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https://www.readbyqxmd.com/read/27860024/capturing-excited-states-in-the-fast-intermediate-exchange-limit-in-biological-systems-using-1-h%C3%A2-nmr-spectroscopy
#1
Emilie Steiner, Judith Schlagnitweit, Patrik Lundström, Katja Petzold
Changes in molecular structure are essential for the function of biomolecules. Characterization of these structural fluctuations can illuminate alternative states and help in correlating structure to function. NMR relaxation dispersion (RD) is currently the only method for detecting these alternative, high-energy states. In this study, we present a versatile (1) H R1ρ RD experiment that not only extends the exchange timescales at least three times beyond the rate limits of (13) C/(15) N R1ρ and ten times for CPMG experiments, but also makes use of easily accessible probes, thus allowing a general description of biologically important excited states...
November 17, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27810802/body-diffusion-weighted-imaging-using-non-cpmg-fast-spin-echo
#2
Eric Gibbons, Patrick Le Roux, Shreyas Vasanawala, John Pauly, Adam Kerr
SS-FSE is a fast technique that does not suffer from off-resonance distortions to the degree that EPI does. Unlike EPI, SS-FSE is ill-suited to diffusion weighted imaging (DWI) due to the Carr-Purcell-Meiboom-Geill (CPMG) condition. Non- CPMG phase cycling does accommodate SS-FSE and DWI but places constraints on reconstruction, which are resolved here through parallel imaging. Additionally, improved echo stability can be achieved by using short duration and highly selective DIVERSE radiofrequency pulses. Here, signal-to-noise ratio (SNR) comparisons between EPI and nCPMG SS-FSE acquisitions and reconstruction techniques give similar values...
October 27, 2016: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/27809381/stability-and-sensitivity-of-water-t2-obtained-with-ideal-cpmg-in-healthy-and-fat-infiltrated-skeletal-muscle
#3
Christopher D J Sinclair, Jasper M Morrow, Robert L Janiczek, Matthew R B Evans, Elham Rawah, Sachit Shah, Michael G Hanna, Mary M Reilly, Tarek A Yousry, John S Thornton
Quantifying muscle water T2 (T2 -water) independently of intramuscular fat content is essential in establishing T2 -water as an outcome measure for imminent new therapy trials in neuromuscular diseases. IDEAL-CPMG combines chemical shift fat-water separation with T2 relaxometry to obtain such a measure. Here we evaluate the reproducibility and B1 sensitivity of IDEAL-CPMG T2 -water and fat fraction (f.f.) values in healthy subjects, and demonstrate the potential of the method to quantify T2 -water variation in diseased muscle displaying varying degrees of fatty infiltration...
December 2016: NMR in Biomedicine
https://www.readbyqxmd.com/read/27782473/fast-accurate-2d-mr-relaxation-exchange-spectroscopy-rexsy-beyond-compressed-sensing
#4
Ruiliang Bai, Dan Benjamini, Jian Cheng, Peter J Basser
Previously, we showed that compressive or compressed sensing (CS) can be used to reduce significantly the data required to obtain 2D-NMR relaxation and diffusion spectra when they are sparse or well localized. In some cases, an order of magnitude fewer uniformly sampled data were required to reconstruct 2D-MR spectra of comparable quality. Nonetheless, this acceleration may still not be sufficient to make 2D-MR spectroscopy practicable for many important applications, such as studying time-varying exchange processes in swelling gels or drying paints, in living tissue in response to various biological or biochemical challenges, and particularly for in vivo MRI applications...
October 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27766699/mulitshot-cartesian-turbo-spin-echo-diffusion-imaging-using-iterative-pocsmuse-reconstruction
#5
Zhe Zhang, Bing Zhang, Ming Li, Xue Liang, Xiaodong Chen, Renyuan Liu, Xin Zhang, Hua Guo
PURPOSE: To report a diffusion imaging technique insensitive to off-resonance artifacts and motion-induced ghost artifacts using mulitshot Cartesian turbo spin-echo (TSE) acquisition and iterative POCS-based reconstruction of multiplexed sensitivity encoded magnetic resonance imaging (MRI) (POCSMUSE) for phase correction. MATERIALS AND METHODS: Phase insensitive diffusion preparation was used to deal with the violation of the Carr-Purcell-Meiboom-Gill (CPMG) conditions of TSE diffusion-weighted imaging (DWI), followed by a mulitshot Cartesian TSE readout for data acquisition...
