Journal of Magnetic Resonance

Publisher: Elsevier


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  • Other titles
    Journal of magnetic resonance (San Diego, Calif.: 1997: Online), Journal of magnetic resonance, JMR
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    Document, Periodical, Internet resource
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    Internet Resource, Computer File, Journal / Magazine / Newspaper

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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: 55Mn pulsed electron nuclear double resonance (ENDOR) experiments were performed at X-band on high spin S = 5/2 Mn2+ ions incorporated at zinc lattice sites in heteroepitaxial ZnO thin films. The films have been prepared by pulsed laser deposition and the manganese ions were doped during the growth process. We examine how the c/a lattice axes ratio of the ZnO films influences the 55Mn hyperfine (hf) and nuclear quadrupole (nq) coupling parameters of the Mn2+ probe ions. The results are compared with those obtained for Mn2+ ions present as impurities in ZnO single crystals and revealed that the 55Mn nq coupling monitors sensitively the structural distortions in the bonding environment of the Mn2+ ions. The experiments provided the full axially symmetric 55Mn hf and nq interaction tensors. The latter is found to be very sensitive to small axial distortions of the MnO4 tetrahedrons. In particular, the 55Mn pulsed ENDOR spectra of the ZnO:Mn thin films are strongly subjected to strain effects in the nq coupling parameter indicating a variation of the local structural parameters for the heteroepitaxial films. In the analysis of the 55Mn pulsed ENDOR spectra the axial and cubic zero field splitting of the Mn2+ ions was taken into account and intensity effects in the ENDOR spectra due to the zero field splitting effects were discussed.
    Journal of Magnetic Resonance 07/2014; 245:79-86.
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    ABSTRACT: We propose analytical functions for T2 distribution to describe transverse relaxation in high- and low-fields NMR experiments on porous media. The method is based on a superstatistics theory, and allows to find the mean and standard deviation of T2, directly from measurements. It is an alternative to multiexponential models for data decay inversion in NMR experiments. We exemplify the method with q-exponential functions and χ(2)-distributions to describe, respectively, data decay and T2 distribution on high-field experiments of fully water saturated glass microspheres bed packs, sedimentary rocks from outcrop and noisy low-field experiment on rocks. The method is general and can also be applied to biological systems.
    Journal of Magnetic Resonance 04/2014; 244C:12-17.
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    ABSTRACT: Spin relaxation in the rotating frame (R1ρ) is a powerful NMR technique for characterizing fast microsecond timescale exchange processes directed toward short-lived excited states in biomolecules. At the limit of fast exchange, only kex=k1+k-1 and Φex=pGpE(Δω)(2) can be determined from R1ρ data limiting the ability to characterize the structure and energetics of the excited state conformation. Here, we use simulations to examine the uncertainty with which exchange parameters can be determined for two state systems in intermediate-to-fast exchange using off-resonance R1ρ relaxation dispersion. R1ρ data computed by solving the Bloch-McConnell equations reveals small but significant asymmetry with respect to offset (R1ρ (ΔΩ)≠R1ρ (-ΔΩ)), which is a hallmark of slow-to-intermediate exchange, even under conditions of fast exchange for free precession chemical exchange line broadening (kex/Δω>10). A grid search analysis combined with bootstrap and Monte-Carlo based statistical approaches for estimating uncertainty in exchange parameters reveals that both the sign and magnitude of Δω can be determined at a useful level of uncertainty for systems in fast exchange (kex/Δω<10) but that this depends on the uncertainty in the R1ρ data and requires a thorough examination of the multidimensional variation of χ(2) as a function of exchange parameters. Results from simulations are complemented by analysis of experimental R1ρ data measured in three nucleic acid systems with exchange processes occurring on the slow (kex/Δω=0.2; pE=∼0.7%), fast (kex/Δω=∼10-16; pE=∼13%) and very fast (kex=39,000s(-1)) chemical shift timescales.
    Journal of Magnetic Resonance 04/2014; 244C:18-29.
