Designing Gradient Coils With Reduced Hot Spot Temperatures
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 9 December 2009
Peter T., While , Larry K., Forbes , Stuart, Crozier
Gradient coil temperature is an important concern in the design and construction of MRI scanners. Closely spaced gradient coil windings cause temperature hot spots within the system as a result of Ohmic heating associated with large current being driven through resistive material, and can strongly affect the performance of the coils. In this paper, a model is presented for predicting the spatial temperature distribution of a gradient coil, including the location and extent of temperature hot spots. Subsequently, a method is described for designing gradient coils with improved temperature distributions and reduced hot spot temperatures. Maximum temperature represents a non-linear constraint and a relaxed fixed point iteration routine is proposed to adjust coil windings iteratively to minimise this coil feature. Several examples are considered that assume different thermal material properties and cooling mechanisms for the gradient system. Coil winding solutions are obtained for all cases considered that display a considerable drop in hot spot temperature (>20%) when compared to standard minimum power gradient coils with equivalent gradient homogeneity, efficiency and inductance. The method is semi-analytical in nature and can be adapted easily to consider other non-linear constraints in the design of gradient coils or similar systems.
Homonuclear dipolar recoupling under ultra-fast magic-angle spinning: probing 19F19F proximities by solid-state NMR
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 16 December 2009
Qiang, Wang , Bingwen, Hu , Olivier, Lafon , Julien, Trébosc , Feng, Deng , and Jean-Paul Amoureux
We describe dipolar recoupling methods that accomplish, at high magic-angle spinning (MAS) frequencies, the excitation of double-quantum (DQ) coherences between spin-1/2 nuclei. We employ rotor-synchronized symmetry-based pulse sequences which are either γ-encoded or non-γ-encoded. The sensitivity and the robustness to both chemical-shift anisotropy and offset are examined. We also compare different techniques to avoid signal folding in the indirect dimension of two-dimensional double-quantum ↔ single-quantum (DQ−SQ) spectra. This comprehensive analysis results in the identification of satisfactory conditions for dipolar 19F−19F recoupling at high magnetic fields and high MAS frequencies. The utility of these recoupling methods is demonstrated with high-resolution DQ−SQ NMR spectra, which allow probing 19F−19F proximities in powered fluoroaluminates.
Intermolecular single-quantum coherence sequences for high-resolution NMR spectra in inhomogeneous fields
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 16 December 2009
Yuqing, Huang , Shuhui, Cai , Xi, Chen , Zhong, Chen
A new pulse sequence based on intermolecular single-quantum coherences (iSQCs) is proposed to obtain high-resolution NMR spectroscopy in inhomogeneous magnetic fields via fast 2D acquisition. Taking the intrinsic properties of iSQCs, the sequence is time-efficient with a narrow spectral width in the indirect dimension. It can recover useful information of chemical shifts, relative peak areas, J coupling constants, and multiplet patterns even when the field inhomogeneity is severe enough to erase almost all spectroscopic information. Moreover, good solvent suppression efficiency can be achieved by this sequence even with imperfect radio-frequency pulse flip angles. Spatially localized iSQC spectroscopy was performed on a sample packed with pig brain tissue and cucumber to show the feasibility of the sequence in in vivo magnetic resonance spectroscopy (MRS). This sequence may provide a promising way for the applications on in vivo and in situ high-resolution NMR spectroscopy.
Echo-time independent signal modulations for Strongly Coupled Systems in Triple Echo Localization schemes: An extension of S-PRESS editing
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 December 2009
Nils, Kickler , Giulio, Gambarota , Ralf, Mekle , Rolf, Gruetter , Robert, Mulkern
The double spin-echo point resolved spectroscopy sequence (PRESS) is a widely used method and standard in clinical MR spectroscopy. Existence of important J-modulations at constant echo times, depending on the temporal delays between the rf-pulses, have been demonstrated recently for strongly coupled spin systems and were exploited for difference editing, removing singlets from the spectrum (strong-coupling PRESS, S-PRESS). A drawback of this method for in vivo applications is that large signal modulations needed for difference editing occur only at relatively long echo times. In this work we demonstrate that, by simply adding a third refocusing pulse (3S-PRESS), difference editing becomes possible at substantially shorter echo times while, as applied to citrate, more favorable lineshapes can be obtained. For the example of an AB system an analytical description of the MR signal, obtained with this triple refocusing sequence (3S-PRESS), is provided.
