Download or read book Protein Structure Determination and Methods Development for Solid State NMR written by Francesco Ravotti and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Development of Solid state NMR Methodologies for Protein Structure Determination Based on Paramagnetic Tagging written by Dwaipayan Mukhopadhyay and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years solid-state NMR has emerged as a valuable tool for elucidating structure and dynamics of large biomolecular systems, especially suited for application in systems ranging from amyloid fibrils, membrane proteins to large protein ligand complexes inaccessible by more traditional structure determination techniques e.g. X-ray crystallography and solution-state NMR. Essential in determination of a biomolecular structure is the acquisition of numerous high quality interatomic distance restraints. However, conventional dipolar coupling based methods lead to significant challenges for accurate determination of critical long range distances. An alternative method to overcome this limitation is the incorporation of paramagnetic centers in proteins and utilization of the very large electron-nucleus couplings. In this dissertation, we combine state of the art proton-detection techniques with development of novel rigid transition metal binding tags, to improve the quality of long range distance restraints generated by measurement of site-specific paramagnetic relaxation enhancements in solid-state NMR.
Download or read book Solid state NMR written by Frances Separovic and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to describe the methodology and applications of solid-state NMR spectroscopy to studies of membrane proteins, membrane-active peptides and model biological membranes. As well as structural studies, this book contains coverage of membrane interactions and molecular motions. Advances in biological solid-state NMR are very pertinent with high-field developments seeing applications in biological membranes and whole cells. Experts who are leaders in the development and application of biological solid-state NMR are chapter contributors. Part of Biophysical Society-IOP series.
Download or read book Hardware and Methods Development for Protein Structure Elucidation by Solid state NMR Spectroscopy written by Eric Karl Paulson and published by . This book was released on 2004 with total page 674 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Annual Reports on NMR Spectroscopy written by Graham A. Webb and published by Academic Press. This book was released on 2013-06-07 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: NMR is an analytical tool used by chemists and physicists to study the structure and dynamics of molecules. In recent years, no other technique has gained such significance as NMR spectroscopy. It is used in all branches of science in which precise structural determination is required and in which the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a premier means for the specialist and non-specialist alike to become familiar with new techniques and applications of NMR spectroscopy. Nuclear magnetic resonance (NMR) is an analytical tool used by chemists and physicists to study the structure and dynamics of molecules In recent years, no other technique has gained such significance as NMR spectroscopy. It is used in all branches of science in which precise structural determination is required and in which the nature of interactions and reactions in solution is being studied Annual Reports on NMR Spectroscopy has established itself as a premier means for the specialist and non-specialist alike to become familiar with new techniques and applications of NMR spectroscopy
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 Applications of Dynamic Nuclear Polarization and Solid state Nuclear Magnetic Resonance for Protein Structure Determination written by Rebecca Maria Mayrhofer and published by . This book was released on 2010 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: Magic Angle Spinning (MAS) solid state nuclear magnetic resonance (SSNMR) is a developing method for determining the structures and studying the dynamics and functions of biological molecules. This method is particularly important for systems, such as amyloidogenic fibrous proteins, that do not crystallize or dissolve well and are therefore not amendable to X-ray or solution NMR techniques. However, due to inherently low sensitivity, NMR experiments may require weeks to obtain spectra with sufficient signal-to-noise ratio. This issue is further exacerbated for biological systems of interest due to their large size and limited mass availability. The sensitivity can be increased by two orders of magnitude by combining MAS NMR with dynamic nuclear polarization (DNP). The application of SSNMR-DNP to protein structure determination is explored using malonic acid and a model peptide system, WT-TTR105-115. A custom built MAS-SSNMR probe is modified for the purpose of MAS-SSNMR DNP experiments.