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    ABSTRACT: Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While (13)C/(13)C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of (15)N nuclei in proteins has been a challenge. Previous studies have shown that the negligible (15)N-(15)N dipolar coupling in peptides or proteins necessitates the use of a very long mixing time (typically several seconds) for effective spin diffusion to occur and considerably slows down a (15)N/(15)N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of (15)N, via the recoupled (1)H-(1)H dipolar couplings enable faster (15)N/(15)N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between (1)H and (15)N nuclei) steps. In fact, less than 300nL (∼1.1micromole quantity) sample is sufficient to acquire the 3D spectrum within 5h. Our results also demonstrate that a 3D (15)N/(15)N/(1)H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D (15)N/(15)N/(1)H and 2D radio frequency-driven dipolar recoupling (RFDR)-based (1)H/(1)H experimental results obtained from a powder sample of N-acetyla-l-(15)N-valyl-l-(15)N-leucine at 70 and 100kHz MAS frequencies are presented.
    Journal of Magnetic Resonance 04/2014; 244C:1-5.
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    ABSTRACT: The time dependence of the diffusion coefficient is a well known property of porous media and commonly obtained by pulsed field gradient (PFG) NMR. In practical materials, its analysis can be complicated by the presence of a broad pore size distribution and multiple fluid phases with different diffusion coefficients. We propose a two-dimensional Diffusion Time Correlation experiment (DTC), which utilizes the double-PFG with a single-direction gradient to yield a two-dimensional correlation function of the diffusion coefficient for two different diffusion times. This correlation map separates out restricted diffusion from the bulk diffusion process and we demonstrate this on a plant and bulk water sample. In its development, we show that the d-PFG should then be thought of as correlating two apparent diffusion coefficients measured by two overlapping gradient waveforms.
    Journal of Magnetic Resonance 04/2014; 244C:6-11.
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    ABSTRACT: Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper. Using one-bond (1)JNH spin-spin coupling constants and hydrogen/deuterium exchange, we demonstrate that a transient intramolecular hydrogen bond is present in the partially helical folding nucleus of GCN(16-31). The data demonstrate that (1)JNH couplings are a sensitive tool for the detection of transient intramolecular hydrogen bonds in challenging systems where the effective/useable protein concentration is low. This includes peptides at natural abundance but also uniformly labeled biomolecules that are limited to low concentrations because of precipitation or aggregation.
    Journal of Magnetic Resonance 04/2014; 243C:93-97.
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    ABSTRACT: Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) are widely used techniques across numerous disciplines. While typically implemented at fields >1T, there has been continuous interest in the methods at much lower fields for reasons of cost, material contrast, or application. There have been numerous demonstrations of MR at much lower fields (from 1μT to 1mT), the so-called ultra-low field (ULF) regime. Approaches to ULF MR have included superconducting quantum interference device (SQUID) sensor technology for ultra-sensitive detection and the use of pulsed pre-polarizing fields to enhance the signal strength. There are many advantages to working in the ULF regime. However, due to the low strength of the measurement field, acquisition of MRI at ULF is more susceptible to ambient fields that cause image distortions. Imaging artifacts can be caused by transients associated with non-ideal field switching and from remnant fields in magnetic shielding, among other causes. In this paper, we introduce a general theoretical framework that describes effects of non-ideal measurement field inversion/rotation due to presence of these transient fields. We illustrate imaging artifacts via simulated and experimental examples.
    Journal of Magnetic Resonance 04/2014; 243C:98-106.
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    ABSTRACT: This study describes the design, construction and operation of a new type of transmit/receive array using ceramic resonators operating in a transverse electromagnetic (TE) mode. Single element function and performance at 298.1MHz (7T) are analyzed and compared to a lumped element design loop coil with comparable geometry. The results show that ceramic resonators working in the TE01δ mode configuration produce similar efficiency, defined as the transmit magnetic field (B1(+)) per square root of the specific absorption rate (SAR), to conventional surface coils. An array consisting of eight ceramic elements was then designed to operate in transmit/receive mode. This array was driven via power/phase splitters by two independent transmit channels and functional cardiac images were produced from a number of healthy volunteers.
    Journal of Magnetic Resonance 04/2014;
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    ABSTRACT: Monitoring the pore system in sedimentary rocks with MRI when fluids are introduced is very important in the study of petroleum reservoirs and enhanced oil recovery. However, the lengthy acquisition time of each image, with pure phase encode MRI, limits the temporal resolution. Spatiotemporal correlations can be exploited to undersample the k-t space data. The stacked frames/profiles can be well approximated by an image matrix with rank deficiency, which can be recovered by nonlinear nuclear norm minimization. Sparsity of the x-t image can also be exploited for nonlinear reconstruction. In this work the results of a low rank matrix completion technique were compared with k-t sparse compressed sensing. These methods are demonstrated with one dimensional SPRITE imaging of a Bentheimer rock core plug and SESPI imaging of a Berea rock core plug, but can be easily extended to higher dimensionality and/or other pure phase encode measurements. These ideas will enable higher dimensionality pure phase encode MRI studies of dynamic flooding processes in low magnetic field systems.