On the applications of μr=-1 metamaterial lenses for magnetic resonance imaging
Publication year: 2009
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 December 2009
Manuel J., Freire , Lukas, Jelinek , Ricardo, Marques , Mikhail, Lapine
In this work some possible applications of negative permeability magnetic metamaterial lenses for magnetic resonance imaging (MRI) are analyzed. It is shown that using magnetic metamaterials lenses it is possible to manipulate the spatial distribution of the radio-frequency (RF) field used in MR systems and, under some circumstances, improve the sensitivity of surface coils. Furthermore a collimation of the RF field, phenomenon that may find application in parallel imaging, is presented. MR images of real tissues are shown in order to prove the suitability of the theoretical analysis for practical applications.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 21 December 2009
Sandra, Garcia , Jeffrey H., Walton , Brandon, Armstrong , Songi, Han , Michael J., McCarthy
We present the development of an Overhauser dynamic nuclear polarization (DNP) instrument at 0.04 T using 1.1 GHz (L-band) electron spin resonance frequencies (ESR) and 1.7 MHz 1H nuclear magnetic resonance frequencies. Using this home-built DNP system, the electron–nucleus coupling factor of 4-oxo-TEMPO dissolved in water was determined as 0.39 ± 0.06 at 0.04 T. The higher coupling factor obtained at this field compared to higher magnetic fields, such as 0.35 T, directly translates to higher enhancement of the NMR signal and opens up a wider time scale window for observing water dynamics interacting with macromolecular systems, including proteins, polymers or lipid vesicles. The higher enhancements obtained will facilitate the observation of water dynamics at correlation times up to 10 ns, that corresponds to more than one order of magnitude slower dynamics than accessible at 0.35 T using X-band ESR frequencies.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 December 2009
Manuel J., Freire , Lukas, Jelinek , Ricardo, Marques , Mikhail, Lapine
In this work some possible applications of negative permeability magnetic metamaterial lenses for magnetic resonance imaging (MRI) are analyzed. It is shown that using magnetic metamaterials lenses it is possible to manipulate the spatial distribution of the radio-frequency (RF) field used in MR systems and, under some circumstances, improve the sensitivity of surface coils. Furthermore a collimation of the RF field, phenomenon that may find application in parallel imaging, is presented. MR images of real tissues are shown in order to prove the suitability of the theoretical analysis for practical applications.
L-Band Overhauser Dynamic Nuclear Polarization
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 21 December 2009
Sandra, Garcia , Jeffrey H., Walton , Brandon, Armstrong , Songi, Han , Michael J., McCarthy
We present the development of an Overhauser dynamic nuclear polarization (DNP) instrument at 0.04 T using 1.1 GHz (L-band) electron spin resonance frequencies (ESR) and 1.7 MHz 1H nuclear magnetic resonance frequencies. Using this home-built DNP system, the electron–nucleus coupling factor of 4-oxo-TEMPO dissolved in water was determined as 0.39 ± 0.06 at 0.04 T. The higher coupling factor obtained at this field compared to higher magnetic fields, such as 0.35 T, directly translates to higher enhancement of the NMR signal and opens up a wider time scale window for observing water dynamics interacting with macromolecular systems, including proteins, polymers or lipid vesicles. The higher enhancements obtained will facilitate the observation of water dynamics at correlation times up to 10 ns, that corresponds to more than one order of magnitude slower dynamics than accessible at 0.35 T using X-band ESR frequencies.
