Progress in Nuclear Magnetic Resonance Spectroscopy最新文献

{"title":"From LASER physics to the para-hydrogen pumped RASER","authors":"S. Appelt ,&nbsp;A. Kentner ,&nbsp;S. Lehmkuhl ,&nbsp;B. Blümich","doi":"10.1016/j.pnmrs.2019.05.003","DOIUrl":"10.1016/j.pnmrs.2019.05.003","url":null,"abstract":"<div><p>The properties of the LASER with respect to self-organization are compared with the key features of the <em>p</em>-H₂ pumped RASER. According to LASER theory the equations of motion for the LASER can be derived from the enslaving principle, i.e. the slowest-changing order parameter (the light field in the resonator) enslaves the rapidly relaxing atomic degrees of freedom. Likewise, it is shown here that the equations of motion for the <em>p</em>-H₂ pumped RASER result from a set of order parameters, where the transverse magnetization of the RASER-active spin states enslaves the electromagnetic modes. The consequences are striking for nuclear magnetic resonance (NMR) spectroscopy, since long-lasting multi-mode RASER oscillations enable unprecedented spectroscopic resolution down to the micro-Hertz regime. Based on the theory for multi-mode RASER operation we analyze the conditions that reveal either the collapse of the entire NMR spectrum, the occurrence of self-organized frequency-combs, or RASER spectra which reflect the <em>J</em>-coupled network of the molecule. Certain RASER experiments involving the protons of ¹⁵N pyridine or 3-picoline molecules pumped with <em>p</em>-H₂ via SABRE (Signal Amplification By Reversible Exchange) show either a single RASER oscillation in the time domain, giant RASER pulses or a complex RASER beat pattern. The corresponding ¹H spectra consist of one narrow line, equidistant narrow lines (frequency-comb), or highly resolved lines reporting NMR properties, respectively. Numerous applications in the areas of material sciences, fundamental physics and medicine involving high precision sensors for magnetic fields, rotational motions or molecular structures become feasible.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 1-32"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48727791","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":"17O NMR studies of organic and biological molecules in aqueous solution and in the solid state","authors":"Gang Wu","doi":"10.1016/j.pnmrs.2019.06.002","DOIUrl":"10.1016/j.pnmrs.2019.06.002","url":null,"abstract":"<div><p>This review describes the latest developments in the field of ¹⁷O NMR spectroscopy of organic and biological molecules both in aqueous solution and in the solid state. In the first part of the review, a general theoretical description of the nuclear quadrupole relaxation process in isotropic liquids is presented at a mathematical level suitable for non-specialists. In addition to the first-order quadrupole interaction, the theory also includes additional relaxation mechanisms such as the second-order quadrupole interaction and its cross correlation with shielding anisotropy. This complete theoretical treatment allows one to assess the transverse relaxation rate (thus the line width) of NMR signals from half-integer quadrupolar nuclei in solution over the entire range of motion. On the basis of this theoretical framework, we discuss general features of quadrupole-central-transition (QCT) NMR, which is a particularly powerful method of studying biomolecules in the slow motion regime. Then we review recent advances in ¹⁷O QCT NMR studies of biological macromolecules in aqueous solution. The second part of the review is concerned with solid-state ¹⁷O NMR studies of organic and biological molecules. As a sequel to the previous review on the same subject [G. Wu, Prog. Nucl. Magn. Reson. Spectrosc. 52 (2008) 118–169], the current review provides a complete coverage of the literature published since 2008 in this area.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 135-191"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.06.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41277846","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":"Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR","authors":"Kai Klöpfer,&nbsp;Franz Hagn","doi":"10.1016/j.pnmrs.2019.08.001","DOIUrl":"10.1016/j.pnmrs.2019.08.001","url":null,"abstract":"<div><p>Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"114 ","pages":"Pages 271-283"},"PeriodicalIF":6.1,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2019.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42323089","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":"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}