Download or read book Development of Solid state NMR Spectroscopy for Membrane Proteins and the Application to Vpu from HIV 1 written by Eugene Chun-Chin Lin and published by . This book was released on 2015 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solid-state nuclear magnetic resonance (NMR) spectroscopy is a robust method to solve the structures of membrane proteins in their native bilayer environments. Two systems have been well established: oriented samples (OS) are referred to proteins incorporated in the magnetic aligned bicelles, and rotationally aligned (RA) samples are referred to proteins undergoing fast rotational diffusion in proteoliposomes. 1H-15N and 1H-13C dipolar couplings are measured as the angular restraints for the structure calculations. New separated-local-field experiment, Dual-PISEMO, is developed for OS solid-state NMR to measure 1H-13C dipolar couplings of the uniformly 13C labeled proteins, which provide both backbone and side-chain conformations. In order to obtain the full assignments and restraints in OS solid-state NMR, 1H-irradiations with mismatched conditions are implemented to improve the crucial step: the magnetization transfer between 15N and 13C. Non-uniform sampling (NUS) is an alternative approach to further the experimental time of high-dimensional solid-state NMR experiments. Compressed sensing (CS) is able to reconstruct the spectra with 25 ~ 33% of data with the optimized sampling scheme, and covariance spectroscopy provides promising results with alternative States sampling scheme, which requires 50% of data or less. Viral protein "u" (Vpu) from HIV-1 is a type I membrane protein consisting of a transmembrane domain and a cytoplasmic domain, which are associated with different biological activities to enhance viral infectivity. It is essential to determine the three-dimensional structure of Vpu in order to understand its mechanisms in the molecular level and to develop new classes of anti-viral drugs. Magic-angle spinning (MAS) experiments providing high-sensitivity and high- resolution spectra, are implemented to study Vpu incorporated into proteoliposomes. 15N, 13C chemical shift and 1H-15N, 1H-13C dipolar couplings are measured and converted to equivalent structural restraints.
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 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 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 Perspectives on Solid State NMR in Biology written by S.R. Kiihne and published by Springer Science & Business Media. This book was released on 2013-03-14 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solid state NMR is rapidly emerging as a universally applicable method for the characterization of ordered structures that cannot be studied with solution methods or diffraction techniques. This proceedings -; from a recent international workshop - captures an image of the latest developments and future directions for solid state NMR in biological research, particularly on membrane proteins. Detailed information on how hormones or drugs bind to their membrane receptor targets is needed, e.g. for rational drug design. Higher fields are bringing clear improvements, and the power of solid state NMR techniques for studying amorphous and membrane associated peptides, proteins and complexes is shown by examples of applications at ultra-high fields. Progress in protein expression, experimental design and data analysis are also presented by leaders in these research areas.
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 Spectroscopy for Biopolymers written by Hazime Saitô and published by Springer Science & Business Media. This book was released on 2006-08-05 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: ‘‘Biopolymers’’ are polymeric materials of biological origin, including globular, membrane, and fibrous proteins, polypeptides, nucleic acids, po- saccharides, lipids, etc. and their assembly, although preference to respe- ive subjects may be different among readers who are more interested in their biological significance or industrial and/or medical applications. Nevert- less, characterizing or revealing their secondary structure and dynamics may be an equally very important and useful issue for both kinds of readers. Special interest in revealing the 3D structure of globular proteins, nucleic acids, and peptides was aroused in relation to the currently active Structural Biology. X-ray crystallography and multidimensional solution NMR sp- troscopy have proved to be the standard and indispensable means for this purpose. There remain, however, several limitations to this end, if one intends to expand its scope further. This is because these approaches are not always straightforward to characterize fibrous or membrane proteins owing to extreme difficulty in crystallization in the former, and insufficient spectral resolution due to sparing solubility or increased effective molecular mass in the presence of surrounding lipid bilayers in the latter.
