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1.  FLAMEnGO 2.0: An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances 
We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires the protein X-ray structure or an NMR structural ensemble with data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) and the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at
PMCID: PMC4161213  PMID: 24915505
FLAMEnGO 2.0; Automatic assignment of methyl groups; Methyl-TROSY; Sparse and ambiguous data
2.  Multiple Acquisition/Multiple Observation Separated Local Field/Chemical Shift Correlation Solid-state Magic Angle Spinning NMR Spectroscopy 
Multiple acquisition spectroscopy (MACSY) experiments that enable multiple free induction decays to be recorded during individual experiments are demonstrated. In particular, the experiments incorporate separated local field spectroscopy into homonuclear and heteronuclear correlation spectroscopy. The measured heteronuclear dipolar couplings are valuable in structure determination as well as in enhancing resolution by providing an additional frequency axis. In one example four different three-dimensional spectra are obtained in a single experiment, demonstrating that substantial potential saving in experimental time is available when multiple multi-dimensional spectra are required as part of solid-state NMR studies.
PMCID: PMC4128693  PMID: 25023566
MACSY; dual acquisition; dual observation; PELF; dipolar couplings; protein NMR; R-INEPT; CXCR1
3.  New spectral-spatial imaging algorithm for full EPR spectra of multiline nitroxides and pH sensitive trityl radicals 
An algorithm is derived and demonstrated that reconstructs an EPR spectral-spatial image from projections with arbitrarily selected gradients. This approach permits imaging wide spectra without the use of the very large sweep widths and gradients that would be required for spectral-spatial imaging with filtered backprojection reconstruction. Each projection is defined as the sum of contributions at the set of locations in the object. At each location gradients shift the spectra in the magnetic field domain, which is equivalent to a phase change in the Fourier-conjugate frequency domain. This permits solution of the problem in the frequency domain. The method was demonstrated for 2D images of phantoms consisting of (i) two tubes containing 14N and 15N nitroxide and (ii) two tubes containing a pH sensitive trityl radical at pH 7.0 and 7.2. In each case spectral slices through the image agree well with the full spectra obtained in the absence of gradient.
PMCID: PMC4134677  PMID: 25058914
4.  Differentiation of Histidine Tautomeric States using 15N Selectively Filtered 13C Solid-State NMR Spectroscopy 
The histidine imidazole ring in proteins usually contains a mixture of three possible tautomeric states (two neutral - τ and π states and a charged state) at physiological pHs. Differentiating the tautomeric states is critical for understanding how the histidine residue participates in many structurally and functionally important proteins. In this work, one dimensional 15N selectively filtered 13C solid-state NMR spectroscopy is proposed to differentiate histidine tautomeric states and to identify all 13C resonances of the individual imidazole rings in a mixture of tautomeric states. When 15N selective 180° pulses are applied to the protonated or non-protonated nitrogen region, the 13C sites that are bonded to the non-protonated or protonated nitrogen sites can be identified, respectively. A sample of 13C,15N labeled histidine powder lyophilized from a solution at pH 6.3 has been used to illustrate the usefulness of this scheme by uniquely assigning resonances of the neutral τ and charged states from the mixture.
PMCID: PMC4136442  PMID: 25026459
Histidine tautomeric states; solid-state MAS NMR; REDOR/TEDOR; selective polarization
5.  Exchange-Induced Relaxation in the Presence of a Fictitious Field 
In the present study we derive a solution for two site fast exchange-induced relaxation in the presence of a fictitious magnetic field as generated by amplitude and frequency modulated RF pulses. This solution provides a means to analyze data obtained from relaxation experiments with the method called RAFFn (Relaxation Along a Fictitious Field of rank n), in which a fictitious field is created in a coordinate frame undergoing multi-fold rotation about n axes (rank n). The RAFF2 technique is relevant to MRI relaxation methods that provide good contrast enhancement for tumor detection. The relaxation equations for n = 2 are derived for the fast exchange regime using density matrix formalism. The method of derivation can be further extended to obtain solutions for n > 2.