Efficient Heteronuclear Dipolar Decoupling in Solid-State Nuclear Magnetic Resonance at Rotary Resonance Conditions
Publication year: 2009
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 21 December 2009
Subhradip, Paul , Venus Singh, Mithu , Narayanan D., Kurur , P.K., Madhu
We introduce here a heteronuclear dipolar decoupling scheme in solid-state nuclear magnetic resonance that performs efficiently at the rotary-resonance conditions, where otherwise dipolar couplings are re-introduced. Results are shown proving the efficiency of this scheme at two magnetic fields under magic-angle spinning frequencies of 30 kHz and 20 kHz.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 22 December 2009
Kanmi, Mao , Marek, Pruski
A simple method is shown for optimization of 1H homonuclear dipolar decoupling at MAS rates exceeding 10 kHz. By monitoring the intensity of a spin-echo under the decoupling conditions, it is possible to optimize the amplitude of the RF magnetic field, the cycle time of the decoupling sequence and the resonance offset within minutes. As a result, the decoupling efficiency can be quickly and reliably fine-tuned without using a reference sample. The utility of this method has been confirmed by studying the resolution patterns for the supercycled PMLG scheme, which were found to be in excellent agreement with earlier theoretical predictions and verified in high-resolution 2D 1H-1H experiments.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 23 December 2009
Luke A., O’Dell , Kristopher J., Harris , Robert W., Schurko
Various amplitude- and phase-modulated excitation pulses for the observation of static NMR powder patterns from half-integer quadrupolar nuclei have been generated using the optimal control routines implemented in SIMPSON 2.0. Such pulses are capable of both excitation of the central transition and signal enhancement by population transfer from the satellites. Enhancements in excess of 100% have been achieved for the central transition of the spin-3/2 87Rb nucleus compared with a selective π/2 pulse. These pulses are shown to be relatively insensitive to changes in RF power and transmitter offsets, and can achieve a more uniform signal enhancement than double frequency sweeps (DFS), resulting in more accurate spectral lineshapes. We also investigate the possibility of “calibration-free” optimized pulses for general use on half-integer quadrupoles with unknown interaction parameters. Such pulses could prove extremely useful for studying low abundance or insensitive nuclei for which experimental optimization of the DFS scheme may be difficult. We demonstrate that a pulse optimized for an arbitrary spin-3/2 system can function well on multiple samples, and can also excite the central transition of higher spin numbers, albeit with a smaller enhancement. The mechanism by which these optimized pulses achieve the signal enhancement is highly complex and, unlike DFS, involves a non-linear excitation of the satellite transition manifold, as well as the generation and manipulation of significant multiple-quantum coherences.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 23 December 2009
Russell R.P., Senthamarai , Ilya, Kuprov , Konstantin, Pervushin
Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library (http://spindynamics.org), which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of αXβ2 Integrin and 440 amino acids NS3 helicase.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Devon, Sheppard , Vitali, Tugarinov
The measurements of longitudinal and transverse 2H spin relaxation rates of backbone amide deuterons (DN) in the [U-13C,15N]-labeled protein ubiquitin show that the utility of amide deuterons as probes of backbone order in proteins is compromised by substantial variability of DN quadrupolar coupling constants (QCC) from one amide site to another. However, using the dynamics parameters of 15N-2H bond vectors evaluated from 15N relaxation data, site-specific QCC values can be estimated directly from DN R1 and R2 rates providing useful information on hydrogen bonding in proteins. In agreement with previous indirect scalar relaxation-based measurements, the DN QCC values estimated directly from R1 and R2 2H relaxation rates correlate with the inverse cube of the x-ray structure-derived hydrogen bond distances in ubiquitin: QCC = (232±2.3) + (118±17) Σi(cosα)ri-3 where r is the inter-nuclear hydrogen bond distance in ångströms, and α is the ND····Oi angle.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
J., Mende , N., Elmiladi , C., Höhl , K., Maier
The influence of acoustic radiation in the form of ultrasound (US) on the nuclear magnetic resonance (NMR) signal of liquids in the presence of piezo- and ferroelectric nanoparticles was investigated. The NMR resonances of 1H and 23Na were influenced by US with a frequency of ωUS = 18.26 MHz. For hydrogen, US with a frequency ωUS = ω0 was used where ω0 is the Larmor frequency of 18.26 MHz. For sodium, US with a frequency ωUS = 2ω0, Na was used with ω0, Na = 9.13 MHz. A detailed description of nanoparticle properties and sample preparation is given. The influence of US on the spin-lattice relaxation time T1 was determined with an inversion recovery sequence for different concentrations of PZT. An elongation of T1 of 1H by 1.7% at a PZT concentration of 0.05% and an elongation of T1 of 23Na by 3% at a PZT concentration of 0.04% was observed. The elongation scales with the concentration of the PZT. An possible explanation of the effect of elongation is discussed.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Kang, Chen , Frank, Delaglio , Nico, Tjandra
