[PDF] Computational Aspects Of Membrance Protein Structure Determination Using Solid State Nuclear Magnetic Resonance eBook

Author : N. Rama Krishna
Publisher : Springer Science & Business Media
Page : 565 pages
File Size : 18,58 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 : Stanley Casimir Howell
Publisher :
Page : 211 pages
File Size : 36,78 MB
Release : 2007
Category :
ISBN :

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Efforts at elucidating the structural biology of membrane proteins represent an ongoing challenge to conventional methods of structure determination. The emergence of new methods for the measurement and application of orientational restraints have offered new avenues of pursuing the determination of membrane protein structures. Presented in this thesis is the evolution of experimental and computation methods necessary to extend NMR based structure determination methods to the polytopic mercuric ion transport proteins of the mer operon. Primary structural efforts are focused upon the bi-spanning protein, MerF, using solution-state NMR methods on protein reconstituted into isotropic and weakly aligned micelles and solid-state NMR methods on protein reconstituted into statically aligned bicelles. The application of the methods developed for MerF are applied to a tri-spanning chimeric protein, MerTf, to extend the NMR based methodology toward the structure determination of the principal mercuric ion transporter, MerT.

Author : Conggang Li
Publisher :
Page : 116 pages
File Size : 39,16 MB
Release : 2007
Category :
ISBN : 9780549022480

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Solid-state nuclear magnetic resonance (NMR) provides a unique approach for structure determination and functional studies of membrane proteins in a native lipid bilayer environment. Here, polarization inversion spin exchange at magic angle (PISEMA) experiments of aligned samples were applied to study the proton channel, M2 protein transmembrane portion (M2-TMD) from influenza A virus and other intact full length membrane proteins. The challenges of membrane protein structure characterization utilizing static aligned sample, including sample preparation, sample stability induced by RF heating, PISEMA experiment set up were discussed.

Author : Jean-Jacques Lacapère
Publisher : Methods in Molecular Biology
Page : 482 pages
File Size : 17,12 MB
Release : 2010-08-06
Category : Science
ISBN :

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Membrane proteins, representing nearly 40% of all proteins, are key components of cells involved in many cellular processes, yet only a small number of their structures have been determined. Membrane Protein Structure Determination: Methods and Protocols presents many detailed techniques for membrane protein structure determination used today by bringing together contributions from top experts in the field. Divided into five convenient sections, the book covers various strategies to purify membrane proteins, approaches to get three dimensional crystals and solve the structure by x-ray diffraction, possibilities to gain structural information for a membrane protein using electron microscopy observations, recent advances in nuclear magnetic resonance (NMR), and molecular modelling strategies that can be used either to get membrane protein structures or to move from atomic structure to a dynamic understanding of a molecular functioning mechanism. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Membrane Protein Structure Determination: Methods and Protocols serves as an ideal reference for scientists seeking to further our knowledge of these vital and versatile proteins as well as our overall understanding of the complicated world of cell biology.

Author : Kala Bharath Pilla
Publisher :
Page : 0 pages
File Size : 48,89 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 : Dmitry Shishmarev
Publisher :
Page : 428 pages
File Size : 39,81 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.