resulting in ultrafast kinetics. The single ensemble of conformations of a global downhill folding protein moves gradually from highly disordered to the unique native structure when thermodynamic parameters that affect the protein's stability are changed (one-state folding). The gradual morphing of a one-state downhill folding protein structure in response to thermodynamic bias is referred to as a conformational rheostat. When such a conformational rheostat is coupled to binding an analyte, it can result in an ultrafast, broad band, and single-molecule analog biosensors. This thesis explores conformational rheostats as the mechanism behind the folding upon binding behavior of intrinsically disordered proteins and as broadband transducers towards engineering high-performance biosensors.The second chapter of this thesis describes a new methodology that we have developed to study the conformational landscape of intrinsically partially disordered proteins (IPDP). This methodology is inspired by the LEGO game, where the sequence of an IPDP is deconstructed into its local structural elements and their possible combinations based on the 3D structure the IPDP acquires upon binding its partners. The local structural elements are hence analogous to LEGO building blocks, and their combinations report on the interactions among them, like the complementary indentations of LEGO pieces. In particular, we chose the IPDP NCBD as model IPDP to develop the proof of concept for the method. Our results showed that even though the NCBD is highly flexible and apparently disordered, there are strong local signals and different sets of long-range transient interactions. These sets of interactions stabilize the overall fold and compete with one another hence resulting in a dynamic ensemble. The methodology developed in Chapter 2 is expected to be extremely useful in characterizing the incipient cooperativity of virtually any IPDP in their unbound form, a capability that is currently unavailable. Chapters 3 and 4 of this thesis deal with the design of a pH biosensor using the downhill folding protein gpW as a scaffold and unfolding coupled to ionization as a transducer. In chapter 3, a methodology for engineering conformational pH transducing into pH insensitive proteins using a histidine grafting approach was developed. The methodology was applied to the protein gpW to demonstrate an engineered, tunable broadband pH transducer based on the conformational rheostat mechanism. Chapter 4 explores general strategies for introducing fluorescence readouts capable of converting the gradual conformational changes of the rheostatic pH transducer into broadband fluorescence-based pH biosensors. Strategies that exploit the Förster Resonance Energy Transfer (FRET) and Photo Induced Electron Transfer (PET) mechanisms were explored as potential means to convert changes in conformation into suitable fluorescence signals were explored and characterized. We discovered that FRET signals using fluorophores in the visible (required for high-sensitivity biosensing) are insensitive to the localized conformational changes associated with conformational rheostats in native-like conditions. In contrast, the very short-range distance dependence of PET (
Author : Charis Ghelis
Publisher : Academic Press
ISBN 13 : 0323140920
Total Pages : 580 pages
Book Rating : 4.3/5 (231 download)
Download or read book Protein Folding written by Charis Ghelis and published by Academic Press. This book was released on 2012-12-02 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.
Author : Trevor P. Creamer
Publisher : Nova Publishers
ISBN 13 : 9781604561074
Total Pages : 330 pages
Book Rating : 4.5/5 (61 download)
Download or read book Unfolded Proteins written by Trevor P. Creamer and published by Nova Publishers. This book was released on 2008 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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)
Author : Prakash Saudagar
Publisher : Springer Nature
ISBN 13 : 9819920795
Total Pages : 287 pages
Book Rating : 4.8/5 (199 download)
Download or read book Protein Folding Dynamics and Stability written by Prakash Saudagar and published by Springer Nature. This book was released on 2023-05-27 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Katelyn Blair Connell
Publisher :
ISBN 13 :
Total Pages : 242 pages
Book Rating : 4.:/5 (769 download)
Download or read book Beyond the Native State written by Katelyn Blair Connell and published by . This book was released on 2010 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. The role of such intermediates is a matter of considerable debate, but it is clear that characterization of these partially folded species is crucial for understanding protein folding and function. A single amino acid change can convert E. coli ribonuclease H from a three-state folder that populates a kinetic intermediate to one that folds in an apparent two-state fashion. We have compared the folding trajectories of the three-state and two-state RNases H, proteins with the same native state topology but altered regional stability, using a protein engineering approach. Our data indicate that that both versions of RNase H fold through a similar trajectory with similar high-energy conformations. This suggests that formation of specific partially folded conformations may be a general feature of protein folding that can promote, rather than hinder, efficient folding. To better understand the robust role this high-energy species plays in folding, we set out to trap the transient intermediate of RNase H at equilibrium by selectively destabilizing the region of the protein known to be unfolded in this species. We find that the intermediate is undetectable in a series of HSQC's, revealing the dynamic nature of this partially folded form on the timescale of NMR detection. This result is in contrast to studies in which the structures of trapped intermediates are solved by NMR, indicating that the they are well-packed and native-like. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding. An analogous intermediate is populated on the kinetic trajectory of RNase H from T. thermophilus, an organism that grows optimally at a temperature 30 oC higher than E. coli. To understand how two proteins that share identical structures can function in such different environments, we looked for differences in their energetics by comparing equilibrium mimics of their high-energy intermediates. We find potential differences in the dynamic properties of the intermediates, which may provide insight into how proteins with the same native structure can exhibit vastly different biophysical behavior. In contrast to globular proteins such as RNase H, repeat proteins are tandem arrays of repeating structural units that have no long-range contacts. In these modular domains, the majority of native contacts could be maintained in the face of partial unfolding. Repeat proteins therefore offer a unique architecture for exploring the extent of cooperativity and roughness on the energy landscape. To understand how a modular system builds cooperativity into its energetics, and to explore the origins and limits of this cooperativity, we studied the behavior of the Notch ankyrin domain in the optical tweezers, a single molecule mechanical tool. The forced unfolding of the Notch ankyrin domain occurs in one or two steps when manipulated in the optical tweezers. Though the unfolding pathway is heterogenous compared to that observed in bulk studies, there is a limit to the degree of uncoupling of individual repeats. We compare these results to the unfolding behavior of the Notch ankyrin domain in the atomic force microscope obtained by our collaborators for this project. This offers some insight into the apparent difference in solution and AFM unfolding of ankyrin repeat proteins.