The concept of cross-spectrum is applied in protein NMR spectroscopy to assist in the backbone sequential resonance assignment. Cross-spectrum analysis is used routinely to reveal correlations in frequency domains as a means to reveal common features contained in multiple time series. Here the cross-spectrum between related NMR spectra, for example HNCO and HN(CA)CO, can be calculated with point-by-point multiplications along their common C’ carbon axis. In the resulting higher order cross-spectrum, an enhanced correlation signal occurs at every common i-1 carbon frequency allowing the amide proton HN (and nitrogen N) resonances from residues i and i-1 to be identified. The cross-spectrum approach is demonstrated using 2D spectra H(N)CO, H(NCA)CO, H(NCO)CACB, and H(N)CACB measured on a 15N/13C double-labeled Ubiquitin sample. These 2D spectra are used to calculate two pseudo-3D cross-spectra, Hi-Hi-1-C’i-1 and Hi-Hi-1-CAi-1CBi-1. We show using this approach, backbone resonances of H, C’, CA, and CB can be fully assigned without ambiguity. The cross-spectrum principle is expected to offer an easy, practical, and more quantitative approach for heteronuclear backbone resonance assignment.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Rafal, Janik , Emily, Ritz , Andrew, Gravelle , Lichi, Shi , Xiaohu, Peng , and Vladimir Ladizhansky
In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly 13C,15N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22 kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600 MHz. To match HORROR condition over all powder orientations, variable amplitude RF fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing interresidue long-range interresidue connectivities (e.g., (N[i]-CO[i-2])) are demonstrated on the model peptide N-Acetyl-Valine-Leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009 Erik Gudmundsona, , Petre Stoicaa, Jian Lib, Andreas Jakobssonc, Michael D. Rowed, John A. S. Smithd and Jun Lingb
The problem of estimating the spectral content of exponentially decaying signals from a set of irregularly sampled data is of considerable interest in several applications, for example in various forms of radio frequency spectroscopy. In this paper, we propose a new nonparametric iterative adaptive approach that provides a solution to this estimation problem. As opposed to commonly used methods in the field, the damping coefficient, or linewidth, is explicitly modelled, which allows for an improved estimation performance. Numerical examples using both simulated data and data from NQR experiments illustrate the benefits of the proposed estimator as compared to currently available nonparametric methods.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2010
J., Seliger , V., Žagar
A modification of nuclear quadrupole double resonance with coupled multiplet is proposed which can be used for the measurement of the dipolar structure of the 17O nuclear quadrupole resonance lines in case of a strong 1H-17O dipolar interaction. The technique is based on magnetic field cycling between a high magnetic field and zero magnetic field and on the simultaneous application of three rf magnetic fields with the frequencies that are close to the three 17O NQR frequencies ν5/2-1/2 > ν5/2-3/2
ν3/2-1/2 during the time spent in zero static magnetic field. When the sum of the two lower irradiation frequencies ν1+ν2 is not equal to the highest irradiation frequencyν, the three-frequency irradiation increases the proton relaxation rate in zero magnetic field and consequently decreases the proton NMR signal at the end of the magnetic field cycle. The new technique is theoretically analyzed and compared to the single-frequency and two-frequency irradiation techniques. It is shown that the sensitivity of the new technique exceeds the sensitivity of the two-frequency irradiation technique. As a test of the new technique we measured the shape of the highest-frequency 17O NQR line in paraelectric KH2PO4.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2010
C. Vinod Chandrana, Jérôme Cunyb, Régis Gautierb, Laurent Le Pollèsb, Chris J. Pickardc and Thomas Bräunigera,
To efficiently obtain multiple-quantum magic-angle spinning (MQMAS) spectra of the nuclide 45Sc (I=7/2), we have combined several previously suggested techniques to enhance the signal-to-noise ratio and to improve spectral resolution for the test sample, scandium sulphate pentahydrate (ScSPH). Whereas the 45Sc-3QMAS spectrum of ScSPH does not offer sufficient resolution to clearly distinguish between the 3 scandium sites present in the crystal structure, these sites are well-resolved in the 5QMAS spectrum. The loss of sensitivity incurred by using MQMAS with 5Q coherence order is partly compensated for by using fast-amplitude modulated (FAM) sequences to improve the efficiency of both 5Q coherence excitation and conversion. Also, heteronuclear decoupling is employed to minimise dephasing of the 45Sc signal during the 5Q evolution period due to dipolar couplings with the water protons in the ScSPH sample. Application of multi-pulse decoupling schemes such as TPPM and SPINAL results in improved sensitivity and resolution in the F1 (isotropic) dimension of the 5QMAS spectrum, the best results being achieved with the recently suggested SWf-TPPM sequence. By numerical fitting of the 45Sc-NMR spectra of ScSPH from 3QMAS, 5QMAS and single-quantum MAS at magnetic fields B0=9.4 T and 17.6 T, the isotropic chemical shift δiso, the quadrupolar coupling constant χ, and the asymmetry parameter η were obtained. Averaging over all experiments, the NMR parameters determined for the 3 scandium sites, designated (a), (b) and (c) are: δiso(a)=-15.5±0.5 ppm, χ(a)=5.60± 0.10 MHz, η(a)=0.06±0.05; δiso(b)=-12.9±0.5 ppm, χ(b)=4.50± 0.10 MHz, η(b)=1.00± 0.00; and δiso(c)=-4.7± 0.2 ppm, χ(c)=4.55± 0.05 MHz, η(c)=0.50±0.02. The NMR scandium species were assigned to the independent crystallographic sites by evaluating their experimental response to proton decoupling, and by density functional theory (DFT) calculations using the PAW and GIPAW approaches, in the following way: Sc(1) to (c), Sc(2) to (a), and Sc(3) to (b). The need to compute NMR parameters using an energy-optimised crystal structure is once again demonstrated.
