Progress in Nuclear Magnetic Resonance Spectroscopy最新文献

{"title":"Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules","authors":"Daniel Joss,&nbsp;Daniel Häussinger","doi":"10.1016/j.pnmrs.2019.08.002","DOIUrl":"10.1016/j.pnmrs.2019.08.002","url":null,"abstract":"<div><p>In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, C_B-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 284-312"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47842141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Magnetic susceptibility and paramagnetism-based NMR","authors":"Giacomo Parigi,&nbsp;Enrico Ravera,&nbsp;Claudio Luchinat","doi":"10.1016/j.pnmrs.2019.06.003","DOIUrl":"10.1016/j.pnmrs.2019.06.003","url":null,"abstract":"<div><p>The magnetic interactions between the nuclear magnetic moment and the magnetic moment of unpaired electron(s) depend on the structure and dynamics of the molecules where the paramagnetic center is located and of their partners. The long-range nature of the magnetic interactions is thus a reporter of invaluable information for structural biology studies, when other techniques often do not provide enough data for the atomic-level characterization of the system. This precious information explains the flourishing of paramagnetism-assisted NMR studies in recent years. Many paramagnetic effects are related to the magnetic susceptibility of the paramagnetic metal. Although these effects have been known for more than half a century, different theoretical models and new approaches have been proposed in the last decade. In this review, we have summarized the consequences for NMR spectroscopy of magnetic interactions between nuclear and electron magnetic moments, and thus of the presence of a magnetic susceptibility due to metals, and we do so using a unified notation.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 211-236"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.06.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47920724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural characterization of bacteriophage viruses by NMR","authors":"Amir Goldbourt","doi":"10.1016/j.pnmrs.2019.06.004","DOIUrl":"10.1016/j.pnmrs.2019.06.004","url":null,"abstract":"<div><p>Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the <em>Acinetobacter</em> phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 192-210"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.06.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48051945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Broadband and multi-resonant sensors for NMR","authors":"Hossein Davoodi,&nbsp;Mazin Jouda,&nbsp;Jan G. Korvink,&nbsp;Neil MacKinnon,&nbsp;Vlad Badilita","doi":"10.1016/j.pnmrs.2019.05.001","DOIUrl":"10.1016/j.pnmrs.2019.05.001","url":null,"abstract":"<div><p>It has always been of considerable interest to study the nuclear magnetic resonance response of multiple nuclei simultaneously, whether these signals arise from internuclear couplings within the same molecule, or from uncoupled nuclei within sample mixtures. The literature contains numerous uncorrelated reports on techniques employed to achieve multi-nuclear NMR detection. This paper consolidates the subset of techniques in which single coil detectors are utilized, and highlights the strengths and weaknesses of each approach, at the same time pointing the way towards future developments in the field of multi-nuclear NMR. We compare the different multi-nuclear NMR techniques in terms of performance, and present a guide to NMR probe designers towards application-based optimum design. We also review the applicability of micro-coils in the context of multi-nuclear methods. Micro-coils benefit from compact geometries and exhibit lower impedance, which provide new opportunities and challenges for the NMR probe designer.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"112 ","pages":"Pages 34-54"},"PeriodicalIF":6.1,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44639658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion","authors":"Atul Rangadurai ,&nbsp;Eric S. Szymaski ,&nbsp;Isaac J. Kimsey ,&nbsp;Honglue Shi ,&nbsp;Hashim M. Al-Hashimi","doi":"10.1016/j.pnmrs.2019.05.002","DOIUrl":"https://doi.org/10.1016/j.pnmrs.2019.05.002","url":null,"abstract":"<div><p>This review describes off-resonance <em>R</em>_1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly ¹³C/¹⁵N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern <em>R</em>_1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the <em>R</em>_1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual ¹³C or ¹⁵N spins are then described for measuring off-resonance <em>R</em>_1ρ(¹³C) and <em>R</em>_1ρ(¹⁵N) in uniformly ¹³C/¹⁵N labeled DNA and RNA samples prepared using commercially available ¹³C/¹⁵N labeled nucleotide triphosphates. Approaches for analyzing <em>R</em>_1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"112 ","pages":"Pages 55-102"},"PeriodicalIF":6.1,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.05.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72224302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational protocols for calculating 13C NMR chemical shifts","authors":"Leonid B. Krivdin","doi":"10.1016/j.pnmrs.2019.05.004","DOIUrl":"10.1016/j.pnmrs.2019.05.004","url":null,"abstract":"<div><p>The most recent results dealing with the computation of ¹³C NMR chemical shifts in chemistry (small molecules, saturated, unsaturated and aromatic compounds, heterocycles, functional derivatives, coordination complexes, carbocations, and natural products) are reviewed, paying special attention to theoretical background and accuracy, the latter involving solvent effects, vibrational corrections, and relativistic effects.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"112 ","pages":"Pages 103-156"},"PeriodicalIF":6.1,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.05.