[PDF] Precise And Accurate Structural Genomics Protein Structure Determination Using Rd And Gft Nmr Spectroscopy eBook

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Page : 161 pages
File Size : 29,76 MB
Release : 2006
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Nuclear magnetic resonance (NMR) has emerged as a powerful tool for determining three-dimensional structures of proteins in solution. The major part of this dissertation describes the efforts to deal with the core steps involved in NMR-base protein structure determination: NMR data collection, NMR data analysis, structure calculation and refinement. NMR data collection has been recognized as one of the major bottlenecks of NMR-base structure determination due to the necessarily long time. Chapter 2 and 3 describe two NMR data collection and analysis protocols for high-quality protein structure determination based on Reduced Dimensionality (RD) and G-matrix Fourier transform (GFT) NMR, respectively. The rapidly collected RD & GFT NMR data enabled high-quality structure determination of four structural genomics target proteins in high-throughput. Chapter 5 introduces the program UBNMR which was developed to facilitate NMR data analysis in general and RD & GFT NMR data pre-processing and data analysis in particular. RD and GFT NMR based protocols, with the aid of UBNMR, are expected to greatly impact on the NMR-based structural biology and structural genomics. In addition to rapid NMR data collection and analysis, structure calculation and refinement are also pivotal for obtaining the high-quality protein structures. Chapter 5 describes the analysis of the newly implemented simultaneous GFT NOESY to obtain an accurate and precise initial structural fold. Chapter 6 presents a protein structure refinement strategy using NOE data collected in supercooled water at low temperatures.

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Page : 30 pages
File Size : 24,54 MB
Release : 2006
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Nuclear magnetic resonance (NMR) has become one of the most common methods for the determination of three-dimensional (3D) solution structures of proteins. On the other hand, bioinformaticians provide powerful tools to study a protein's biological role. The work of this thesis consists of two major parts: (1) the NMR structure determination of the Northeast Structural Genomics Consortium target protein Xanthomonas campestris Xcc2852, and (2) the functional annotation of the NESG Consortium target protein Escherichia coli yhgG. For the 3D structure determination in part (1), we used a standard protocol for NMR-based structural genomics, which enables one to rapidly collect and analyze NMR data. A set of G-matrix Fourier Transform (GFT) NMR experiments were used and feasibility and robustness of the protocol is exemplified. In the bioinformatics study of part (2), sophisticated sequence and structure alignment algorithms were used to explore the possible function of target protein yhgG.

Author : Daniel Chasman
Publisher : CRC Press
Page : 534 pages
File Size : 37,53 MB
Release : 2003-03-18
Category : Medical
ISBN : 0824748166

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This text offers in-depth perspectives on every aspect of protein structure identification, assessment, characterization, and utilization, for a clear understanding of the diversity of protein shapes, variations in protein function, and structure-based drug design. The authors cover numerous high-throughput technologies as well as computational methods to study protein structures and residues. A valuable reference, this book reflects current trends in the effort to solve new structures arising from genome initiatives, details methods to detect and identify errors in the prediction of protein structural models, and outlines challenges in the conversion of routine processes into high-throughput platforms.

Author : Alexander McPherson
Publisher : Academic Press
Page : 226 pages
File Size : 36,62 MB
Release : 2010
Category : Medical
ISBN : 9780123812780

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Structural genomics is the systematic determination of 3-dimensional structures of proteins representative of the range of protein structure and function found in nature. The goal is to build a body of structural information that will predict the structure and potential function for almost any protein from knowledge of its coding sequence. This is essential information for understanding the functioning of the human proteome, the ensemble of tens of thousands of proteins specified by the human genome. While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large scale cloning, expression and purification. One main advantage of this approach is economy of scale. Key Features *Examines the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography and NMR spectroscopy * Looks at structural genomics as a foundation of drug discovery as discovering new medicines is becoming more challenging and the pharmaceutical industry is looking to new technologies to help in this mission

Author : Kala Bharath Pilla
Publisher :
Page : 0 pages
File Size : 32,37 MB
Release : 2015
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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 : Alexander McPherson
Publisher : Academic Press
Page : 241 pages
File Size : 38,75 MB
Release : 2010-09-09
Category : Science
ISBN : 0123819636

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Structural genomics is the systematic determination of 3-D structures of proteins representative of the range of protein structure and function found in nature. The goal is to build a body of structural information that will predict the structure and potential function for almost any protein from knowledge of its coding sequence. This is essential information for understanding the functioning of the human proteome, the ensemble of tens of thousands of proteins specified by the human genome. While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large-scale cloning, expression and purification. One main advantage of this approach is economy of scale. Examines the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography and NMR spectroscopy Looks at structural genomics as a foundation of drug discovery as discovering new medicines is becoming more challenging and the pharmaceutical industry is looking to new technologies to help in this mission

Author : P. Jolles
Publisher : Birkhäuser
Page : 240 pages
File Size : 38,46 MB
Release : 2013-03-11
Category : Science
ISBN : 3034884583

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A wealth of information has accumulated over the last few years on the human genome. The new insights have completely changed the focus of protein analysis. It is no longer time-consuming analysis of unknown products, but rather selective identifications of individual forms, modifications and processings, and overall analysis of global protein outputs from cells and tissues in health and disease. This book gears to the rising need of sensitive, accurate, and fast separation and identification techniques in proteomics. It discusses current methodologies of modern protein analysis, from isolation and sample preparation, over analysis and identification, to final characterization. Several evaluations concentrate on the now productive approaches of two-dimensional gel electrophoresis and mass spectrometry, but alternative methods and further perspectives are also outlined. The book includes an overlook over current databases to connect protein analysis data with all available information,...

Author : Derek J. Chadwick
Publisher : John Wiley & Sons
Page : 282 pages
File Size : 37,78 MB
Release : 2008-04-30
Category : Science
ISBN : 0470514159

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How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.