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 21 December 2009
Subhradip, Paul , Venus Singh, Mithu , Narayanan D., Kurur , P.K., Madhu
We introduce here a heteronuclear dipolar decoupling scheme in solid-state nuclear magnetic resonance that performs efficiently at the rotary-resonance conditions, where otherwise dipolar couplings are re-introduced. Results are shown proving the efficiency of this scheme at two magnetic fields under magic-angle spinning frequencies of 30 kHz and 20 kHz.
Homonuclear dipolar decoupling under fast MAS: Resolution patterns and simple optimization strategy
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 22 December 2009
Kanmi, Mao , Marek, Pruski
A simple method is shown for optimization of 1H homonuclear dipolar decoupling at MAS rates exceeding 10 kHz. By monitoring the intensity of a spin-echo under the decoupling conditions, it is possible to optimize the amplitude of the RF magnetic field, the cycle time of the decoupling sequence and the resonance offset within minutes. As a result, the decoupling efficiency can be quickly and reliably fine-tuned without using a reference sample. The utility of this method has been confirmed by studying the resolution patterns for the supercycled PMLG scheme, which were found to be in excellent agreement with earlier theoretical predictions and verified in high-resolution 2D 1H-1H experiments.
Optimized Excitation Pulses for the Acquisition of Static NMR Powder Patterns from Half-Integer Quadrupolar Nuclei
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 23 December 2009
Luke A., O’Dell , Kristopher J., Harris , Robert W., Schurko
Various amplitude- and phase-modulated excitation pulses for the observation of static NMR powder patterns from half-integer quadrupolar nuclei have been generated using the optimal control routines implemented in SIMPSON 2.0. Such pulses are capable of both excitation of the central transition and signal enhancement by population transfer from the satellites. Enhancements in excess of 100% have been achieved for the central transition of the spin-3/2 87Rb nucleus compared with a selective π/2 pulse. These pulses are shown to be relatively insensitive to changes in RF power and transmitter offsets, and can achieve a more uniform signal enhancement than double frequency sweeps (DFS), resulting in more accurate spectral lineshapes. We also investigate the possibility of “calibration-free” optimized pulses for general use on half-integer quadrupoles with unknown interaction parameters. Such pulses could prove extremely useful for studying low abundance or insensitive nuclei for which experimental optimization of the DFS scheme may be difficult. We demonstrate that a pulse optimized for an arbitrary spin-3/2 system can function well on multiple samples, and can also excite the central transition of higher spin numbers, albeit with a smaller enhancement. The mechanism by which these optimized pulses achieve the signal enhancement is highly complex and, unlike DFS, involves a non-linear excitation of the satellite transition manifold, as well as the generation and manipulation of significant multiple-quantum coherences.
Benchmarking NMR experiments: a relational database of protein pulse sequences
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 23 December 2009
Russell R.P., Senthamarai , Ilya, Kuprov , Konstantin, Pervushin
Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library (http://spindynamics.org), which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of αXβ2 Integrin and 440 amino acids NS3 helicase.
