Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate . When is greater than the chemical shift difference between free and bound, which typically equates to an affinity weaker than about 3 μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows to be determined from measurement of peak positions, provided the measurements are made appropriately. H shifts are influenced to a large extent by through-space interactions, whereas C and C shifts are influenced more by through-bond effects. N and C′ shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure N HSQC spectra, calculate the geometrical distance moved by the peak, weighting N shifts by a factor of about 0.14 compared to H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of CH signals. Slow to intermediate exchange rates lead to line broadening, and make values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by simultaneous fitting of many measured shift changes, or more simply by adding substoichiometric amounts of ligand. The chemical shift changes can be used as restraints for docking ligand onto protein. By use of quantitative calculations of ligand-induced chemical shift changes, it is becoming possible to determine not just the position but also the orientation of ligands.
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
Although scalar-coupling provides important structural information, the resulting signal splittings significantly reduce the resolution of NMR spectra. Limited resolution is a particular problem in proton NMR experiments, resulting in part from the limited proton chemical shift range (∼10 ppm) but even more from the splittings due to scalar coupling to nearby protons. “Pure shift” NMR spectroscopy (also known as broadband homonuclear decoupling) has been developed for disentangling overlapped proton NMR spectra. The resulting spectra are considerably simplified as they consist of single lines, reminiscent of proton-decoupled C-13 spectra at natural abundance, with no multiplet structure. The different approaches to obtaining pure shift spectra are reviewed here and several applications presented. Pure shift spectra are especially useful for highly overlapped proton spectra, as found for example in reaction mixtures, natural products and biomacromolecules.
In this review we focus on the technology associated with low-field NMR. We present the current state-of-the-art in low-field NMR hardware and experiments, considering general magnet designs, rf performance, data processing and interpretation. We provide guidance on obtaining the optimum results from these instruments, along with an introduction for those new to low-field NMR. The applications of lowfield NMR are now many and diverse. Furthermore, niche applications have spawned unique magnet designs to accommodate the extremes of operating environment or sample geometry. Trying to capture all the applications, methods, and hardware encompassed by low-field NMR would be a daunting task and likely of little interest to researchers or industrialists working in specific subject areas. Instead we discuss only a few applications to highlight uses of the hardware and experiments in an industrial environment. For details on more particular methods and applications, we provide citations to specialized review articles.
Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR.
► Description of the major methods for detecting GABA in the human brain using MRS. ► Literature review of studies using MRS of GABA, categorized as methodological, neuroscience, pharmacological, and clinical. ► Summary tables of methodological parameters and major findings.
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied , , or in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other ‘omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
NMR spectroscopy is a most powerful tool for the determination of complex structures and interactions, and can be performed on components with various physical phases. NMR provides significant level of molecular information and can be performed on samples that have had little or no-pretreatment makes it highly appropriate for environmental analysis. Solution-state NMR affords high resolution spectra and thus provides excellent information on structure and interactions even for very complex environmental mixtures. Presaturation Utilizing Relaxation Gradients and Echoes (PURGE) is extremely effective at selectively removing the water signal and when only the minimal irradiation field is used even signals from non-exchangeable protons from under the water signal can be recovered to some extent. Numerous NMR parameters can be utilized to provide a range of information as to the molecular orientation, motion and interactions at the molecular scale.
A history of the UK NMR Discussion group (NMRDG) was compiled by Les Sutcliffe and John Lindon and uploaded in a wwebsite. The site provided information on the early days of NMR spectroscopy in the country and a history of the formation and evolution of the NMRDG till 2009. A full set of programs of the one day and other short scientific meetings of the Group from 1964 was included. The Group also organized a series of international conferences along with the Royal Society of Chemistry from 1969 till 2003 and a full set of the programs of these meetings was found on the site. A number of distinguished resonance practitioners who were based in the UK were provided with obituaries after their death. The authors wanted to receive additional information and images for the history web site and needed to be notified of any errors and omissions.
Valuable information about the local environment of the aluminum nucleus can be obtained through Al-27 Nuclear Magnetic Resonance (NMR) parameters like the isotropic chemical shift, scalar and quadrupolar coupling constants, and relaxation rate. With nearly 250 scientific articles per year dealing with Al-27 NMR spectroscopy, this analytical tool has become popular because of the recent progress that has made the acquisition and interpretation of the NMR data much easier. The application of Al-27 NMR techniques to various classes of compounds, either in solution or solid-state, has been shown to be extremely informative concerning local structure and chemistry of aluminum in its various environments. The development of experimental methodologies combined with theoretical approaches and modeling has contributed to major advances in spectroscopic characterization especially in materials sciences where long-range periodicity and classical local NMR probes are lacking. In this review we will present an overview of results obtained by Al-27 NMR as well as the most relevant methodological developments over the last 25 years, concerning particularly on progress in the application of liquid- and solid-state Al-27 NMR to the study of aluminum-based materials such as aluminum polyoxoanions, zeolites, aluminophosphates, and metal organic-frameworks. (C) 2016 Elsevier B.V. All rights reserved.
