Download or read book New Methods for Automated NMR Data Analysis and Protein Structure Determination written by Felician Dancea and published by . This book was released on 2004 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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.

Download or read book New Methods for Automated NMD Data Analysis and Protein Structure Determination written by Felician Dancea and published by . This book was released on 2005 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book New Approaches to Protein NMR Automation written by Babak Alipanahi Ramandi and published by . This book was released on 2011 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of a protein molecule is the key to understanding its biological and physiological properties. A major problem in bioinformatics is to efficiently determine the three-dimensional structures of query proteins. Protein NMR structure de- termination is one of the main experimental methods and is comprised of: (i) protein sample production and isotope labelling, (ii) collecting NMR spectra, and (iii) analysis of the spectra to produce the protein structure. In protein NMR, the three-dimensional struc- ture is determined by exploiting a set of distance restraints between spatially proximate atoms. Currently, no practical automated protein NMR method exists that is without human intervention. We first propose a complete automated protein NMR pipeline, which can efficiently be used to determine the structures of moderate sized proteins. Second, we propose a novel and efficient semidefinite programming-based (SDP) protein structure determination method. The proposed automated protein NMR pipeline consists of three modules: (i) an automated peak picking method, called PICKY, (ii) a backbone chemical shift assign- ment method, called IPASS, and (iii) a protein structure determination method, called FALCON-NMR. When tested on four real protein data sets, this pipeline can produce structures with reasonable accuracies, starting from NMR spectra. This general method can be applied to other macromolecule structure determination methods. For example, a promising application is RNA NMR-assisted secondary structure determination. In the second part of this thesis, due to the shortcomings of FALCON-NMR, we propose a novel SDP-based protein structure determination method from NMR data, called SPROS. Most of the existing prominent protein NMR structure determination methods are based on molecular dynamics coupled with a simulated annealing schedule. In these methods, an objective function representing the error between observed and given distance restraints is minimized; these objective functions are highly non-convex and difficult to optimize. Euclidean distance geometry methods based on SDP provide a natural formulation for realizing a three-dimensional structure from a set of given distance constraints. However, the complexity of the SDP solvers increases cubically with the input matrix size, i.e., the number of atoms in the protein, and the number of constraints. In fact, the complexity of SDP solvers is a major obstacle in their applicability to the protein NMR problem. To overcome these limitations, the SPROS method models the protein molecule as a set of intersecting two- and three-dimensional cliques. We adapt and extend a technique called semidefinite facial reduction for the SDP matrix size reduction, which makes the SDP problem size approximately one quarter of the original problem. The reduced problem is solved nearly one hundred times faster and is more robust against numerical problems. Reasonably accurate results were obtained when SPROS was applied to a set of 20 real protein data sets.

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 2006-05-09 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.

Download or read book New Computational Methods for 3D NMR Data Analysis and Protein Structure Determination in High dimensional Internal Coordinate Space written by Garry Paul Gippert and published by . This book was released on 1995 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: New computational methods were developed for the determination of primary chemical shift assignments and measurement of three-bond scalar J-coupling constants using multi-dimensional NMR data; and high-dimensional, systematic search for poly-peptide conformations subject to distance geometry constraints. Two methods were developed for conformational search in a space consisting of variable torsion angles. Method I performs a recursive search for linear chains. Method II performs a binary tree search for linear or branched systems. Trial conformations are rejected based on distance and scalar coupling bounds violations, including novel bounds on distance ratios, coupling ratios, and a 'degenerate' treatment of equivalent and prochiral atoms. A hierarchical arrangement of sub-searches is used to prune the high-dimensional space. The binary search (Method II) employs Unix 'pipes' and may be distributed over a computer network in a multi-processor environment, and may additionally utilize bounds on relative orientations of chain segments. 1H, 13C and 15N chemical shift assignments were obtained for recombinant poplar plastocyanin (rPc) from homonuclear and heteronuclear 2D and 3D NMR spectra. A semi-automated reduction of 3D NH-based spectra into a series of interleaved 1D vectors facilitated the sequential assignment process. Sidechain assignments were completed by the prediction and interactive, visual correction of crosspeak locations based on expected scalar and through-space connectivities. A similar procedure was used to identify correct beta-strand alignment based on total integrated NOE volume. Secondary proton chemical shifts were compared for five homologous plastocyanins. Distinct chemical shift variations were correlated with changes in primary sequence and led to a critical analysis of structural differences observed within the protein family. Scalar J-coupling constants between backbone HN and H-alpha protons of rPc were measured in three different NMR spectra--by lineshape analysis for 1H COSY and 3D HNCA-J crosspeaks, and curve fitting to modulated 1H, 15N-HSQC crosspeak intensities. Solution measurements of J(HN,H-alpha) were compared to values predicted from the high-resolution X-ray crystal structure using the Karplus relationship. Notable deviations occur for residues that are involved in intermolecular backbone contacts in the crystal, or are likely to be due to conformational averaging in solution, and includes a subset of residues in the copper-binding loop.