Estimating Quadrupole Couplings of Amide Deuterons in Proteins from Direct Measurements of 2H Spin Relaxation Rates
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Devon, Sheppard , Vitali, Tugarinov
The measurements of longitudinal and transverse 2H spin relaxation rates of backbone amide deuterons (DN) in the [U-13C,15N]-labeled protein ubiquitin show that the utility of amide deuterons as probes of backbone order in proteins is compromised by substantial variability of DN quadrupolar coupling constants (QCC) from one amide site to another. However, using the dynamics parameters of 15N-2H bond vectors evaluated from 15N relaxation data, site-specific QCC values can be estimated directly from DN R1 and R2 rates providing useful information on hydrogen bonding in proteins. In agreement with previous indirect scalar relaxation-based measurements, the DN QCC values estimated directly from R1 and R2 2H relaxation rates correlate with the inverse cube of the x-ray structure-derived hydrogen bond distances in ubiquitin: QCC = (232±2.3) + (118±17) Σi(cosα)ri-3 where r is the inter-nuclear hydrogen bond distance in ångströms, and α is the ND····Oi angle.
Nuclear acoustic resonance in fluids using piezoelectric nanoparticles
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
J., Mende , N., Elmiladi , C., Höhl , K., Maier
The influence of acoustic radiation in the form of ultrasound (US) on the nuclear magnetic resonance (NMR) signal of liquids in the presence of piezo- and ferroelectric nanoparticles was investigated. The NMR resonances of 1H and 23Na were influenced by US with a frequency of ωUS = 18.26 MHz. For hydrogen, US with a frequency ωUS = ω0 was used where ω0 is the Larmor frequency of 18.26 MHz. For sodium, US with a frequency ωUS = 2ω0, Na was used with ω0, Na = 9.13 MHz. A detailed description of nanoparticle properties and sample preparation is given. The influence of US on the spin-lattice relaxation time T1 was determined with an inversion recovery sequence for different concentrations of PZT. An elongation of T1 of 1H by 1.7% at a PZT concentration of 0.05% and an elongation of T1 of 23Na by 3% at a PZT concentration of 0.04% was observed. The elongation scales with the concentration of the PZT. An possible explanation of the effect of elongation is discussed.
A Practical Implementation of Cross-spectrum in Protein Backbone Resonance Assignment
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Kang, Chen , Frank, Delaglio , Nico, Tjandra
The concept of cross-spectrum is applied in protein NMR spectroscopy to assist in the backbone sequential resonance assignment. Cross-spectrum analysis is used routinely to reveal correlations in frequency domains as a means to reveal common features contained in multiple time series. Here the cross-spectrum between related NMR spectra, for example HNCO and HN(CA)CO, can be calculated with point-by-point multiplications along their common C’ carbon axis. In the resulting higher order cross-spectrum, an enhanced correlation signal occurs at every common i-1 carbon frequency allowing the amide proton HN (and nitrogen N) resonances from residues i and i-1 to be identified. The cross-spectrum approach is demonstrated using 2D spectra H(N)CO, H(NCA)CO, H(NCO)CACB, and H(N)CACB measured on a 15N/13C double-labeled Ubiquitin sample. These 2D spectra are used to calculate two pseudo-3D cross-spectra, Hi-Hi-1-C’i-1 and Hi-Hi-1-CAi-1CBi-1. We show using this approach, backbone resonances of H, C’, CA, and CB can be fully assigned without ambiguity. The cross-spectrum principle is expected to offer an easy, practical, and more quantitative approach for heteronuclear backbone resonance assignment.
Inter-residue carbonyl-carbonyl polarization transfer experiments in uniformly 13C,15N-labeled peptides and proteins
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009
Rafal, Janik , Emily, Ritz , Andrew, Gravelle , Lichi, Shi , Xiaohu, Peng , and Vladimir Ladizhansky
In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly 13C,15N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22 kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600 MHz. To match HORROR condition over all powder orientations, variable amplitude RF fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing interresidue long-range interresidue connectivities (e.g., (N[i]-CO[i-2])) are demonstrated on the model peptide N-Acetyl-Valine-Leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.