PMCID: PMC4308052  PMID: 24911888
fictitious fields; relaxations; exchange; high rotating frames
6.  Heteronuclear refocusing by nonlinear phase and amplitude modulation on a single transmitter channel 
The application of low magnetic fields to heteronuclear NMR has expanded recently alongside the emergence of methods for achieving near unity polarization of spin ensembles, independent of magnetic field strength. The parahydrogen induced hyperpolarization methods in particular, often use a hybrid arrangement where a high field spectrometer is used to detect or image polarized molecules that have been conjured on a separate, dedicated polarizer instrument operating at fields in the mT regime where yields are higher. For controlling polarizer chemistry, spare TTL channels of portable NMR spectrometers can be used to pulse program reaction timings in synchrony with heteronuclear RF transformations. The use of a spectrometer as a portable polarizer control module has the advantage of allowing detection in situ, simplifying the process of optimizing polarization yields prior to in vivo experimental trials. Suitable heteronuclear spectrometers compatible with this application are becoming more common, but are still sparsely available in comparison to a large existing infrastructure of single channel NMR consoles. To determine if one of these single channel spectrometers could be used for heteronuclear NMR, the feasibility of rotating a pair of heteronuclear spins (13C and 1H) at 12 mT was investigated in this study. Nonlinear phase and amplitude modulated waveforms designed to simultaneously refocus magnetization at 128 kHz (13C) and 510 kHz (1H) were generated numerically with optimal control. Although precise quantitative comparisons were not attempted due to limitations of the experimental setup, signals refocused at heteronuclear frequencies with this PANORAMIC approach (Precession And Nutation for Observing Rotation At Multiple Intervals about the Carrier) yielded amplitudes comparable to signals which were refocused using traditional block pulses on heteronuclear channels. Using this PANORAMIC approach to heteronuclear NMR at low field would reduce expense as well as hardware complexity and bulk, weighed against the caveat that elaborate pulses are required. More work will be necessary to test this method on the targeted application of parahydrogen induced hyperpolarization as well as to quantify efficiency, but upon further development we anticipate that this method may offer a viable ‘software’ approach to heteronuclear manipulations of spins at low magnetic fields.
PMCID: PMC4206526  PMID: 24954513
Single channel spectrometer; Low field NMR; Parahydrogen induced polarization; Phase modulation; Amplitude modulation; Broadband NMR; Transmitter multiplexing; PANORAMIC; Optimal control
7.  Zero field splitting fluctuations induced phase relaxation of Gd3+ in frozen solutions at cryogenic temperatures 
Distance measurements using double electron–electron resonance (DEER) and Gd3+ chelates for spin labels (GdSL) have been shown to be an attractive alternative to nitroxide spin labels at W-band (95 GHz). The maximal distance that can be accessed by DEER measurements and the sensitivity of such measurements strongly depends on the phase relaxation of Gd3+ chelates in frozen, glassy solutions. In this work, we explore the phase relaxation of Gd3+-DOTA as a representative of GdSL in temperature and concentration ranges typically used for W-band DEER measurements. We observed that in addition to the usual mechanisms of phase relaxation known for nitroxide based spin labels, GdSL are subjected to an additional phase relaxation mechanism that features an increase in the relaxation rate from the center to the periphery of the EPR spectrum. Since the EPR spectrum of GdSL is the sum of subspectra of the individual EPR transitions, we attribute this field dependence to transition dependent phase relaxation. Using simulations of the EPR spectra and its decomposition into the individual transition subspectra, we isolated the phase relaxation of each transition and found that its rate increases with |ms|. We suggest that this mechanism is due to transient zero field splitting (tZFS), where its magnitude and correlation time are scaled down and distributed as compared with similar situations in liquids. This tZFS induced phase relaxation mechanism becomes dominant (or at least significant) when all other well-known phase relaxation mechanisms, such as spectral diffusion caused by nuclear spin diffusion, instantaneous and electron spin spectral diffusion, are significantly suppressed by matrix deuteration and low concentration, and when the temperature is sufficiently low to disable spin lattice interaction as a source of phase relaxation.
PMCID: PMC4495766  PMID: 25442776
Gd3+; Phase relaxation; Zero field splitting; W-band EPR; Spin labels
8.  3D15N/15N/1H Chemical Shift Correlation Experiment Utilizing an RFDR-based 1H/1H Mixing Period at 100 kHz MAS 
Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While 13C/13C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of 15N nuclei in proteins has been a challenge. Previous studies have shown that the negligible 15N-15N 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 15N/15N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of 15N, via the recoupled 1H-1H dipolar couplings enable faster 15N/15N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between 1H and 15N nuclei) steps. In fact, less than 300 nL (~1.1 micromole quantity) sample is sufficient to acquire the 3D spectrum within 5 hours. Our results also demonstrate that a 3D 15N/15N/1H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D 15N/15N/1H and 2D radio frequency-driven dipolar recoupling (RFDR)-based 1H/1H experimental results obtained from a powder sample of N-acetyla-L-15N-valyl-L-15N-leucine at 70 and 100 kHz MAS frequencies are presented.