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 Current Developments in Solid State NMR Spectroscopy written by Norbert Müller and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Why to apply solid-state NMR? - By now, we should have learned that NMR is mainly used for the study of molecules in solution, while x-ray diffraction is the method of choice for solids. Based on this fact, the two recent 'NMR-Nobelprizes' went indeed into the liquid phase: my own one eleven years ago, and particularly the most recent one to Kurt Wuthrich. His prize is beyond any doubts very well justified. His contribution towards the study of biomolecules in solution, in their native (or almost native) environment is truly monumental. We all will profit from it indirectly when one of our future diseases will be cured with better drugs, based on the insightful knowledge gained through liquid-state NMR. Two fields of NMR are still left out of the Nobel Prize game: magnetic reso nance imaging (MRI) and solid-state NMR. The disrespect for MRI in Stockholm is particularly difficult to understand; but this is not a subject to be discussed at the present place. Solid-state NMR is the third of the three great fields of NMR, powerful already today and very promising for the near future.
Download or read book Solid state NMR Studies of Membrane Proteins and Membrane Protein Complexes written by Lindsay J. Sperling and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins help control nearly every process in the cell, which is why approximately 50% of pharmaceuticals currently on the market target membrane proteins. Knowledge of structure-function relationships of these proteins could be leveraged to produce more efficient drugs. However, the traits that make membrane proteins so interesting also make them difficult targets for traditional structure elucidation techniques. X-ray crystallography relies on the use of single crystals, production of which are elusive for membrane proteins due to their inherent dynamic loops and stretches of hydrophobic residues, which contribute to aggregation and/or loss of function without the presence of a lipid environment. Solution NMR experiences difficulty dealing with slow molecular tumbling due to the large sizes of membrane proteins. Conversely, solid-state NMR (SSNMR) has no inherent size limitation and does not require the use of crystals, which presents SSNMR with the unique capability to study membrane proteins in native environments at atomic-resolution. However, this technique is still a relatively new tool for solving structures of biomolecules. Here, we begin to develop strategies for solid-state NMR de novo structure determination. We provide a 0́−divide-and-conquer0́+ investigation of an E. coli 41 kDa membrane protein complex, DsbA/DsbB. We begin by completing chemical shift assignments, the first step in structure determination in NMR studies, of the 21 kDa protein DsbA to optimize sensitivity and resolution of data collection and analysis of large systems. We then use this study to drive forward structural examination of the disulfide bond forming system DsbA/DsbB. Finally, SSNMR techniques are used to study a 144 kDa cytochrome bo3 ubiquinol oxidase demonstrating the power of this technique to investigate large membrane complexes in native environments.
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 Sample Preparation of Membrane Proteins Suitable for Solid State MAS NMR and Development of Assignment Strategies written by Matthias Hiller and published by . This book was released on 2009 with total page 120 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 Solid State NMR Spectroscopy written by Melinda J. Duer and published by John Wiley & Sons. This book was released on 2008-04-15 with total page 592 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is for those familiar with solution-state NMR who are encountering solid-state NMR for the first time. It presents the current understanding and applications of solid-state NMR with a rigorous but readable approach, making it easy for someone who merely wishes to gain an overall impression of the subject without details. This dual requirement is met through careful construction of the material within each chapter. The book is divided into two parts: "Fundamentals" and "Further Applications." The section on Fundamentals contains relatively long chapters that deal with the basic theory and practice of solid-state NMR. The essential differences and extra scope of solid-state NMR over solution-state is dealt with in an introductory chapter. The basic techniques that all chapters rely on are collected into a second chapter to avoid unnecessary repetition later. Remaining chapters in the "Fundamentals" part deal with the major areas of solid-state NMR which all solid-state NMR spectroscopists should know about. Each begins with an overview of the topic that puts the chapter in context. The basic principles upon which the techniques in the chapter rely are explained in a separate section. Each of these chapters exemplifies the principles and techniques with the applications most commonly found in current practice. The "Further Applications" section contains a series of shorter chapters which describe the NMR techniques used in other, more specific areas. The basic principles upon which these techniques rely will be expounded only if not already in the Fundamentals part.
Download or read book Structural Characterization of Membrane Proteins by Solid state NMR Spectroscopy written by Karsten Seidel and published by . This book was released on 2008 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural Characterization of Membrane Proteins by Solid state NMR Spectroscopy written by and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
