Characterization of Local Motions in Proteins Detected by Nuclear Magnetic Resonance Relaxation Studies PDF Download
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Author: Mark William Frederick Fischer
Publisher:
ISBN:
Category :
Languages : en
Pages : 364
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Book Description
Author: Mark William Frederick Fischer
Publisher:
ISBN:
Category :
Languages : en
Pages : 364
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Book Description
Author: Alexandra Ahlner
Publisher: Linköping University Electronic Press
ISBN: 9175191032
Category : Nuclear magnetic resonance spectroscopy
Languages : en
Pages : 79
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Book Description
Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins. To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the soft- ware also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multi-dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at C? positions in proteins, using the CPMG dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals. To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of EphB2 and its signaling mechanism.
Author: John L. Markley
Publisher: Oxford University Press
ISBN: 0195357426
Category : Science
Languages : en
Pages : 375
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Book Description
This book presents a critical assessment of progress on the use of nuclear magnetic resonance spectroscopy to determine the structure of proteins, including brief reviews of the history of the field along with coverage of current clinical and in vivo applications. The book, in honor of Oleg Jardetsky, one of the pioneers of the field, is edited by two of the most highly respected investigators using NMR, and features contributions by most of the leading workers in the field. It will be valued as a landmark publication that presents the state-of-the-art perspectives regarding one of today's most important technologies.
Author: Martin Zacharias
Publisher: World Scientific
ISBN: 1848163398
Category : Science
Languages : en
Pages : 401
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Book Description
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.
Author: Yutaka Ito
Publisher: Royal Society of Chemistry
ISBN: 1839160934
Category : Science
Languages : en
Pages : 322
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Book Description
In-cell NMR spectroscopy is a relatively new field. Despite its short history, recent in-cell NMR-related publications in major journals indicate that this method is receiving significant general attention. This book provides the first informative work specifically focused on in-cell NMR. It details the historical background of in-cell NMR, host cells for in-cell NMR studies, methods for in-cell biological techniques and NMR spectroscopy, applications, and future perspectives. Researchers in biochemistry, biophysics, molecular biology, cell biology, structural biology as well as NMR analysts interested in biological applications will all find this book valuable reading.
Author: Eric Michael Johnson
Publisher:
ISBN:
Category :
Languages : en
Pages : 147
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Book Description
An accurate understanding of the role of conformational dynamics in proteins requires data at multiple timescales and sites within the protein of interest. Considerable progress has been achieved in characterizing the picosecond-to-nanosecond (ps-ns) dynamics of the protein backbone via NMR relaxation measurements of the 15N nucleus. More recent developments in the measurement of 2H quadrupolar relaxation rates are enabling an extensive characterization of the dynamics in methyl-containing side-chains as well. The aim of the present study is to characterize the effects of Ca2+ binding on the side-chain dynamics of the protein calbindin D9k. Calbindin is a small (~8.7 kD), single domain protein of the EF-hand family. It contains two Ca2+ binding sites that exhibit high positive cooperativity. Longitudinal, transverse, quadrupolar order, transverse antiphase and double quantum relaxation rates are reported for both the apo (Ca2+-free) and Ca2+-loaded states of the protein at two magnetic field strengths. The relatively large size of the data set allows for a detailed analysis of the underlying conformational dynamics by spectral density mapping and model-free fitting procedures. The results indicate that a methyl group's distance from the Ca2+ binding sites is a significant determinant of its conformational dynamics. Several methyl groups segregate into two limiting classes, one proximal and the other distal to the binding sites. Methyl groups in these two classes respond differently to Ca2+ binding, both in terms of the timescale and amplitude of their fluctuations. Ca2+ binding elicits a partial immobilization among methyl groups in the proximal class, which is consistent with previous studies of calbindin's backbone dynamics. The distal class, however, exhibits a trend that could not be inferred from the backbone data in that its mobility actually increases with Ca2+ binding. We have introduced the term polar dynamics to describe this type of organization across the molecule. The trend may represent an important mechanism by which calbindin achieves high affinity binding while minimizing the corresponding conformational entropy loss.