    Journal of Magnetic Resonance 04/2014; 243C:114-121.
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    ABSTRACT: The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide templates. Here we describe a new implicit solvation potential, EEFx (Effective Energy Function for XPLOR-NIH), for NMR-restrained structure calculations of proteins in XPLOR-NIH. The key components of EEFx are an energy term for solvation energy that works together with other nonbonded energy functions, and a dedicated force field for conformational and nonbonded protein interaction parameters. The initial results obtained with EEFx show that significant improvements in structural quality can be obtained. EEFx is computationally efficient and can be used both to fold and refine structures. Overall, EEFx improves the quality of protein conformation and nonbonded atomic interactions. Moreover, such benefits are accompanied by enhanced structural precision and enhanced structural accuracy, reflected in improved agreement with the cross-validated dipolar coupling data. Finally, implementation of EEFx calculations is straightforward and computationally efficient. Overall, EEFx provides a useful method for the practical calculation of experimental protein structures in a physically realistic environment.
    Journal of Magnetic Resonance 04/2014; 243C:54-64.
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    ABSTRACT: The aim of this study was to develop and compare two methods for quantification of metabolite concentrations in human skeletal muscle using phased-array receiver coils at 3T. Water suppressed and un-suppressed spectra were recorded from the quadriceps muscle (vastus medialis) in 8 healthy adult volunteers, and from a calibration phantom containing 69mM/L N-acetyl aspartate. Using the phantom replacement technique, trimethylamine specifically [TMA] and creatine [Cr] concentrations were estimated, and compared to those values obtained by using the water reference method. Quadriceps [TMA] concentrations were 9.5±2.4 and 9.6±4.1mmol/kg wet weight using the phantom replacement and water referencing methods respectively, while [Cr] concentrations were 26.8±12.2 and 24.1±5.3mmol/kg wet weight respectively. Reasonable agreement between water referencing and phantom replacement methods was found, although for [Cr] variation was significantly higher for the phantom replacement technique. The relative advantages and disadvantages of each approach are discussed.
    Journal of Magnetic Resonance 04/2014; 243C:81-84.
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    ABSTRACT: Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In these cases, sparse isotopic labeling (single or small subsets of amino acids) combined with long range paramagnetic constraints and improved computational modeling offer an alternative. This perspective provides a brief overview of this approach and two discussions of potential applications; one involving a very large system (an Hsp90 homolog) in which perdeuteration is possible and methyl-TROSY sequences can potentially be used to improve resolution, and one involving ligand placement in a glycosylated protein where resolution is achieved by single amino acid labeling (the sialyltransferase, ST6Gal1). This is not intended as a comprehensive review, but as a discussion of future prospects that promise impact on important questions in the structural biology area.
    Journal of Magnetic Resonance 04/2014; 241:32-40.
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    ABSTRACT: Multi-dimensional NMR spectra have traditionally been processed with the fast Fourier transformation (FFT). The availability of high field instruments, the complexity of spectra of large proteins, the narrow signal dispersion of some unstructured proteins, and the time needed to record the necessary increments in the indirect dimensions to exploit the resolution of the highfield instruments make this traditional approach unsatisfactory. New procedures need to be developed beyond uniform sampling of the indirect dimensions and reconstruction methods other than the straight FFT are necessary. Here we discuss approaches of non-uniform sampling (NUS) and suitable reconstruction methods. We expect that such methods will become standard for multi-dimensional NMR data acquisition with complex biological macromolecules and will dramatically enhance the power of modern biological NMR.
    Journal of Magnetic Resonance 04/2014; 241:60-73.
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    ABSTRACT: Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.
    Journal of Magnetic Resonance 04/2014; 241:115-25.
  • Journal of Magnetic Resonance 04/2014; 241:1-2.
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    ABSTRACT: Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space.
    Journal of Magnetic Resonance 04/2014; 241:53-9.