Author : Alka Dwevedi
Publisher : Springer
ISBN 13 : 3319125923
Total Pages : 61 pages
Book Rating : 4.3/5 (191 download)
Download or read book Protein Folding written by Alka Dwevedi and published by Springer. This book was released on 2014-12-01 with total page 61 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Cláudio M. Gomes
Publisher : Springer
ISBN 13 : 331900882X
Total Pages : 63 pages
Book Rating : 4.3/5 (19 download)
Download or read book Protein Folding written by Cláudio M. Gomes and published by Springer. This book was released on 2019-02-25 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Yawen Bai
Publisher : Springer Science & Business Media
ISBN 13 : 1597451894
Total Pages : 332 pages
Book Rating : 4.5/5 (974 download)
Download or read book Protein Folding Protocols written by Yawen Bai and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.
Author :
Publisher : Elsevier
ISBN 13 : 0080497187
Total Pages : 479 pages
Book Rating : 4.0/5 (84 download)
Download or read book Energetics of Biological Macromolecules, Part E written by and published by Elsevier. This book was released on 2004-04-02 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Author : Donald B Wetlaufer
Publisher : Routledge
ISBN 13 : 1000305031
Total Pages : 171 pages
Book Rating : 4.0/5 (3 download)
Download or read book The Protein Folding Problem written by Donald B Wetlaufer and published by Routledge. This book was released on 2019-06-21 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins in living systems carry out a great variety of specific functions, each of which depends on the precise three-dimensional structure of a particular protein. Proteins are synthesized in the form of a flexible polypeptide chain that is capable of assuming a vast number of configurations; the transformation of this chain into a specific, relatively rigid three-dimensional structure is called folding--a remarkable process of self-organization. It is known that the amino acid sequences of some proteins have sufficient information to determine their three-dimensional structures. There are other proteins whose folding requires additional information beyond that found in the sequence of the mature protein. This book introduces the central problem of folding mechanisms as well as a number of other closely related issues. This book is neither a textbook nor a treatise. Rather, it is an attempt by several investigators to convey the excitement and challenges of those aspects of the folding problem in which they are actively engaged. The contributors give brief introductions to protein folding from the perspectives of molecular architecture, stability and dynamics, phage genetics, DNA exons, general physiology, and natural selection. They point out emerging new directions, including the suggestion of a class of diseases that result from protein folding defects.
Author : Astrid Sigel
Publisher : Walter de Gruyter GmbH & Co KG
ISBN 13 : 3110434334
Total Pages : 596 pages
Book Rating : 4.1/5 (14 download)
Download or read book Lead: Its Effects on Environment and Health written by Astrid Sigel and published by Walter de Gruyter GmbH & Co KG. This book was released on 2017-04-10 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17, entitled Lead: Its Effects on Environment and Health of the series Metal Ions in Life Sciences centers on the interrelations between biosystems and lead. The book provides an up-to-date review of the bioinorganic chemistry of this metal and its ions; it covers the biogeochemistry of lead, its use (not only as gasoline additive) and anthropogenic release into the environment, its cycling and speciation in the atmosphere, in waters, soils, and sediments, and also in mammalian organs. The analytical tools to determine and to quantify this toxic element in blood, saliva, urine, hair, etc. are described. The properties of lead(II) complexes formed with amino acids, peptides, proteins (including metallothioneins), nucleobases, nucleotides, nucleic acids, and other ligands of biological relevance are summarized for the solid state and for aqueous solutions as well. All this is important for obtaining a coherent picture on the properties of lead, its effects on plants and toxic actions on mammalian organs. This and more is treated in an authoritative and timely manner in the 16 stimulating chapters of Volume 17, which are written by 36 internationally recognized experts from 13 nations. The impact of this recently again vibrant research area is manifested in nearly 2000 references, over 50 tables and more than 100 illustrations (half in color). Lead: Its Effects on Environment and Health is an essential resource for scientists working in the wide range from material sciences, inorganic biochemistry all the way through to medicine including the clinic ... not forgetting that it also provides excellent information for teaching.