Download or read book Towards Automating Protein Structure Determination from NMR Data written by Xin Gao and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Development Towards High throughput NMR based Protein Structure Determination written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book NMR with Biological Macromolecules in Solution written by Kurt Wüthrich and published by World Scientific Publishing Company. This book was released on 2021 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book provides insights into the research of the Kurt Wüthrich laboratories from 1996-2020. During this time period, the technique of nuclear magnetic resonance (NMR) spectroscopy in solution went through several breakthroughs, while maturing into a standard method of structural biology. With the introduction of TROSY (transverse relaxation-optimized spectroscopy), the range of accessible molecular sizes was extended about thirty-fold, and efficient protein structure determination resulted from the demands of the structural genomics initiative. Applications in fundamental biology and biomedicine include studies of prion proteins and prion diseases (TSEs), the SARS-Corona virus proteome, trans-membrane signalling by G protein-coupled receptors (GPCRs), and signal transfer by pheromones.Key publications from the Kurt Wüthrich laboratories are placed in perspective, providing insights into new aspects of NMR spectroscopy in structural biology. In addition to methods development, this includes applications in diverse areas of biological research, such as prion proteins and their role in transmissible spongiform encephalopathies (TSEs), trans-membrane signal transfer by G protein-coupled receptors (GPCRs), structural characterization of the SARS-Corona virus proteome, metabolic-flux profiling in bacterial cultures, and signal transfers by pheromones.

Download or read book Automated Determination of Protein Structures from NMR Data by Iterative Analysis of Self consistent Contact Patterns written by Yuanpeng Janet Huang and published by . This book was released on 2001 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book A Probabilistic Approach to the Automation of NMR Protein Structure Determination written by Arash Bahrami and published by . This book was released on 2009 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book New Approaches for Automated Protein NMR Structure Determination Based on Experimental NOESY Spectra written by Torsten Herrmann and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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.

Download or read book Structure and Biophysics New Technologies for Current Challenges in Biology and Beyond written by Joseph D. Puglisi and published by Springer Science & Business Media. This book was released on 2007-04-26 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of articles from the proceedings of the ISSBMR 7th Course: Structure and Biophysics - New Technologies for Current Challenges in Biology and Beyond. This NATO Advanced Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture in June 2005. It presents state of the art information on NMR spectroscopy and its place in the broader field of biophysics.

Download or read book Modern Magnetic Resonance written by Graham A. Webb and published by Springer Science & Business Media. This book was released on 2007-05-26 with total page 1889 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive collection of the applications of Nuclear Magnetic Resonance (NMR), Magnetic Resonance Imaging (MRI) and Electron-Spin Resonance (ESR). Covers the wide ranging disciplines in which these techniques are used: * Chemistry; * Biological Sciences; * Pharmaceutical Sciences; * Medical uses; * Marine Science; * Materials Science; * Food Science. Illustrates many techniques through the applications described, e.g.: * High resolution solid and liquid state NMR; * Low resolution NMR, especially important in food science; * Solution State NMR, especially important in pharmaceutical sciences; * Magnetic Resonance Imaging, especially important for medical uses; * Electron Spin Resonance, especially important for spin-labelling in food, marine and medical studies.

Download or read book Biomolecular NMR Spectroscopy written by Andrew J. Dingley and published by IOS Press. This book was released on 2011 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Magnetic Resonance (NMR) spectroscopy is the most powerful technique for characterization of biomolecular structures at atomic resolution in the solution state. This timely book, entitled "Biomolecular NMR Spectroscopy," focuses on the latest state-of-the-art NMR techniques for characterization of biological macromolecules in the solid and solution state. The editors, Dr. Andrew Dingley (University of Auckland, New Zealand) and Dr. Steven Pascal (Massey University, New Zealand) have organized the book into four sections, covering the following topics: sample preparation, structure and dynamics of proteins, structure and dynamics of nucleic acids and protein-nucleic acid complexes, and rapid and hybrid techniques--

Download or read book Protein Structure written by Eshel Faraggi and published by BoD – Books on Demand. This book was released on 2012-04-20 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the dawn of recorded history, and probably even before, men and women have been grasping at the mechanisms by which they themselves exist. Only relatively recently, did this grasp yield anything of substance, and only within the last several decades did the proteins play a pivotal role in this existence. In this expose on the topic of protein structure some of the current issues in this scientific field are discussed. The aim is that a non-expert can gain some appreciation for the intricacies involved, and in the current state of affairs. The expert meanwhile, we hope, can gain a deeper understanding of the topic.