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This volume is the scientific chronicle of the NATO Advanced Research Workshop on Computational Aspects of the Study of Biological Macro molecules by Nuclear Magnetic Resonance Spectroscopy, which was held June 3-8, 1990 at Il Ciocco, near Barga, Italy. The use of computers in the study of biological macromolecules by NMR spectroscopy is ubiquitous. The applications are diverse, including data col lection, reduction, and analysis. Furthermore, their use is rapidly evolv ing, driven by the development of new experimental methods in NMR and molecular biology and by phenomenal increases in computational perfor mance available at reasonable cost. Computers no longer merely facilitate, but are now absolutely essential in the study of biological macromolecules by NMR, due to the size and complexity of the data sets that are obtained from modern experiments. The Workshop, and this proceedings volume, provide a snapshot of the uses of computers in the NMR of biomolecules. While by no means exhaustive, the picture that emerges illustrates both the· importance and the diversity of their application.
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.
The theoretical and computational aspects of nuclear magnetic resonance (NMR) spectroscopy underlie the many diverse applications of NMR to studies of biomolecular dynamics, kinetics, and structure. The challenging aspects of biomolecular NMR spectroscopy can be divided into three major steps: (a) data acquisition and processing (development of methods for fast data collection and signal identification); (b) accurate mapping of spectral frequencies to atoms in the covalent structure of the molecule (as required for investigations of biomolecular dynamics and kinetics as well as structure calculation); (c) structure calculation and validation. I have investigated possibilities for improving current computational methods for each of these steps. In order to accelerate the process of NMR data acquisition, I have incorporated fast data collection methods into our probabilistic approach to simultaneous reduced-dimensionality data collection and assignment (discussed in Chapter 2). In order to simplify the process of assigning spectral frequencies derived from conventional triple-resonance NMR data to atoms of proteins, I designed a semi-automated method and trained an undergraduate student to implement it. In addition, because one of the important requirements of scientific research is the reproducibility of the study, I designed and developed a novel validation method called ARECA, for verifying the accuracy of chemical shift assignments (described in Chapter 3). A quote from one of the anonymous reviewers of our paper describing the method highlights its importance and practicality: "The new chemical shift validation method, ARECA, described in this work represents a fresh approach to a difficult problem, that has been an Achilles heel to protein NMR for more than three decades. ... I believe ARECA will become a very valuable addition to the 'must-use' tools of protein NMR spectroscopists." In order to facilitate applications of NMR for users with limited NMR expertise, I have introduced a framework (discussed in Chapter 4) for calculating three-dimensional structures of proteins from NMR data. This framework was designed to simplify the process while emphasizing the important role of validation in NMR studies
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).
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.
This book covers new techniques in protein NMR, from basic principles to state-of-the-art research. It covers a spectrum of topics ranging from a “toolbox” for how sequence-specific resonance assignments can be obtained using a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome. Further topics include the novel applications of Overhauser dynamic nuclear polarization methods (DNP), assessing protein structure, and aspects of solid-state NMR of macroscopically aligned membrane proteins. This book is an ideal resource for students and researchers in the fields of biochemistry, chemistry, and pharmacology and NMR physics. Comprehensive and intuitively structured, this book examines protein NMR and new novel applications that include the latest technological advances. This book also has the features of: • A selection of various applications and cutting-edge advances, such as novel applications of Overhauser dynamic nuclear polarization methods (DNP) and a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome • A pedagogical approach to the methodology • Engaging the reader and student with a clear, yet critical presentation of the applications
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.
This volume covers state-of-the-art applications of solid-state and solution nuclear magnetic resonance( NMR) spectroscopy to study protein structure, dynamics and interactions. Chapters detail various aspects of data acquisition and processing, determination of the structure, multi-timescale dynamics of entities ranging from individual proteins to large macromolecular complexes to intact viral assemblies. The final two chapters will highlight the promise of NMR beyond field strengths of 1 GHz to study the structure, dynamics and interactions of a larger class of proteins and protein complexes of extraordinary biological interest. Written in the highly successful Methods in Molecular Biology series format, chapters provide detailed laboratory protocols and troubleshooting tips that would be of great practical help to NMR spectroscopists with different levels of expertise.
This book discusses the paradigm-shifting phenomenon of intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and functional IDP regions (IDPRs). The properties of IDPs and IDPRs are highly complementary to those deriving from the presence of a unique and well-defined three-dimensional fold. Ignored for a long time in high-resolution studies of proteins, intrinsic protein disorder is now recognized as one of the key features for a large variety of cellular functions, where structural flexibility presents a functional advantage in terms of binding plasticity and promiscuity and this volume explores this exciting new research. Recent progress in the field has radically changed our perspective to study IDPs through NMR: increasingly complex IDPs can now be characterized, a wide range of observables can be determined reporting on the structural and dynamic properties, computational methods to describe the structure and dynamics are in continuous development and IDPs can be studied in environments as complex as whole cells. This volume communicates the new exciting possibilities offered by NMR and presents open questions to foster further developments. Intrinsically Disordered Proteins Studied by NMR Spectroscopy provides a snapshot to researchers entering the field as well as providing a current overview for more experienced scientists in related areas.