Download or read book Membrane Protein Structure Determination written by Jean-Jacques Lacapère and published by Methods in Molecular Biology. This book was released on 2010-08-06 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Solid state NMR approaches for protein structure determination written by Matthias Huber and published by . This book was released on 2012 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Development of Solid state NMR Spectroscopy for Membrane Proteins written by Jiaozhi George Lu and published by . This book was released on 2014 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Atomic-resolution membrane protein structures can be determined by solid-state Nuclear Magnetic Resonance (NMR) spectroscopy, and the unique advantage of the approach is that membrane proteins reside in near-native lipid bilayer environment at physiological pH and temperature, which minimizes the potential distortions of the protein structure caused by the environment. Here, the full-length mercury transporter protein, MerF, is the focus of the structural studies, and the protein is an essential part of the bacterial mercury detoxification system that has been exploited as a potential engineering target for mercury bioremediation strategies. The backbone structures of the full-length MerF are determined in two environments, (i) magnetically aligned bicelles by oriented-sample (OS) solid-state NMR and (ii) proteoliposome by rotationally aligned (RA) solid-state NMR; and notably, both environments provide the planar lipid bilayer environment for the protein. The structural study of MerF in aligned bicelle has initially been challenging for the OS solid-state NMR, and consequently, methods have been developed to tackle the two major obstacles, the spectral resolution and resonance assignments. New pulse sequence, MSHOT-Pi4/Pi, has demonstrated a reduction of the 1H resonance line width by more than a factor of two, a significant improvement in spectral resolution. New resonance assignment method, Dipolar Coupling Correlated Isotropic Chemical Shift (DCCICS) Analysis, has been developed that is able to transfer resonance assignment from isotropic NMR methods to OS solid-state NMR spectra. The combined usage of several resonance assignment strategies and special tactics, such as applying DCCICS to the new high-resolution proton-evolved local field experiments for terminal and loop residues, has resulted in the complete assignment of all backbone immobile residues of the full-length MerF protein in magnetically aligned bicelle. Meanwhile, RA solid-state NMR is developed in the lab as a new method that combines the strength of magic-angle-spinning (MAS) solid-state NMR in obtaining resonance assignment and the concept of molecular alignment from OS solid-state NMR in obtaining angular restraints. In applying to the structural study of MerF, the method is further incorporated with multi-contact cross polarization and sequential backbone "walk" with three three-dimensional experiments, and the first structure of full-length MerF is determined with the method. In comparison to the previously determined structure of the truncated MerF (MerFt), the full-length structure reveals that the protein truncation has caused large conformational rearrangement at a place more than ten residues away from the truncation site, which serves as an example to demonstrate the importance of studying the full-length unmodified proteins by structural biologists. Additionally, the structure reveals that both mercury-binding sites are located at the intracellular side of the membrane, hinting at the observation of a conformation that allows intramolecular transfer of mercury ions. Subsequently after the complete assignment of MerF in OS solid-state NMR, the MerF structure determined by RA solid-state NMR is further improved by incorporating additional angular restraints from OS solid-state NMR and by the new treatment of dihedral restraints derived from the experimental study of C-terminal dynamics. Lastly, as a side project, the theoretical foundation of MSHOT-Pi4 pulse sequence is further explored. The observation that the pulse sequence selectively improves the resolution of membrane protein samples but not of standard single crystal sample has been analytically generalized as the principle of "motion-adapted" pulse sequence, where it is found that the interference between sample's spatial rotational motion and the radio-frequency pulse rotation in the quantum spin space is the cause of the selectivity. As a related endeavor, the mechanisms of dilute spin exchange and the magic-angle 1H spin-lock pulses have been analyzed theoretically and demonstrated in standard and biological samples. Mixed-order proton-relay mechanism is proposed to be the main contributor to dilute spin exchange in stationary aligned sample, and once more, the difference of pulse performance between standard and biological samples is observed that may be a consequence of several causes including sample motion. In conclusion, the development of various methods in OS and RA solid-state NMR are likely to find their usage in future structural studies of membrane proteins; the theoretical principle of motion-adapted property opens up new avenue to develop pulse sequences for membrane protein samples; and the atomic-resolution backbone structures of MerF contribute information for structural biologist and for the mechanistic study of mercury transportation.