PMCID: PMC4062578  PMID: 24801998
solid-state NMR; ultrafast MAS; proton-detection; RFDR; peptide
9.  A framework for accurate determination of the T2 distribution from multiple echo magnitude MRI images 
Measurement of the T2 distribution in tissues provides biologically relevant information about normal and abnormal microstructure and organization. Typically, the T2 distribution is obtained by fitting the magnitude MR images acquired by a multi-echo MRI pulse sequence using an inverse Laplace transform (ILT) algorithm. It is well known that the ideal magnitude MR signal follows a Rician distribution. Unfortunately, studies attempting to establish the validity and efficacy of the ILT algorithm assume that these input signals are Gaussian distributed. Violation of the normality (or Gaussian) assumption introduces unexpected artifacts, including spurious cerebrospinal fluid (CSF)-like long T2 components; bias of the true geometric mean T2 values and in the relative fractions of various components; and blurring of nearby T2 peaks in the T2 distribution. Here we apply and extend our previously proposed magnitude signal transformation framework to map noisy Rician-distributed magnitude multi-echo MRI signals into Gaussian-distributed signals with high accuracy and precision. We then perform an ILT on the transformed data to obtain an accurate T2 distribution. Additionally, we demonstrate, by simulations and experiments, that this approach corrects the aforementioned artifacts in magnitude multi-echo MR images over a large range of signal-to-noise ratios.
PMCID: PMC4086921  PMID: 24859198
T2 distribution; MRI; multi-echo; magnitude; Rician; Gaussian; signal; probability integral transform
10.  Remote sensing of sample temperatures in nuclear magnetic resonance using photoluminescence of semiconductor quantum dots 
Knowledge of sample temperatures during nuclear magnetic resonance (NMR) measurements is important for acquisition of optimal NMR data and proper interpretation of the data. Sample temperatures can be difficult to measure accurately for a variety of reasons, especially because it is generally not possible to make direct contact to the NMR sample during the measurements. Here I show that sample temperatures during magic-angle spinning (MAS) NMR measurements can be determined from temperature-dependent photoluminescence signals of semiconductor quantum dots that are deposited in a thin film on the outer surface of the MAS rotor, using a simple optical fiber-based setup to excite and collect photoluminescence. The accuracy and precision of such temperature measurements can be better than ±5 K over a temperature range that extends from approximately 50 K (−223° C) to well above 310 K (37° C). Importantly, quantum dot photoluminescence can be monitored continuously while NMR measurements are in progress. While this technique is likely to be particularly valuable in low-temperature MAS NMR experiments, including experiments involving dynamic nuclear polarization, it may also be useful in high-temperature MAS NMR and other forms of magnetic resonance.
PMCID: PMC4090140  PMID: 24859817
11.  Acceleration of Natural-Abundance Solid-State MAS NMR Measurements on Bone by Paramagnetic Relaxation from Gadolinium-DTPA 
Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylenetriamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.
PMCID: PMC4094129  PMID: 24881032
Solid-state NMR; paramagnetic relaxation enhancement; ultrafast MAS; Gd-DTPA; Bone
12.  Synthesis and evaluation of nitroxide-based oligoradicals for low-temperature dynamic nuclear polarization in solid state NMR 
We describe the synthesis of new nitroxide-based biradical, triradical, and tetraradical compounds and the evaluation of their performance as paramagnetic dopants in dynamic nuclear polarization (DNP) experiments in solid state nuclear magnetic resonance (NMR) spectroscopy with magic-angle spinning (MAS). Under our experimental conditions, which include temperatures in the 25–30 K range, a 9.4 T magnetic field, MAS frequencies of 6.2–6.8 kHz, and microwave irradiation at 264.0 GHz from a 800 mW extended interaction oscillator source, the most effective compounds are triradicals that are related to the previously-described compound DOTOPA-TEMPO (see Thurber et al., 2010), but have improved solubility in glycerol/water solvent near neutral pH. Using these compounds at 30 mM total nitroxide concentration, we observe DNP enhancement factors of 92–128 for cross-polarized 13C NMR signals from 15N,13C-labeled melittin in partially protonated glycerol/water, and build-up times of 2.6–3.8 s for 1H spin polarizations. Net sensitivity enhancements with biradical and tetraradical dopants, taking into account absolute 13C NMR signal amplitudes and build-up times, are approximately 2–4 times lower than with the best triradicals.
