Download or read book Solid State NMR Structural Studies of Proteins Modified with Paramagnetic Tags written by Ishita Sengupta and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Finally, in Chapter 5, we present solid-state NMR studies of the K28C mutant of protein GB1 intentionally modified with 2-[1,4,7,10-tetraazacyclododecan-1-yl]-ethanethiol (TETAC) side chains with a high affinity for transition metal ions like Cu2+, ZnZn2+, Co2+ etc.
Download or read book Development of New Paramagnetic Tags for Solid state NMR Structural Studies of Natively Diamagnetic Proteins written by Jayasimha Arachchige and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Solid state NMR is a powerful technique, which can be used for structural and dynamic studies of complex biological macromolecules. However, the paucity of structural restraints available using conventional techniques complicates the structural studies of proteins by solid-state NMR. Recently, it has been shown that large numbers of long range distance restraints in the form of paramagnetic relaxation enhancements (PREs) and pseudocontact shifts (PCS) can be derived from proteins containing paramagnetic centers.
Download or read book Solid state NMR Structural Studies of Proteins Using Cyclen Based Paramagnetic Metal Chelating Probes written by Rajith Madushanka Jayasinha Arachchige and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The capability of solid-state NMR spectroscopy to provide site-specific atomic-level information makes it one of the main tools used in the structural and dynamic analysis of complex non-crystalline biological macromolecules. However, the challenges associated with measurements of unambiguous long-range distance restraints between nuclear spins by conventional solid-state NMR methods have a significant impact on the ability to determine three-dimensional structures of proteins and nucleic acids. Recently, it has been shown that paramagnetism-based solid-state NMR methods can be utilized to overcome this scarcity of long-range structural information. Electron-nucleus through space dipolar interactions in proteins containing paramagnetic metal centers lead to NMR spectral effects including paramagnetic relaxation enhancements (PREs) and pseudocontact shifts (PCSs), which can provide structural restraints up to 30 A° and beyond exceeding by four to five-fold the length scales accessible by conventional methods. For natively diamagnetic proteins with no endogenous paramagnetic metal centers can be introduced by covalently linking to the protein small molecule tags containing high affinity metal binding motifs. The focus of this research was to develop new thiol-reactive mono and bidentate compact paramagnetic metal chelating probes based on the cyclen manifold for improved solid-state NMR PRE and PCS measurements in natively diamagnetic proteins. The single arm TETAC tag was able to overcome the key shortcomings associated with the more bulky and flexible EDTA type metal-binding tags used in initial paramagnetic solid-state NMR studies. Relative to PREs, the magnitude of which depends primarily on the electron-nucleus distance, the measurements of PCS effects are far more challenging due to an additional dependence on the location of the nucleus in the frame of the g-tensor of the unpaired electron spin of the paramagnetic center. Specifically, such measurements are susceptible to the flexibility of the paramagnetic tag, which can considerably reduce the PCS magnitude or average the effect altogether. To alleviate this problem compact cyclen based tags, which can rigidly be attached to the protein via two disulfide bridges, were designed. The new double arm tags, 2,2'-(1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(N-(2-(pyridin-2-yldisulfanyl)ethyl)acetamide) and 2,2'-(4,10-bis(2-(pyridin-2-yldisulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane-1,7-diyl)diacetic acid, are able to immobilize paramagnetic Co(II) ions on the model 56 amino acid residue protein, B1 immunoglobulin-binding domain of protein G, and successfully overcome the PCS averaging issues associated with the monodentate metal chelating probes. In addition, the same tags loaded with Cu(II) enable solid-state NMR PRE measurements to be performed to yield additional restraints on the protein structure.
Download or read book NMR of Proteins written by Clore and published by CRC Press. This book was released on 1993 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Determination of structures of larger proteins in solution by three- and four-dimensional heteronuclear magnetic resonance spectroscopy. Methodological advances in protein NMR. Determination of high-resolution NMR structures of proteins. Multidimensional NMR studies of immunosuppressant/immunophilin complexes. NMR studies of the structure and role of modules involved in protein-protein interactions. NMR structural studies of membrane proteins. Heteronuclear NMR studies of the molecular synamics of staphylococcal nuclease. Study of protein dynamics by NMR. The folding, stability and dynamics of T4 lysozyme: a perspective using nuclear magnetic resonance.