Download or read book Development and Application of Solid state NMR Methods for Investigating Protein Structure and Dynamics written by Martin D. Gelenter and published by . This book was released on 2021 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solid-state nuclear magnetic resonance spectroscopy (SSNMR) is uniquely well-suited among spectroscopic and microscopy techniques for studying the structure and dynamics of biomacromolecules with atomic length-scale resolution. The development and application of advanced SSNMR techniques facilitates the study of novel systems to understand protein structure and function.
Download or read book Towards Closing the Gap written by Matthew Fritz and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The overall theme of this thesis is the development and application of an integrated approach to accurately measure and compute anisotropic NMR parameters, chemical shift and dipolar tensors, in microcrystalline proteins and organic solids. Protein structures determined by solid state magic angle spinning (MAS) NMR use local dipolar correlations in conjunction with the qualitative torsion angle restraints derived from isotropic chemical shifts. Despite progress in the last two decades in the development of MAS NMR for protein structure determination, current methods are still time-consuming and error-prone. In large proteins and protein assemblies, multiple samples prepared with different isotopic labels and many multidimensional MAS NMR experiments on each of these samples are required for obtaining distance restraints. Even then, the distance restraints are local and do not exceed 5-7 Å. Existing protocols can potentially be improved, both in speed and accuracy, by adding information about chemical shift tensors and long-range distance restraints.
Download or read book Advances in Biological Solid State NMR written by Frances Separovic and published by Royal Society of Chemistry. This book was released on 2014 with total page 632 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Biological NMR brings the reader up to date with chapters from international leaders of this growing field, covering the most recent developments in the methodology and applications of solid state NMR to studies of membrane interactions and molecular motions
Download or read book Methodology and Applications of High Resolution Solid state NMR to Structure Determination of Proteins written by Józef Romuald Lewandowski and published by . This book was released on 2008 with total page 878 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of methodological developments and applications of solid-state NMR for assignment and high resolution structure determination of microcrystalline proteins and amyloid fibrils are presented. Magic angle spinning spectroscopy on uniformly and selectively "C and '5N labeled samples is performed at magnetic fields from 11.7 to 21.1 T and spinning frequencies from 9 to 65 kHz.Dynamic Nuclear Polarization on nanocrystals of amyloidogenic peptide GNNQQNY is presented demonstrating that 'H-'H spin diffusion can efficiently transfer the enhanced polarization across the solute that is not in an intimate contact with the polarizing agent.An improved theoretical treatment of Rotational Resonance Width (R2W) experiments and its application to determination of precise 13C-13C distance is presented. A general theory of second averaging in modulation frame for designing solid-state NMR experiments is introduced and discussed in the context of two methods: Cosine Modulated Rotary Resonance (CMpRR) for performing a broadband double-quantum 13C-13C recoupling without the need for additional 'H decoupling and Cosine Modulated recoupling with Chemical Shift reintroduction (COMICS) that provides a general frequency selective method for measuring precise 13C-13C distances in uniformly labeled solids. Cosine Modulated Adiabatic Recoupling (CMAR) - an adiabatic extension of the CMpRR, that is particularly robust with respect to rf inhomogeneity, is also introduced. A number of applications CMpRR at 21.1 T to proteins with varying degrees of macroscopic order are presented. A second order Third Spin Assisted Recoupling (TSAR) mechanism is introduced and discussed in detail. The heteronuclear TSAR - Proton Assisted Insensitive Nuclei Cross-Polarization (PAIN-CP) and homonuclear Proton Assisted Recoupling (PAR) yield long distance 13C_1-N, 3C-_13C and 15N- 5N restraints in uniformly labeled systems with spinning frequencies up to 65 kHz that are used for protein structure calculation. Structure, dynamics and polymorphism of amyloidogenic peptide GNNQQNY from the yeast protein sup35p are investigated. Finally, PAIN-CP and '3C-13C PAR are used for high resolution de novo structure determination of 10.4 kDa Crh protein dimer.
Download or read book Experimental Approaches of NMR Spectroscopy written by The Nuclear Magnetic Resonance Society of Japan and published by Springer. This book was released on 2017-11-23 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 Protein Structure Determination by Paramagnetic NMR and Computational Hybrid Approach written by Kala Bharath Pilla and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
