Structure Computation And Dynamics In Protein Nmr

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
ISBN 13 : 0306459531
Total Pages : 565 pages
Book Rating : 4.35/5 ( download)

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Download or read book Structure Computation and Dynamics in Protein NMR written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 1999-06-30 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.

Author : N. Rama Krishna
Publisher : Springer
ISBN 13 : 9780306459535
Total Pages : 584 pages
Book Rating : 4.31/5 ( download)

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Download or read book Structure Computation and Dynamics in Protein NMR written by N. Rama Krishna and published by Springer. This book was released on 1999-06-30 with total page 584 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
ISBN 13 : 0306470837
Total Pages : 400 pages
Book Rating : 4.37/5 ( download)

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Download or read book Modern Techniques in Protein NMR written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 2006-03-16 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 16 marks the beginning of a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. This volume is being followed by Volume 17 with the subtitle Structure Computation and Dynamics in Protein NMR. Volumes 16 and 17 present some of the recent, significant advances in biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volumes some of the world’s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains advances in two broad categories: the first, Large Proteins, Complexes, and Membrane Proteins, and second, Pulse Methods. Volume 17, which will follow covers major advances in Computational Methods, and Structure and Dynamics. In the opening chapter of Volume 16, Marius Clore and Angela Gronenborn give a brief review of NMR strategies including the use of long range restraints in the structure determination of large proteins and protein complexes. In the next two chapters, Lewis Kay and Ron Venters and their collaborators describe state-of-t- art advances in the study of perdeuterated large proteins. They are followed by Stanley Opella and co-workers who present recent developments in the study of membrane proteins. (A related topic dealing with magnetic field induced residual dipolar couplings in proteins will appear in the section on Structure and Dynamics in Volume 17).

Author : Lawrence Berliner
Publisher : Springer
ISBN 13 : 9780306389818
Total Pages : 345 pages
Book Rating : 4.19/5 ( download)

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Download or read book Biological Magnetic Resonance written by Lawrence Berliner and published by Springer. This book was released on 1978-11-01 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological magnetic resonance (NMR and EPR) is a rapidly expanding area of research with much activity in most universities and research institutions. International conferences are held biennially with an increasing number of participants. With the introduction of sophisticated and continuously im proving instrumentation, biological magnetic resonance is approaching the state of a common physical method in biochemical, biomedical, and bio logical research. The lack of monograpbs on the subject had been con spicuous for a long time. This gap started to close only recently. However, because of the rapid expansion and intensive research, many texts are dated by the time of their appearance. Therefore we have undertaken the editing of a series that is intended to provide the practicing chemist, biochemist, or biologist with the advances and progress in selected contemporary topics. In seeking to make the series as authoritative as possible, we have invited authors who have not only made significant contributions but who are also currently active in their fields. We hope that their expertise as well as their first hand experience as reflected in the chapters of this volume will be of benefit to the reader, inter alia, in planning his own experiments and in critically evaluating the current literature.

Author : John L. Markley
Publisher : Oxford University Press
ISBN 13 : 0195357426
Total Pages : 375 pages
Book Rating : 4.24/5 ( download)

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Download or read book Biological NMR Spectroscopy written by John L. Markley and published by Oxford University Press. This book was released on 1997-01-30 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Jean-Paul Renaud
Publisher : John Wiley & Sons
ISBN 13 : 1118900502
Total Pages : 1367 pages
Book Rating : 4.05/5 ( download)

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Download or read book Structural Biology in Drug Discovery written by Jean-Paul Renaud and published by John Wiley & Sons. This book was released on 2020-01-09 with total page 1367 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins

Author : Gordon S. Rule
Publisher : Springer Science & Business Media
ISBN 13 : 1402035004
Total Pages : 543 pages
Book Rating : 4.05/5 ( download)

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Download or read book Fundamentals of Protein NMR Spectroscopy written by Gordon S. Rule and published by Springer Science & Business Media. This book was released on 2006-02-16 with total page 543 pages. Available in PDF, EPUB and Kindle. Book excerpt: NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. End of chapter exercises are included to emphasize important concepts. Fundamentals of Protein NMR Spectroscopy not only offer students a systematic, in-depth, understanding of modern NMR spectroscopy and its application to biomolecular systems, but will also be a useful reference for the experienced investigator.

Author : Alexandra Ahlner
Publisher : Linköping University Electronic Press
ISBN 13 : 9175191032
Total Pages : 79 pages
Book Rating : 4.34/5 ( download)

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Download or read book Improved Methods for Characterization of Protein Dynamics by NMR spectroscopy and Studies of the EphB2 Kinase Domain written by Alexandra Ahlner and published by Linköping University Electronic Press. This book was released on 2015-04-15 with total page 79 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : A. Kristina Downing
Publisher : Springer Science & Business Media
ISBN 13 : 1592598099
Total Pages : 494 pages
Book Rating : 4.90/5 ( download)

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Download or read book Protein NMR Techniques written by A. Kristina Downing and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: When I was asked to edit the second edition of Protein NMR Techniques, my first thought was that the time was ripe for a new edition. The past several years have seen a surge in the development of novel methods that are truly revolutionizing our ability to characterize biological macromolecules in terms of speed, accuracy, and size limitations. I was particularly excited at the prospect of making these techniques accessible to all NMR labs and for the opportunity to ask the experts to divulge their hints and tips and to write, practically, about the methods. I commissioned 19 chapters with wide scope for Protein NMR Techniques, and the volume has been organized with numerous themes in mind. Chapters 1 and 2 deal with recombinant protein expression using two organisms, E. coli and P. pastoris, that can produce high yields of isotopically labeled protein at a reasonable cost. Staying with the idea of isotopic labeling, Chapter 3 describes methods for perdeuteration and site-specific protonation and is the first of several chapters in the book that is relevant to studies of higher molecular weight systems. A different, but equally powerful, method that uses molecular biology to “edit” the spectrum of a large molecule using segmental labeling is presented in Chapter 4. Having successfully produced a high molecular weight target for study, the next logical step is data acquisition. Hence, the final chapter on this theme, Chapter 5, describes TROSY methods for stru- ural studies.

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
ISBN 13 : 0306479362
Total Pages : 345 pages
Book Rating : 4.66/5 ( download)

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Download or read book Protein NMR for the Millennium written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein NMR for the Millennium is the third volume in a special thematic series devoted to the latest developments in protein NMR under the Biological Magnetic Resonance umbrella. This book is divided into three major sections dealing with significant recent advances in the study of large proteins in solution and solid state, structure refinement, and screening of bioactive ligands. Key Features: TROSY, Segmental isotope labeling of proteins, Hydrogen bond scalar couplings, Structure refinement based on residual dipolar couplings, Written by the world's foremost experts who have provided broad leadership in advancing the protein NMR field.