PMCID: PMC4106245  PMID: 24887201
Magic-angle spinning; Cross-effect DNP; Hyperpolarization; Electron paramagnetic resonance
13.  Evaluating the Uncertainty in Exchange Parameters Determined from Off-Resonance R1ρ Relaxation Dispersion for Systems in Fast Exchange 
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 Φıx = 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 χ2 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 = 39,000 s−1) chemical shift timescales.
PMCID: PMC4222517  PMID: 24819426
Rotating-frame relaxation dispersion; fast exchange; excited state; dynamics; DNA; RNA
14.  A Practical Implicit Solvent Potential for NMR Structure Calculation 
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.
PMCID: PMC4037354  PMID: 24747742
15.  Finite-Pulse Radio Frequency Driven Recoupling with Phase Cycling for 2D 1H/1H Correlation at Ultrafast MAS Frequencies 
The first-order recoupling sequence radio frequency driven dipolar recoupling (RFDR) is commonly used in single-quantum/single-quantum homonuclear correlation 2D experiments under magic angle spinning (MAS) to determine homonuclear proximities. From previously reported analysis of the use of XY-based super-cycling schemes to enhance the efficiency of the finite-pulse-RFDR (fp-RFDR) pulse sequence, XY814 phase cycling was found to provide the optimum performance for 2D correlation experiments on low-γ nuclei. In this study, we analyze the efficiency of different phase cycling schemes for proton-based fp-RFDR experiments. We demonstrate the advantages of using a short phase cycle, XY4, and its super-cycle XY414 that only recouples the zero-quantum homonuclear dipolar coupling, for the fp-RFDR sequence in 2D 1H/1H correlation experiments at ultrafast MAS frequencies. The dipolar recoupling efficiencies of XY4, XY414 and XY814 phase cycling schemes are compared based on results obtained from 2D 1H/1H correlation experiments, utilizing the fp-RFDR pulse sequence, on powder samples of U-13C,15N-L-alanine, N-acetyl-15N-L-valyl-15N-L-leucine, and glycine. Experimental results and spin dynamics simulations show that XY414 performs the best when a high RF power is used for the 180° pulse, whereas XY4 renders the best performance when a low RF power is used. The effects of RF field inhomogeneity and chemical shift offsets are also examined. Overall, our results suggest that a combination of fp-RFDR-XY414 employed in the recycle delay with a large RF-field to decrease the recycle delay, and fp-RFDR-XY4 in the mixing period with a moderate RF-field, is a robust and efficient method for 2D single-quantum/single-quantum 1H/1H correlation experiments at ultrafast MAS frequencies.
PMCID: PMC4037380  PMID: 24713171
Ultrafast MAS; Dipolar recoupling; RFDR; Proton Detection
16.  Proton Magnetic Resonance Spectroscopy of Skeletal Muscle: A Comparison of Two Quantitation Techniques 
Rationale and Objectives
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 3 Tesla.
Materials and Methods
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 69 mM/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 ± 4.1 mmol/kg wet weight using the phantom replacement and water referencing methods respectively, while [Cr] concentrations were 26.8 ± 12.2 and 24.1 ± 5.3 mmol/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.
PMCID: PMC4050659  PMID: 24792959
MR Spectroscopy; Muscle; Quantitation; Phantom Replacement
17.  Performance of RINEPT is Amplified by Dipolar Couplings Under Ultrafast MAS Conditions 
The refocused insensitive nuclei enhanced by polarization transfer (RINEPT) technique is commonly used for heteronuclear polarization transfer in solution and solid-state NMR spectroscopy. Suppression of dipolar couplings, either by fast molecular motions in solution or by a combination of MAS and multiple pulse sequences in solids, enables the polarization transfer via scalar couplings. However, the presence of unsuppressed dipolar couplings could alter the functioning of RINEPT, particularly under fast/ultrafast MAS conditions. In this study, we demonstrate, through experiments on rigid solids complemented by numerical simulations, that the polarization transfer efficiency of RINEPT is dependent on the MAS frequency. In addition, we show that heteronuclear dipolar coupling is the dominant factor in the polarization transfer, which is strengthened by the presence of 1H-1H dipolar couplings. In fact, the simultaneous presence of homonuclear and heteronuclear dipolar couplings is the premise for the polarization transfer by RINEPT, whereas the scalar coupling plays an insignificant role under ultrafast MAS conditions on rigid solids. Our results additionally reveal that the polarization transfer efficiency decreases with the increasing duration of RF pulses used in the RINEPT sequence.
