[PDF] Protein Structure Determination By Paramagnetic Nmr And Computational Hybrid Approach eBook

Author : Kala Bharath Pilla
Publisher :
Page : 0 pages
File Size : 21,81 MB
Release : 2015
Category :
ISBN :

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Computational modelling of proteins that rely on either de novo or evolutionary based approaches often produce poor quality structures, primarily due to the limitations in their algorithms or forcefields. Traditional experimental techniques such as X-ray crystallography depend on narrow set of crystallographic conditions while solution/solid state nuclear magnetic resonance (NMR) spectroscopy relies on cumbersome spectral analysis and complete resonance assignments. These traditional approaches are slow and costly endeavours. Computational/experimental hybrid approaches on the other hand provide a new avenue for reliable, rapid and cost-effective structure determination. Paramagnetic NMR offers easy generation of useful and sparse structural information which can be implemented as restraints in structure prediction algorithms. Pseudocontact shifts (PCS) are the most powerful of structural restraints generated by paramagnetic NMR which are long range in nature and can be easily obtained by simple 2D NMR experiments. This thesis demonstrates different approaches involved in protein structure calculations using PCS restraints in Rosetta. Chapter 2 demonstrates structure determination using PCS restraints exclusively obtained from protein samples in microcrystalline state by magic angle spinning (MAS) NMR spectroscopy. Chapter 3 discusses the implementation of using PCS data from multiple metal centres to precisely determine the location of spins in space in a manner analogues to GPS-satellites. Chapter 4 extends the usage of PCS data from multiple metal centres to capture distinct conformational states in proteins. Chapter 5 demonstrates new techniques especially developed for structure determination of large proteins involving super secondary structure motifs (Smotifs) and data driven iterative resampling. These different computational techniques serve the goal of determining accurate 3D models using minimal experimental data, which are applicable to proteins systems that are currently beyond the realm of traditional experimental approaches.

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
Page : 565 pages
File Size : 29,66 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.

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Page : 0 pages
File Size : 38,62 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 : 30,55 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.

Author : The Nuclear Magnetic Resonance Society of Japan
Publisher : Springer
Page : 634 pages
File Size : 15,26 MB
Release : 2017-11-23
Category : Science
ISBN : 9811059667

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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.