October 20, 2016: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/27739464/nmr-based-serum-metabolomics-reveals-a-distinctive-signature-in-patients-with-lupus-nephritis
#6
Anupam Guleria, Avadhesh Pratap, Durgesh Dubey, Atul Rawat, Smriti Chaurasia, Edavalath Sukesh, Sanat Phatak, Sajal Ajmani, Umesh Kumar, Chunni Lal Khetrapal, Paul Bacon, Ramnath Misra, Dinesh Kumar
Management of patient with Lupus Nephritis (LN) continues to remain a challenge for the treating physicians because of considerable morbidity and even mortality. The search of biomarkers in serum and urine is a focus of researchers to unravel new targets for therapy. In the present study, the utility of NMR-based serum metabolomics has been evaluated for the first time in discriminating LN patients from non-nephritis lupus patients (SLE) and further to get new insights into the underlying disease processes for better clinical management...
October 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27689530/me-cagebird-r-x-cpmg-hsqmbc-a-phase-sensitive-multiplicity-edited-long-range-hsqc-with-absorptive-line-shapes
#7
Harri Koskela, Ilkka Kilpeläinen, Sami Heikkinen
ME-CAGEBIRD(r,X)-CPMG-HSMBC pulse sequence is a phase sensitive, carbon multiplicity edited 2D-experiment for detecting heteronuclear correlations originating from long-range (1)H, (13)C-couplings, (n)JCH. The presented method allows measurement of (n)JCH-values as well as is capable of separating different carbon types in subspectra ((13)C/(13)CH2 and (13)CH/(13)CH3) with minimal amount of cross talk i.e. cross peaks from wrong carbon multiplicity. Pure lineshapes and clean subspectra are achieved by utilizing CPMG in polarization transfer period, CRISIS-approach in multiplicity editing period and zero-quantum filtration...
September 17, 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27661784/an-improved-19-f-cpmg-scheme-for-detecting-binding-of-polyfluorinated-molecules-to-biological-receptors
#8
Luis Pablo Calle, Juan Félix Espinosa
No abstract text is available yet for this article.
September 23, 2016: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/27643912/-14-n-solid-state-nmr-spectroscopy-of-amino-acids
#9
Stanislav L Veinberg, Zachary W Friedl, Austin W Lindquist, Brianna Kispal, Kristopher J Harris, Luke A O'Dell, Robert W Schurko
(14) N ultra-wideline solid-state NMR (SSNMR) spectra were obtained for 16 naturally occurring amino acids and four related derivatives by using the WURST-CPMG (wideband, uniform rate, and smooth truncation Carr-Purcell-Meiboom-Gill) pulse sequence and frequency-stepped techniques. The (14) N quadrupolar parameters were measured for the sp(3) nitrogen moieties (quadrupolar coupling constant, CQ , values ranged from 0.8 to 1.5 MHz). With the aid of plane-wave DFT calculations of the (14) N electric-field gradient tensor parameters and orientations, the moieties were grouped into three categories according to the values of the quadrupolar asymmetry parameter, ηQ : low (≤0...
December 5, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/27628670/workflow-for-integrated-processing-of-multicohort-untargeted-1-h-nmr-metabolomics-data-in-large-scale-metabolic-epidemiology
#10
Ibrahim Karaman, Diana L S Ferreira, Claire L Boulangé, Manuja R Kaluarachchi, David Herrington, Anthony C Dona, Raphaële Castagné, Alireza Moayyeri, Benjamin Lehne, Marie Loh, Paul S de Vries, Abbas Dehghan, Oscar H Franco, Albert Hofman, Evangelos Evangelou, Ioanna Tzoulaki, Paul Elliott, John C Lindon, Timothy M D Ebbels
Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robust processing pipelines that can ensure reliable data for statistical analysis. The COMBI-BIO project incorporates serum from ∼8000 individuals, in three cohorts, profiled by six assays in two phases using both (1)H NMR and UPLC-MS...
October 6, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27627661/protein-observed-fluorine-nmr-is-a-complementary-ligand-discovery-method-to-1-h-cpmg-ligand-observed-nmr
#11
Andrew K Urick, Luis Pablo Calle, Juan F Espinosa, Haitao Hu, William C K Pomerantz
To evaluate its potential as a ligand discovery tool, we compare a newly developed 1D protein-observed fluorine NMR (PrOF NMR) screening method with the well-characterized ligand-observed (1)H CPMG NMR screen. We selected the first bromodomain of Brd4 as a model system to benchmark PrOF NMR because of the high ligandability of Brd4 and the need for small molecule inhibitors of related epigenetic regulatory proteins. We compare the two methods' hit sensitivity, triaging ability, experiment speed, material consumption, and the potential for false positives and negatives...
