Progress in Nuclear Magnetic Resonance Spectroscopy最新文献

{"title":"Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations","authors":"Jean-Philippe Demers ,&nbsp;Pascal Fricke ,&nbsp;Chaowei Shi ,&nbsp;Veniamin Chevelkov ,&nbsp;Adam Lange","doi":"10.1016/j.pnmrs.2018.06.002","DOIUrl":"10.1016/j.pnmrs.2018.06.002","url":null,"abstract":"<div><p>In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions.</p><p>This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells <em>in situ</em>. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces.</p><p>Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"109 ","pages":"Pages 51-78"},"PeriodicalIF":6.1,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.06.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36760942","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":"Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments","authors":"Sigrid Milles,&nbsp;Nicola Salvi,&nbsp;Martin Blackledge,&nbsp;Malene Ringkjøbing Jensen","doi":"10.1016/j.pnmrs.2018.07.001","DOIUrl":"10.1016/j.pnmrs.2018.07.001","url":null,"abstract":"<div><p>Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments. We describe the complementarity of different NMR parameters for quantifying the conformational propensities of IDPs in their isolated and phosphorylated states, and we discuss the challenges associated with obtaining structural models of dynamic protein-protein complexes involving IDPs. In addition, we review recent progress in understanding the conformational behavior of IDPs in cell-like environments such as in the presence of crowding agents, in membrane-less organelles and in the complex environment of the human cell.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"109 ","pages":"Pages 79-100"},"PeriodicalIF":6.1,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36760944","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":"Pros and cons of ultra-high-field MRI/MRS for human application","authors":"Mark E. Ladd ,&nbsp;Peter Bachert ,&nbsp;Martin Meyerspeer ,&nbsp;Ewald Moser ,&nbsp;Armin M. Nagel ,&nbsp;David G. Norris ,&nbsp;Sebastian Schmitter ,&nbsp;Oliver Speck ,&nbsp;Sina Straub ,&nbsp;Moritz Zaiss","doi":"10.1016/j.pnmrs.2018.06.001","DOIUrl":"10.1016/j.pnmrs.2018.06.001","url":null,"abstract":"<div><p>Magnetic resonance imaging and spectroscopic techniques are widely used in humans both for clinical diagnostic applications and in basic research areas such as cognitive neuroimaging. In recent years, new human MR systems have become available operating at static magnetic fields of 7 T or higher (≥300 MHz proton frequency). Imaging human-sized objects at such high frequencies presents several challenges including non-uniform radiofrequency fields, enhanced susceptibility artifacts, and higher radiofrequency energy deposition in the tissue. On the other side of the scale are gains in signal-to-noise or contrast-to-noise ratio that allow finer structures to be visualized and smaller physiological effects to be detected. This review presents an overview of some of the latest methodological developments in human ultra-high field MRI/MRS as well as associated clinical and scientific applications. Emphasis is given to techniques that particularly benefit from the changing physical characteristics at high magnetic fields, including susceptibility-weighted imaging and phase-contrast techniques, imaging with X-nuclei, MR spectroscopy, CEST imaging, as well as functional MRI. In addition, more general methodological developments such as parallel transmission and motion correction will be discussed that are required to leverage the full potential of higher magnetic fields, and an overview of relevant physiological considerations of human high magnetic field exposure is provided.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"109 ","pages":"Pages 1-50"},"PeriodicalIF":6.1,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36760938","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":"Recent advances in solid-state nuclear magnetic resonance spectroscopy of exotic nuclei","authors":"César Leroy,&nbsp;David L. Bryce","doi":"10.1016/j.pnmrs.2018.08.002","DOIUrl":"10.1016/j.pnmrs.2018.08.002","url":null,"abstract":"<div><p>We present a review of recent advances in solid-state nuclear magnetic resonance (SSNMR) studies of exotic nuclei. Exotic nuclei may be spin-1/2 or quadrupolar, and typically have low gyromagnetic ratios, low natural abundances, large quadrupole moments (when <em>I</em> &gt; 1/2), or some combination of these properties, generally resulting in low receptivities and/or prohibitively broad line widths. Some nuclides are little studied for other reasons, also rendering them somewhat exotic. We first discuss some of the recent progress in pulse sequences and hardware development which continues to enable researchers to study new kinds of materials as well as previously unfeasible nuclei. This is followed by a survey of applications to a wide range of exotic nuclei (including e.g., ⁹Be, ²⁵Mg, ³³S, ³⁹K, ⁴³Ca, ^47/49Ti, ⁵³Cr, ⁵⁹Co, ⁶¹Ni, ⁶⁷Zn, ⁷³Ge, ⁷⁵As, ⁸⁷Sr, ¹¹⁵In, ¹¹⁹Sn, ^121/123Sb, ^135/137Ba, ^185/187Re, ²⁰⁹Bi), most of them quadrupolar. The scope of the review is the past ten years, <em>i.e.</em>, 2007–2017.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"109 ","pages":"Pages 160-199"},"PeriodicalIF":6.1,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36760941","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":"Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy","authors":"Jean-Nicolas Dumez","doi":"10.1016/j.pnmrs.2018.08.001","DOIUrl":"10.1016/j.pnmrs.2018.08.001","url":null,"abstract":"<div><p>A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"109 ","pages":"Pages 101-134"},"PeriodicalIF":6.1,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36760939","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":"A quarter of a century of SERF: The progress of an NMR pulse sequence and its application","authors":"Stefan Berger","doi":"10.1016/j.pnmrs.2018.10.001","DOIUrl":"10.1016/j.pnmrs.2018.10.001","url":null,"abstract":"<div><p>SERF, an NMR pulse sequence for selectively measuring a spin coupling constant without interference from other couplings, was published by the current author almost 25 years ago in 1995. Since then, about 35 modifications and extensions of the original have been published by other groups and applied to many chemical problems. This review discusses these modifications and provides pertinent examples. A comparative and critical evaluation of these developments is given in tabular form. The last part focuses on the chemical results.