Author: Melinda J. Duer
Publisher: John Wiley & Sons
ISBN: 0470999381
Category : Science
Languages : en
Pages : 592
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Book Description
This book is for those familiar with solution-state NMR who are encountering solid-state NMR for the first time. It presents the current understanding and applications of solid-state NMR with a rigorous but readable approach, making it easy for someone who merely wishes to gain an overall impression of the subject without details. This dual requirement is met through careful construction of the material within each chapter. The book is divided into two parts: "Fundamentals" and "Further Applications." The section on Fundamentals contains relatively long chapters that deal with the basic theory and practice of solid-state NMR. The essential differences and extra scope of solid-state NMR over solution-state is dealt with in an introductory chapter. The basic techniques that all chapters rely on are collected into a second chapter to avoid unnecessary repetition later. Remaining chapters in the "Fundamentals" part deal with the major areas of solid-state NMR which all solid-state NMR spectroscopists should know about. Each begins with an overview of the topic that puts the chapter in context. The basic principles upon which the techniques in the chapter rely are explained in a separate section. Each of these chapters exemplifies the principles and techniques with the applications most commonly found in current practice. The "Further Applications" section contains a series of shorter chapters which describe the NMR techniques used in other, more specific areas. The basic principles upon which these techniques rely will be expounded only if not already in the Fundamentals part.
Author: Graham A. Webb
Publisher: Springer Science & Business Media
ISBN: 1402039107
Category : Technology & Engineering
Languages : en
Pages : 1889
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Book Description
A comprehensive collection of the applications of Nuclear Magnetic Resonance (NMR), Magnetic Resonance Imaging (MRI) and Electron-Spin Resonance (ESR). Covers the wide ranging disciplines in which these techniques are used: * Chemistry; * Biological Sciences; * Pharmaceutical Sciences; * Medical uses; * Marine Science; * Materials Science; * Food Science. Illustrates many techniques through the applications described, e.g.: * High resolution solid and liquid state NMR; * Low resolution NMR, especially important in food science; * Solution State NMR, especially important in pharmaceutical sciences; * Magnetic Resonance Imaging, especially important for medical uses; * Electron Spin Resonance, especially important for spin-labelling in food, marine and medical studies.
Author: The Nuclear Magnetic Resonance Society of Japan
Publisher: Springer
ISBN: 9811059667
Category : Science
Languages : en
Pages : 634
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Book Description
This book describes the advanced developments in methodology and applications of NMR spectroscopy to life science and materials science. Experts who are leaders in the development of new methods and applications of life and material sciences have contributed an exciting range of topics that cover recent advances in structural determination of biological and material molecules, dynamic aspects of biological and material molecules, and development of novel NMR techniques, including resolution and sensitivity enhancement. First, this book particularly emphasizes the experimental details for new researchers to use NMR spectroscopy and pick up the potentials of NMR spectroscopy. Second, the book is designed for those who are involved in either developing the technique or expanding the NMR application fields by applying them to specific samples. Third, the Nuclear Magnetic Resonance Society of Japan has organized this book not only for NMR members of Japan but also for readers worldwide who are interested in using NMR spectroscopy extensively.
Author: Aron W. Fenton
Publisher: Humana Press
ISBN: 9781617793332
Category : Science
Languages : en
Pages : 0
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Book Description
Despite considerable variability within the scientific community, allosteric regulation can best be defined functionally as how a macromolecule binds one ligand differently when a second ligand is or is not pre-bound to the macromolecule, which constitutes a vital aspect of protein structure/function. In Allostery: Methods and Protocols, expert researchers in the field provide key techniques to investigate this biological phenomenon. Focusing on heterotropic systems with some coverage of homotropic systems, this volume covers the monitoring of allosteric function, allosteric conformational changes, and allosteric changes in protein dynamics/sub-population distribution, as well as topics such as macromolecular and ligand engineering of allosteric functions and computational aids in the study of allostery. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Allostery: Methods and Protocols aids scientists in continuing to study ligand-induced, through-protein effects on protein function (ligand binding/catalysis), a phenomenon that is well recognized through the history of the life sciences and very poorly understood at the molecular level.