PMCID: PMC4057659  PMID: 24792960
Ultrafast MAS; Polarization Transfer; RINEPT; Solid-State NMR; Dipolar Couplings
18.  Fast and robust measurement of microstructural dimensions using temporal diffusion spectroscopy 
Mapping axon sizes non-invasively is of interest for neuroscientists and may have significant clinical potential because nerve conduction velocity is directly dependent on axon size. Current approaches to measuring axon sizes using diffusion-weighted MRI, e.g. q-space imaging with pulsed gradient spin echo (PGSE) sequences usually require long scan times and high q-values to detect small axons (diameter <2 μm). The oscillating gradient spin echo (OGSE) method has been shown to be able to achieve very short diffusion times and hence may be able to detect smaller axons with high sensitivity. In the current study, OGSE experiments were performed to measure the inner diameters of hollow microcapillaries with a range of sizes (~1.5–19.3 μm) that mimic axons in the human central nervous system. The results suggest that OGSE measurements, even with only moderately high frequencies, are highly sensitive to compartment sizes, and a minimum of two ADC values with different frequencies may be sufficient to extract the microcapillary size accurately. This suggests that the OGSE method may serve as a fast and robust measurement method for mapping axon sizes non-invasively.
PMCID: PMC4008665  PMID: 24583517
Temporal diffusion spectroscopy; OGSE; Axon size; Oscillating gradient; Microcapillary
19.  Mean square optimal NUFFT approximation for efficient non-Cartesian MRI reconstruction 
The fast evaluation of the discrete Fourier transform of an image at non-uniform sampling locations is key to efficient iterative non-Cartesian MRI reconstruction algorithms. Current non-uniform fast Fourier transform (NUFFT) approximations rely on the interpolation of oversampled uniform Fourier samples. The main challenge is high memory demand due to oversampling, especially when multi-dimensional datasets are involved. The main focus of this work is to design an NUFFT algorithm with minimal memory demands. Specifically, we introduce an analytical expression for the expected mean square error in the NUFFT approximation based on our earlier work. We then introduce an iterative algorithm to design the interpolator and scale factors.Experimental comparisons show that the proposed optimized NUFFT scheme provides considerably lower approximation errors than our previous scheme that rely on worst case error metrics. The improved approximations are also seen to considerably reduce the errors and artifacts in non-Cartesian MRI reconstruction.
PMCID: PMC4008684  PMID: 24637054
interpolators; non-uniform fast Fourier transform; histogram; non-Cartesian MRI
20.  19F Spin-lattice Relaxation of Perfluoropolyethers: Dependence on Temperature and Magnetic Field Strength (7.0-14.1T) 
Fluorine (19F) MRI of perfluorocarbon labeled cells has become a powerful technique to track the migration and accumulation of cells in living organisms. It is common to label cells for 19F MRI with nanoemulsions of perfluoropolyethers that contain a large number of chemically equivalent fluorine atoms. Understanding the mechanisms of 19F nuclear relaxation, and in particular the spin-lattice relaxation of these molecules, is critical to improving experimental sensitivity. To date, the temperature and magnetic field strength dependence of spin-lattice relaxation rate constant (R1) for perfluoropolyethers has not been described in detail. In this study, we evaluated R1 of linear perfluoropolyether (PFPE) and cyclic perfluoro-15-crown-5 ether (PCE) at three magnetic field strengths (7.0, 9.4, and 14.1 T) and at temperatures ranging from 256-323K. Our results show that R1 of perfluoropolyethers is dominated by dipole-dipole interactions and chemical shift anisotropy. R1 increased with magnetic field strength for both PCE and PFPE. In the temperature range studied, PCE was in the fast motion regime (ωτc < 1) at all field strengths, but for PFPE, R1 passed through a maximum, from which the rotational correlation time was estimated. The importance of these measurements for the rational design of new 19F MRI agents and methods is discussed.