Spectral Estimation of Irregularly Sampled Exponentially Decaying Signals with Applications to RF Spectroscopy
Publication year: 2009Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 December 2009 Erik Gudmundsona, , Petre Stoicaa, Jian Lib, Andreas Jakobssonc, Michael D. Rowed, John A. S. Smithd and Jun Lingb
The problem of estimating the spectral content of exponentially decaying signals from a set of irregularly sampled data is of considerable interest in several applications, for example in various forms of radio frequency spectroscopy. In this paper, we propose a new nonparametric iterative adaptive approach that provides a solution to this estimation problem. As opposed to commonly used methods in the field, the damping coefficient, or linewidth, is explicitly modelled, which allows for an improved estimation performance. Numerical examples using both simulated data and data from NQR experiments illustrate the benefits of the proposed estimator as compared to currently available nonparametric methods.
Measurement of dipolar structure of 17O nuclear quadrupole resonance lines by three-frequency irradiation
Publication year: 2010Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2010
J., Seliger , V., Žagar
A modification of nuclear quadrupole double resonance with coupled multiplet is proposed which can be used for the measurement of the dipolar structure of the 17O nuclear quadrupole resonance lines in case of a strong 1H-17O dipolar interaction. The technique is based on magnetic field cycling between a high magnetic field and zero magnetic field and on the simultaneous application of three rf magnetic fields with the frequencies that are close to the three 17O NQR frequencies ν5/2-1/2 > ν5/2-3/2
ν3/2-1/2 during the time spent in zero static magnetic field. When the sum of the two lower irradiation frequencies ν1+ν2 is not equal to the highest irradiation frequencyν, the three-frequency irradiation increases the proton relaxation rate in zero magnetic field and consequently decreases the proton NMR signal at the end of the magnetic field cycle. The new technique is theoretically analyzed and compared to the single-frequency and two-frequency irradiation techniques. It is shown that the sensitivity of the new technique exceeds the sensitivity of the two-frequency irradiation technique. As a test of the new technique we measured the shape of the highest-frequency 17O NQR line in paraelectric KH2PO4.Improving sensitivity and resolution of MQMAS spectra: a 45Sc-NMR case study of scandium sulphate pentahydrate
Publication year: 2010Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2010
C. Vinod Chandrana, Jérôme Cunyb, Régis Gautierb, Laurent Le Pollèsb, Chris J. Pickardc and Thomas Bräunigera,
To efficiently obtain multiple-quantum magic-angle spinning (MQMAS) spectra of the nuclide 45Sc (I=7/2), we have combined several previously suggested techniques to enhance the signal-to-noise ratio and to improve spectral resolution for the test sample, scandium sulphate pentahydrate (ScSPH). Whereas the 45Sc-3QMAS spectrum of ScSPH does not offer sufficient resolution to clearly distinguish between the 3 scandium sites present in the crystal structure, these sites are well-resolved in the 5QMAS spectrum. The loss of sensitivity incurred by using MQMAS with 5Q coherence order is partly compensated for by using fast-amplitude modulated (FAM) sequences to improve the efficiency of both 5Q coherence excitation and conversion. Also, heteronuclear decoupling is employed to minimise dephasing of the 45Sc signal during the 5Q evolution period due to dipolar couplings with the water protons in the ScSPH sample. Application of multi-pulse decoupling schemes such as TPPM and SPINAL results in improved sensitivity and resolution in the F1 (isotropic) dimension of the 5QMAS spectrum, the best results being achieved with the recently suggested SWf-TPPM sequence. By numerical fitting of the 45Sc-NMR spectra of ScSPH from 3QMAS, 5QMAS and single-quantum MAS at magnetic fields B0=9.4 T and 17.6 T, the isotropic chemical shift δiso, the quadrupolar coupling constant χ, and the asymmetry parameter η were obtained. Averaging over all experiments, the NMR parameters determined for the 3 scandium sites, designated (a), (b) and (c) are: δiso(a)=-15.5±0.5 ppm, χ(a)=5.60± 0.10 MHz, η(a)=0.06±0.05; δiso(b)=-12.9±0.5 ppm, χ(b)=4.50± 0.10 MHz, η(b)=1.00± 0.00; and δiso(c)=-4.7± 0.2 ppm, χ(c)=4.55± 0.05 MHz, η(c)=0.50±0.02. The NMR scandium species were assigned to the independent crystallographic sites by evaluating their experimental response to proton decoupling, and by density functional theory (DFT) calculations using the PAW and GIPAW approaches, in the following way: Sc(1) to (c), Sc(2) to (a), and Sc(3) to (b). The need to compute NMR parameters using an energy-optimised crystal structure is once again demonstrated.
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