[PDF] Computational Aspects Of Protein Nmr eBook

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Page : 0 pages
File Size : 42,60 MB
Release : 2015
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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

Author : Jeffrey C. Hoch
Publisher : Springer Science & Business Media
Page : 457 pages
File Size : 38,51 MB
Release : 2013-11-21
Category : Medical
ISBN : 147579794X

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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.

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
Page : 565 pages
File Size : 16,19 MB
Release : 2006-05-09
Category : Medical
ISBN : 0306470845

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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
Page : 400 pages
File Size : 16,93 MB
Release : 2006-03-16
Category : Medical
ISBN : 0306470837

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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 : Dmitry Shishmarev
Publisher :
Page : 428 pages
File Size : 30,78 MB
Release : 2014
Category : Nuclear magnetic resonance spectroscopy
ISBN :

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Nuclear magnetic resonance (NMR) spectroscopy is a powerful research technique widely used for establishing three-dimensional structures, dynamic properties and intermolecular interactions of proteins. Its non-destructiveness, high information content and applicability for a broad range of samples, both in solution and in the solid state, renders it one of the best tools in the modern structural biology. Liquid-state NMR spectroscopy, however, also has some drawbacks, such as relatively low inherent sensitivity, complexity of the resultant spectra, high time demands and poor suitability for the analysis of large biomolecular complexes and membrane proteins. Due to the variety of aspects that might be improved and optimised, it's been a target of constant development for the last few decades and still is a primary focus of modern biochemical science. The goal of my PhD projects was to understand and improve several aspects and techniques of liquid-state protein NMR spectroscopy, employing both computational and experimental analysis. In the present thesis, I describe the results of my work on a wide variety of topics. The first project is devoted to optimisations of experiments suffering from the radiation damping effect. The second project is a computational analysis aimed at investigations of the applicability of mobile lanthanide-binding tags in protein-ligand interaction studies. The third project is an investigation of the structure and functions of single-stranded DNA-binding protein (SSB) using solution NMR, targeted at the elucidation of the mechanism by which the protein plays its role in the metabolism of single-stranded DNA.

Author : Lawrence Berliner
Publisher : Springer
Page : 193 pages
File Size : 40,30 MB
Release : 2015-08-24
Category : Science
ISBN : 1489976213

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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

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Page : 0 pages
File Size : 31,79 MB
Release : 2013
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Three-dimensional structures of proteins determined in solution by NMR spectroscopy have the unique advantage of revealing details of molecular structure and dynamics in a physiologically relevant state; however, the many tedious steps needed to solve and validate a structure make this method challenging. The barriers to NMR structure determination become higher for larger proteins whose spectra are harder to resolve. It is clear that advances need to be made in automating protein structure determination by NMR spectroscopy. The goal of my research has been to use computational methods to advance the development of high-throughput NMR spectroscopy. Accelerating and streamlining the structure determination process will enable investigators to spend less time solving structures and more time investigating challenging biomolecular systems. My goals have been to develop an automation protocol that integrates multiple steps, ensures the robustness of each step, incorporates iterative corrections, and includes visualization tools to validate and extend the results. I developed PINE-SPARKY as a graphical interface for checking and extending automated assignments made by the PINE-NMR server. ADAPT-NMR directs fast data collection by reduced dimensionality on the basis of ongoing NMR assignments. I helped develop a version of ADAPT-NMR (originally only for Varian spectrometers) for Bruker spectrometers, and I created ADAPT-NMR Enhancer as a visualization tool for validating and extending assignments made by ADAPT-NMR on either spectrometer system. I developed the PONDEROSA package to automate the next steps. PONDEROSA carries out automatic picking of 3D-NOESY peaks and iterative structure determinations with the protein sequence and the assignments as inputs. These automation and visualization tools cover almost all of the steps involved in protein structure determination by NMR spectroscopy. As a practical test of this technology, I solved the structure of the 2A proteinase from the human rhinovirus. As a side project, I built a relational database (PACSY DB) that combines information from the Protein Data Bank (PDB) and the Biological Magnetic Resonance data Bank (BMRB) and incorporates tools for structure analysis. PACSY DB can carry out complex queries that combine atomic coordinates, NMR parameters, and structural features of proteins.

Author : John L. Markley
Publisher : Oxford University Press
Page : 375 pages
File Size : 36,56 MB
Release : 1997-01-30
Category : Science
ISBN : 0195357426

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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.