PMCID: PMC4008704  PMID: 24594752
21.  Proton-Detected 2D Radio Frequency Driven Recoupling Solid-state NMR Studies on Micelle-associated Cytochrome-b5 
Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.
PMCID: PMC4020179  PMID: 24657390
Membrane protein; cytochrome-b5; RFDR; NOESY
22.  Dipolar Assisted Assignment Protocol (DAAP) for MAS solid-state NMR of Rotationally Aligned Membrane Proteins in Phospholipid Bilayers 
A method for making resonance assignments in magic angle spinning solid-state NMR spectra of membrane proteins that utilizes the range of hetero-nuclear dipolar coupling frequencies in combination with conventional chemical shift based assignment methods is demonstrated. The dipolar assisted assignment protocol (DAAP) takes advantage of the rotational alignment of the membrane proteins in liquid crystalline phospholipid bilayers. Improved resolution is obtained by combining the magnetically inequivalent heteronuclear dipolar frequencies with isotropic chemical shift frequencies. Spectra with both dipolar and chemical shift frequency axes assist with resonance assignments. DAAP can be readily extended to three- and four- dimensional experiments and to include both backbone and side chain sites in proteins.
PMCID: PMC4043445  PMID: 24698983
23.  Minimum Acquisition Methods for Simultaneously Imaging T1, T2, and Proton Density with B1 Correction and No Spin-echoes 
The spin lattice (T1) and spin-spin (T2) relaxation times, along with the proton density (PD) contain almost all of the information that 1H MRI routinely uses in clinical diagnosis and research, but are seldom imaged directly. Here, three methods for directly imaging T1, T2, and PD with the least possible number of acquisitions–three, are presented. All methods utilize long 0° self-refocusing adiabatic pre-pulses instead of spin-echoes to encode the T2 information prior to a conventional gradient-echo MRI sequence. T1 information is encoded by varying the flip-angle (FA) in the ‘Dual-τ Dual-FA’ and ‘Four-FA’ methods, or the sequence repetition period, TR, in the ‘Dual-τ Dual-TR’ method. Inhomogeneity in the FA distribution and slice-selection profile are recognized as the main error sources for T1 measurements. The former is remedied by integrating an extra FA-dependent acquisition into the ‘Four-FA’ method to provide self-corrected T1, T2, PD, and FA in just four acquisitions-again, the minimum possible. Slice profile errors–which manifest as differences between 2D and 3D T1 measurements, can be addressed by Bloch equation analysis and experimental calibration. All three methods are validated in phantom studies, and the ‘Dual-τ Dual-FA’ and ‘Four-FA’ methods are validated in human brain studies using standard partial saturation and spin-echo methods for reference. The new methods offer a minimum-acquisition option for imaging single-component T1, T2, and PD. Four-FA’ performs best overall in accuracy, with high efficiency per unit accuracy versus existing methods when B1-inhomogeneity is appropriately addressed.
PMCID: PMC4058094  PMID: 24705365
MRI; spin-spin relaxation; spin-latice relaxation; proton density; measurement; B1 Correction
24.  Imaging of Nitroxides at 250 MHz using Rapid-Scan Electron Paramagnetic Resonance 
Projections for 2D spectral-spatial images were obtained by continuous wave and rapid-scan electron paramagnetic resonance using a bimodal cross-loop resonator at 251 MHz. The phantom consisted of three 4 mm tubes containing different 15N,2H-substituted nitroxides. Rapid-scan and continuous wave images were obtained with 5 min total acquisition times. For comparison, images also were obtained with 29 s acquisition time for rapid scan and 15 min for continuous wave. Relative to continuous wave projections obtained for the same data acquisition time, rapid-scan projections had significantly less low-frequency noise and substantially higher signal-to-noise at higher gradients. Because of the improved image quality for the same data acquisition time, linewidths could be determined more accurately from the rapid-scan images than from the continuous wave images.
PMCID: PMC4081024  PMID: 24650729
25.  Perspectives in Magnetic Resonance: NMR in the Post-FFT Era 
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-unifom 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.
PMCID: PMC3964371  PMID: 24656081
non-uniform sampling; protein backbone chemical shift assignments; maximum entropy reconstruction; iterative soft threshold reconstruction; reduced time multidimensional NMR spectroscopy

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