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49067756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diffusion MRI in the brain – Theory and concepts","authors":"J-Donald Tournier","doi":"10.1016/j.pnmrs.2019.03.001","DOIUrl":"10.1016/j.pnmrs.2019.03.001","url":null,"abstract":"<div><p>Over the past two decades, diffusion MRI has become an essential tool in neuroimaging investigations. This is due to its sensitivity to the motion of water molecules as they diffuse through the microstructural environment, allowing diffusion MRI to be used as a ‘probe’ of tissue microstructure. Furthermore, this sensitivity is strongly direction-dependent, notably in brain white matter, due to the alignment of structures that restrict or hinder the motion of water molecules, notably axonal membranes. This provides a means of inferring the orientation of fibres <em>in vivo</em>, and by use of appropriate fibre-tracking algorithms, of delineating the path of white matter tracts in the brain. The ability to perform so-called tractography in humans <em>in vivo</em> non-invasively is unique to diffusion MRI, and is now used in applications such as neurosurgery planning and more broadly within investigations of brain connectomics. This review describes the theory and concepts of diffusion MRI and describes its most important areas of application in the brain, with a strong focus on tractography.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"112 ","pages":"Pages 1-16"},"PeriodicalIF":6.1,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49391939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NMR application in unconventional shale reservoirs – A new porous media research frontier","authors":"Yi-Qiao Song,&nbsp;Ravinath Kausik","doi":"10.1016/j.pnmrs.2019.03.002","DOIUrl":"10.1016/j.pnmrs.2019.03.002","url":null,"abstract":"<div><p>Unconventional shale reservoirs have greatly contributed to the recent surge in petroleum production in the United States and are expected to lead the US oil production to a historical high in 2018. The complexity of the rocks and fluids in these reservoirs presents a significant challenge to the traditional approaches to the evaluation of geological formations due to the low porosity, permeability, complex lithology and fluid composition. NMR has emerged as the key measurement for evaluating these reservoirs, for quantifying their petrophysical parameters, fluid properties, and determining productivity. Measurement of the <span><math><mrow><msub><mrow><mi>T</mi></mrow><mrow><mn>1</mn></mrow></msub><mo>/</mo><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></mrow></math></span> ratio by 2D NMR has been found to be critical for identifying the fluid composition of kerogen, bitumen, light/heavy oils, gases and brine in these formations. This paper will first provide a brief review of the theories of relaxation, measurement methods, and data inversion techniques and then will discuss several examples of applications of these NMR methods for understanding various aspects of the unconventional reservoirs. At the end, we will briefly discuss a few other topics, which are still in their developmental stages, such as solid state NMR, and their potential applications for shale rock evaluation.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"112 ","pages":"Pages 17-33"},"PeriodicalIF":6.1,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42544258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Paramagnetic NMR in solution and the solid state","authors":"Andrew J. Pell ,&nbsp;Guido Pintacuda ,&nbsp;Clare P. Grey","doi":"10.1016/j.pnmrs.2018.05.001","DOIUrl":"10.1016/j.pnmrs.2018.05.001","url":null,"abstract":"<div><p>The field of paramagnetic NMR has expanded considerably in recent years. This review addresses both the theoretical description of paramagnetic NMR, and the way in which it is currently practised. We provide a review of the theory of the NMR parameters of systems in both solution and the solid state. Here we unify the different languages used by the NMR, EPR, quantum chemistry/DFT, and magnetism communities to provide a comprehensive and coherent theoretical description. We cover the theory of the paramagnetic shift and shift anisotropy in solution both in the traditional formalism in terms of the magnetic susceptibility tensor, and using a more modern formalism employing the relevant EPR parameters, such as are used in first-principles calculations. In addition we examine the theory first in the simple non-relativistic picture, and then in the presence of spin-orbit coupling. These ideas are then extended to a description of the paramagnetic shift in periodic solids, where it is necessary to include the bulk magnetic properties, such as magnetic ordering at low temperatures. The description of the paramagnetic shift is completed by describing the current understanding of such shifts due to lanthanide and actinide ions. We then examine the paramagnetic relaxation enhancement, using a simple model employing a phenomenological picture of the electronic relaxation, and again using a more complex state-of-the-art theory which incorporates electronic relaxation explicitly. An additional important consideration in the solid state is the impact of bulk magnetic susceptibility effects on the form of the spectrum, where we include some ideas from the field of classical electrodynamics. We then continue by describing in detail the solution and solid-state NMR methods that have been deployed in the study of paramagnetic systems in chemistry, biology, and the materials sciences. Finally we describe a number of case studies in paramagnetic NMR that have been specifically chosen to highlight how the theory in part one, and the methods in part two, can be used in practice. The systems chosen include small organometallic complexes in solution, solid battery electrode materials, metalloproteins in both solution and the solid state, systems containing lanthanide ions, and multi-component materials used in pharmaceutical controlled-release formulations that have been doped with paramagnetic species to measure the component domain sizes.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"111 ","pages":"Pages 1-271"},"PeriodicalIF":6.1,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37290327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein sample preparation for solid-state NMR investigations","authors":"Denis Lacabanne ,&nbsp;Marie-Laure Fogeron ,&nbsp;Thomas Wiegand ,&nbsp;Riccardo Cadalbert ,&nbsp;Beat H. Meier ,&nbsp;Anja Böckmann","doi":"10.1016/j.pnmrs.2019.01.001","DOIUrl":"10.1016/j.pnmrs.2019.01.001","url":null,"abstract":"<div><p>Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"110 ","pages":"Pages 20-33"},"PeriodicalIF":6.1,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.01.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36998191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}