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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.
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.
This volume and its companion, Volume 338, supplement Volumes 176, 177, 239, and 261. Chapters are written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules.
The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences. Nuclear Magnetic Resonance of Biological Macromolecules, Part C is written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules. * One of the most highly respected publications in the field of biochemistry since 1955 * Frequently consulted, and praised by researchers and reviewers alike * Truly an essential publication for anyone in any field of the life sciences
This volume and its companion, Volume 339, supplement Volumes 176, 177, 239, and 261. Chapters are written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules.
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.
From within complex structures of organisms and cells down to the molecular level, biological processes all involve movement. Muscular fibers slide on each other to activate the muscle, as polymerases do along nucleic acids for replicating and transcribing the genetic material. Cells move and organize themselves into organs by recognizing each other through macromolecular surface-specific interactions. These recognition processes involve the mu tual adaptation of structures that rely on their flexibility. All sorts of conformational changes occur in proteins involved in through-membrane signal transmission, showing another aspect of the flexibility of these macromolecules. The movement and flexibility are inscribed in the polymeric nature of essential biological macromolecules such as proteins and nucleic acids. For instance, the well-defined structures formed by the long protein chain are held together by weak noncovalent interac tions that design a complex potential well in which the protein floats, permanently fluctuating between several micro- or macroconformations in a wide range of frequencies and ampli tudes. The inherent mobility of biomolecular edifices may be crucial to the adaptation of their structures to particular functions. Progress in methods for investigating macromolecular structures and dynamics make this hypothesis not only attractive but more and more testable.
Computational chemistry is increasingly used in most areas of molecular science including organic, inorganic, medicinal, biological, physical, and analytical chemistry. Researchers in these fields who do molecular modelling need to understand and stay current with recent developments. This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
First multi-year cumulation covers six years: 1965-70.
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.