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"108 ","pages":"Pages 74-114"},"PeriodicalIF":6.1,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36770646","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":"MR approaches in neurodegenerative disorders","authors":"Andrew M. Blamire","doi":"10.1016/j.pnmrs.2018.11.001","DOIUrl":"10.1016/j.pnmrs.2018.11.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Neurodegenerative disease is the umbrella term which refers to a range of clinical conditions causing degeneration of neurons within the central nervous system leading to loss of brain function and eventual death. The most prevalent of these is Alzheimer’s disease (AD), which affects approximately 50 million people worldwide and is predicted to reach 75 million by 2030. Neurodegenerative diseases can only be fully diagnosed at post mortem by neuropathological assessment of the type and distribution of protein deposits which characterise each different condition, but there is a clear role for imaging technologies in aiding patient diagnoses in life. Magnetic resonance imaging (MRI) and spectroscopy (MRS) techniques have been applied to study these conditions for many years. In this review, we consider the range of MR-based measurements and describe the findings in AD, but also contrast these with the second most common dementia, dementia with Lewy bodies (DLB).&lt;/p&gt;&lt;p&gt;The most definitive observation is the major structural brain changes seen in AD using conventional T1-weighted (T1w) MRI, where medial temporal lobe structures are notably atrophied in most symptomatic patients with AD, but often preserved in DLB. Indeed these findings are sufficiently robust to have been incorporated into clinical diagnostic criteria. Diffusion tensor imaging (DTI) reveals widespread changes in tissue microstructure, with increased mean diffusivity and decreased fractional anisotropy reflecting the degeneration of the white matter structures. There are suggestions that there are subtle differences between AD and DLB populations. At the metabolic level, atrophy-corrected MRS demonstrates reduced density of healthy neurons in brain areas with altered perfusion and in regions known to show higher deposits of pathogenic proteins.&lt;/p&gt;&lt;p&gt;As studies have moved from patients with advanced disease and clear dysfunction to patients with earlier presentation such as with mild cognitive impairment (MCI), which in some represents the first signs of their ensuing dementia, the ability of MRI to detect differences has been weaker and further work is still required, ideally in much larger cohorts than previously studied.&lt;/p&gt;&lt;p&gt;The vast majority of imaging research in dementia populations has been univariate with respect to the MR-derived parameters considered. To date, none of these measurements has uniquely replicated the patterns of tissue involvement seen by neuropathology, and the ability of MR techniques to deliver a non-invasive diagnosis eludes us. Future opportunities may lie in combining MR and nuclear medicine approaches (position emission tomography, PET) to provide a more complete view of structural and metabolic changes. Such developments will require multi-variate analyses, possibly combined with artificial intelligence or deep learning algorithms, to enhance our ability to combine the array of image-derived information, genetic, gender and lifestyle factors.&lt;","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"108 ","pages":"Pages 1-16"},"PeriodicalIF":6.1,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36770644","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":"Theoretical calculations of carbon-hydrogen spin-spin coupling constants","authors":"Leonid B. Krivdin","doi":"10.1016/j.pnmrs.2018.10.002","DOIUrl":"10.1016/j.pnmrs.2018.10.002","url":null,"abstract":"<div><p>Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10–15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"108 ","pages":"Pages 17-73"},"PeriodicalIF":6.1,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36770645","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":"Chemical shift-based methods in NMR structure determination","authors":"Santrupti Nerli ,&nbsp;Andrew C. McShan ,&nbsp;Nikolaos G. Sgourakis","doi":"10.1016/j.pnmrs.2018.03.002","DOIUrl":"10.1016/j.pnmrs.2018.03.002","url":null,"abstract":"<div><p>Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on <em>ab initio</em> fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"106 ","pages":"Pages 1-25"},"PeriodicalIF":6.1,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37203502","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":"Solid-state MAS NMR resonance assignment methods for proteins","authors":"Victoria A. Higman","doi":"10.1016/j.pnmrs.2018.04.002","DOIUrl":"10.1016/j.pnmrs.2018.04.002","url":null,"abstract":"<div><p>The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D ¹³C-detected experiments have been used for the assignment of backbone and side-chain ¹³C and ¹⁵N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.</p></div>","PeriodicalId":20740,"journal":{"name":"Progress in Nuclear Magnetic Resonance Spectroscopy","volume":"106 ","pages":"Pages 37-65"},"PeriodicalIF":6.1,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pnmrs.2018.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37203498","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}