Studying proteins with the help of paramagnetic lanthanide ions is becoming increasingly popular. By choosing the attachment sites of paramagnetic tags, it is possible to study such protein properties site-selectively without having to solve again the 3D structure of the entire protein, as required in X-ray crystallography or cryo-electron microscopy. In particular, owing to the long-range nature of paramagnetic effects, lanthanide tags lend themselves to site-specific studies where the tag must be sufficiently far from the site of interest not to interfere. To support site-specific NMR studies, it will be useful to develop improved methods for labeling the site of interest with NMR isotopes, e.g. by segmental isotopic labeling or residue-specific labeling. In view of the general importance of NMR spectroscopy in drug development, the availability of protein crystal structures also provides fertile ground for further developments of lanthanide tagging techniques to support fragment-based drug design.
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.
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.
Spatial encoding, as encompassing the monitoring of spin evolutions on the basis of selective frequency-swept pulses and of magnetic field gradients, provides a new way for measuring NMR spectra or MRI images. In contrast to time-domain schemes or to continuous-wave approaches, these new RF/gradient combinations can act together to create interaction-dependent spatial patterns of spin magnetizations or coherences extending throughout a sample. These patterns can then be read-out with the aid of a second set of gradients while digitizing the data, to endow NMR/MRI acquisitions with hitherto unavailable capabilities. The present Review described various facets of these new approaches to monitor NMR spectra and MRI images. We began with a thorough introduction on how to visualize the effects of swept RF pulses - be them of an excitation or refocusing nature - applied in the presence of linear field gradients. It was then discussed how, in a spectroscopic setting, the idea of spatial encoding can be exploited to compress an nD spectroscopic NMR experiment into a single-scan. Numerous acquisition schemes capable of retrieving this kind of results for a variety of 2D experiments were presented, and their relative merits and limitations were surveyed. Similar ideas were shown to have applications in other spectroscopic aradigms involving multi-scan experiments, such as Hadamard spectroscopy. It was once again shown that by partitioning the sample and exciting different patterns for each site, one could produce a single-scan, sub-second version of a complex experiment. Similar versions of multi-scan phase cycling have also been demonstrated . The final part extended these spatially-selective encoding concepts in what we believe are novel imaging sequences, though related to decades-old developments in this field. By suitable excitation protocols, the spins in the sample can, in these MRI settings, be made to interfere destructively - except within a particular voxel which can be chosen at will. This voxel can be shifted along a predefined trajectory, set by shaping the acquisition gradients, yielding a signal proportional to the spin density along that path. Therefore, spatially encoded imaging differs from conventional Fourier imaging by acquiring images in real rather than in k-space. The point-by-point nature of the ensuing approach can then address a number of challenging measurements, including the single-scan acquisition of images arising from different chemical sites, or in the presence of field inhomogeneities. Overall, it is hoped that as the technical details underlying these new methods become clearer and as their user-base expands, further improvements will materialize and new, unforeseen applications of spatial-encoding will emerge - both in the spectroscopy and imaging realms. (Figure presented).
The increasing interest towards application of NMR in food science is revealed both by the constantly increasing number of papers and reviews on this topic and by international and national congresses dedicated to this field. The strength of the H metabolomic approach is the capacity to look at all the components of a mixture at once allowing a metabolite quantitative analysis and thus generating many data from which it is necessary to extract the required information. The application of chemometric methods can reduce the dimension of the NMR data identifying possible patterns among samples. Relative deuterium concentration and specific deuterium-site locations have also been determined in other alcoholic beverages, fruit juices, aromas and perfumes, fats and oils, milk, and drug. Metabolic profiling requires identification and quantification of a number of selected metabolites, belonging to various classes of compounds, in a given sample often without a separation procedure.
► F molecular tags and labeling protocols for F NMR studies of proteins are reviewed and contrasted. ► F NMR biosynthetic labeling strategies are presented. ► Experimental challenges (loss of function through labeling, line broadening, assignment ambiguities) are discussed. ► Approaches to the study of protein topology, using F NMR, are presented. ► Current examples of protein NMR studies are given.
The development of NMR instrumentation, methods, and applications of mobile NMR, with particular attention to single-sided NMR is discussed. Inside-out NMR is a form of single-sided or unilateral NMR, where an NMR sensor much smaller than the object is placed near the object to acquire signals from the object volume near the sensor. Mobile NMR holds great promise in a variety of fields, in particular in medicine, materials science, chemical engineering and space science. A very promising area of application of mobile NMR is process control by sensors installed in the production line. The development of NMR methods for mobile NMR is driven by two sources. One is the need for more information from, and better accuracy of, well-logging instruments. The other is scientific curiosity about doing NMR in low and inhomogeneous fields with inexpensive instrumentation and with it the drive for expanding the range of applications of NMR.