Download or read book The Development of Proton Detection Based Paramagnetic Solid state NMR Methods as a General Structural Biology Tool written by Justin K. Thomas and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Determination of high-resolution three-dimensional structures of biological macromolecules is essential to studying their physiological functions. In recent years direct proton detection based magic angle spinning solid-state NMR has emerged as a widely applicable atomic-resolution structural tool that permits structure and dynamics studies of biological systems that are challenging for the usual structural techniques such as cryo-electron microscopy, X-ray crystallography, and solution-state NMR. In spite of remarkable recent progress in the accurate structural elucidation of biosystems, the widespread application of solid-state NMR for structural studies of large biosystems is hampered due to the dearth of unambiguous long-distance structural restraints. The conventional solid-state NMR approaches rely on upon through space 13C-13C and 13C-15N magnetic dipole-dipole coupling measurement to obtain structural restraints, which become vanishingly small for distances in the 5-6 Å regime and beyond. The paucity of long-range restraints from traditional through space dipolar coupling measurement-based approaches can be circumvented by site-specific incorporation of paramagnetic center to modified locations of a natively diamagnetic protein using a covalently bound paramagnetic tag. The introduction paramagnetic center in the diamagnetic system leads to the generation of large electron-nuclear hyperfine coupling interactions – which manifest themselves in NMR spectra as pseudocontact shifts (PCSs) and paramagnetic relaxation enhancement (PREs). The measurement of the magnitude of the electron-nuclear interactions can be used to obtain long-distance structural restraints for high-resolution structure calculation. In the solution state, PCSs and PREs measurements have been extensively utilized as long-range structural restraints for the analysis of the structure and interactions of biological macromolecules. However, the widespread applications of PCSs and PREs in solid-state NMR for structural studies have been limited because of the unavailability of compact non-native tags that can rigidly incorporate a paramagnetic metal center into protein in a residue-specific manner. In this thesis, we combined paramagnetic solid-state NMR approaches and proton detection-based solid-state NMR experiments to develop new solid-state NMR methodologies for the structural investigation of biomacromolecules. In chapter 1, we describe basic theoretical concepts of solid-state NMR, paramagnetic solid-state NMR, and direct proton detection-based pulse schemes. In chapter 2, we discuss the Pseudocontact shifts (PCSs) measurements in a natively diamagnetic protein using proton-detected solid-state NMR spectroscopy facilitated by Co2+ binding tag. The compact and rigid tag restricted the mobility of the metal in the solid phase by two-point attachment. In chapter 3, we describe a new method developed for measuring PREs restraints from aliphatic side-chain regions of the natively diamagnetic protein. We utilized new developed metal binding tag and reduced adjoining protonation (RAP) isotopic labeling strategy to site-specific measure side-chain PREs. In chapter 4, we applied direct proton detection-based sequential assignment experiments and radiofrequency driven dipolar recoupling (RFDR) schemes for structural investigation of Gerstmann-Straüssler-Scheinker (GSS) disease-associated Y145Stop human prion protein amyloids.
Download or read book Protein NMR written by Lawrence Berliner and published by Springer. This book was released on 2015-08-24 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers new techniques in protein NMR, from basic principles to state-of-the-art research. It covers a spectrum of topics ranging from a “toolbox” for how sequence-specific resonance assignments can be obtained using a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome. Further topics include the novel applications of Overhauser dynamic nuclear polarization methods (DNP), assessing protein structure, and aspects of solid-state NMR of macroscopically aligned membrane proteins. This book is an ideal resource for students and researchers in the fields of biochemistry, chemistry, and pharmacology and NMR physics. Comprehensive and intuitively structured, this book examines protein NMR and new novel applications that include the latest technological advances. This book also has the features of: • A selection of various applications and cutting-edge advances, such as novel applications of Overhauser dynamic nuclear polarization methods (DNP) and a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome • A pedagogical approach to the methodology • Engaging the reader and student with a clear, yet critical presentation of the applications
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 High resolution Structural Studies of Paramagnetic Proteins by Multidimensional Solid state Nuclear Magnetic Resonance Spectroscopy written by Philippe S. Nadaud and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Nuclear magnetic resonance (NMR) is one of the major spectroscopic techniques available for the characterization of molecular structure and conformational dynamics with atomic level detail. NMR relies on the intrinsic magnetic properties of certain nuclear isotopes, such as 1H, 13C, 15N, and 31P, which provide convenient, site-specific structural probes when placed inside a large external magnetic field. Recent developments in solid-state NMR (SSNMR) spectroscopy promise to enable detailed structural studies to be performed for important biological macromolecules, which are inherently insoluble but at the same time cannot be readily crystallized for analysis by X-ray diffraction. Prominent examples of systems of this type include large macromolecular complexes, membrane-bound peptides and proteins important in cell signaling, and fibrillar protein aggregates associated with the development of systemic and neurodegenerative human disorders, including Alzheimer's and Parkinson's diseases and type II diabetes.
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 High Resolution Structural Studies of Membrane Proteins Using Solid State NMR written by Lubica Aslimovska and published by . This book was released on 2007 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Dynamic and Structural Studies of Membrane Proteins by Oriented Sample Solid State NMR written by Emmanuel Oluwaseyi Awosanya and published by . This book was released on 2020 with total page 97 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Modern NMR Methodology written by Henrike Heise and published by Springer. This book was released on 2014-07-08 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: NMR Spectroscopy for Chemical Analysis at Low Magnetic Fields, by Stefan Glöggler, Bernhard Blümich, Stephan Appelt Dynamic Nuclear Hyperpolarization in Liquids, by Ulrich L. Günther NMR with Multiple Receivers, by Eriks Kupce TROSY NMR Spectroscopy of Large Soluble Proteins, by Yingqi Xu, Stephen Matthews Solid-State NMR Spectroscopy of Proteins, by Henrik Müller, Manuel Etzkorn, Henrike Heise Paramagnetic Solid-State Magic-Angle Spinning NMR Spectroscopy, by Guido Pintacuda, Gwendal Kervern
Download or read book DNA Helicases and DNA Motor Proteins written by Maria Spies and published by Springer Science & Business Media. This book was released on 2012-11-19 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.
Download or read book Solid state NMR Studies of Protein Structures and Molecular Dynamics written by Valérie Copié and published by . This book was released on 1990 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Calcium Orthophosphates written by Sergey V. Dorozhkin and published by CRC Press. This book was released on 2012-06-04 with total page 863 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to a great chemical similarity with the biological calcified tissues, many calcium orthophosphates possess remarkable biocompatibility and bioactivity. Materials scientists use this property extensively to construct artificial bone grafts that are either entirely made of or only surface-coated with the biologically relevant calcium orthophospha