October 5, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27593185/quantifying-disease-activity-in-fatty-infiltrated-skeletal-muscle-by-ideal-cpmg-in-duchenne-muscular-dystrophy
#12
Ami Mankodi, Courtney A Bishop, Sungyoung Auh, Rexford D Newbould, Kenneth H Fischbeck, Robert L Janiczek
The purpose of this study was to explore the use of iterative decomposition of water and fat with echo asymmetry and least-squares estimation Carr-Purcell-Meiboom-Gill (IDEAL-CPMG) to simultaneously measure skeletal muscle apparent fat fraction and water T2 (T2,w) in patients with Duchenne muscular dystrophy (DMD). In twenty healthy volunteer boys and thirteen subjects with DMD, thigh muscle apparent fat fraction was measured by Dixon and IDEAL-CPMG, with the IDEAL-CPMG also providing T2,w as a measure of muscle inflammatory activity...
October 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/27527986/enhancing-the-sensitivity-of-cpmg-relaxation-dispersion-to-conformational-exchange-processes-by-multiple-quantum-spectroscopy
#13
Tairan Yuwen, Pramodh Vallurupalli, Lewis E Kay
A triple-quantum (1) H Carr-Purcell-Meiboom-Gill NMR relaxation dispersion experiment is presented that uses methyl group probes as reporters of conformational exchange in highly deuterated, methyl-protonated proteins. Significantly larger dispersion profiles, by as much as a factor of nine, can be obtained relative to single-quantum approaches, thus offering very significant advantages in applications involving interconverting conformers with only small changes in structure or in studies of rare states that are at very low populations...
September 12, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27507493/hydrothermal-changes-in-wheat-starch-monitored-by-two-dimensional-nmr
#14
R Kovrlija, C Rondeau-Mouro
The temperature-dependent changes in wheat starch powder and wheat starch-water mixtures were monitored in real-time throughout the heating/cooling program using a classical one-dimensional T1 method and a novel bi-dimensional approach to correlate spin-lattice and spin-spin relaxation times (T1-T2) including acquisition of the FID signal. The influence of two controlling factors (i.e. water content (11%, 35-50%, wet basis) and temperature (20-90°C and back to 20°C)) on water distribution and starch transformation was investigated...
January 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27473413/evaluating-the-influence-of-initial-magnetization-conditions-on-extracted-exchange-parameters-in-nmr-relaxation-experiments-applications-to-cpmg-and-cest
#15
Tairan Yuwen, Ashok Sekhar, Lewis E Kay
Transient excursions of native protein states to functionally relevant higher energy conformations often occur on the μs-ms timescale. NMR spectroscopy has emerged as an important tool to probe such processes using techniques such as Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion and Chemical Exchange Saturation Transfer (CEST). The extraction of kinetic and structural parameters from these measurements is predicated upon mathematical modeling of the resulting relaxation profiles, which in turn relies on knowledge of the initial magnetization conditions at the start of the CPMG/CEST relaxation elements in these experiments...
August 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27414761/effects-of-off-resonance-spins-on-the-performance-of-the-modulated-gradient-spin-echo-sequence
#16
Igor Serša, Franci Bajd, Aleš Mohorič
Translational molecular dynamics in various materials can also be studied by diffusion spectra. These can be measured by a constant gradient variant of the modulated gradient spin echo (MGSE) sequence which is composed of a CPMG RF pulse train superimposed to a constant magnetic field gradient. The application of the RF train makes the effective gradient oscillating thus enabling measurements of diffusion spectra in a wide range of frequencies. However, seemingly straightforward implementation of the MGSE sequence proved to be complicated and can give overestimated results for diffusion if not interpreted correctly...
September 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27387012/ligand-binding-enhances-millisecond-conformational-exchange-in-xylanase-b2-from-streptomyces-lividans
#17
Donald Gagné, Chitra Narayanan, Nhung Nguyen-Thi, Louise D Roux, David N Bernard, Joseph S Brunzelle, Jean-François Couture, Pratul K Agarwal, Nicolas Doucet
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame...
August 2, 2016: Biochemistry
https://www.readbyqxmd.com/read/27376553/rapid-and-simple-determination-of-t1-relaxation-times-in-time-domain-nmr-by-continuous-wave-free-precession-sequence
#18
Tiago Bueno Moraes, Tatiana Monaretto, Luiz Alberto Colnago
Longitudinal (T1) and transverse (T2) relaxation times have been widely used in time-domain NMR (TD-NMR) to determine several physicochemical properties of petroleum, polymers, and food products. The measurement of T2 through the CPMG pulse sequence has been used in most of these applications because it denotes a rapid, robust method. On the other hand, T1 has been occasionally used in TD-NMR due to the long measurement time required to collect multiple points along the T1 relaxation curve. Recently, several rapid methods to measure T1 have been proposed...
September 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27344611/obtaining-t1-t2-distribution-functions-from-1-dimensional-t1-and-t2-measurements-the-pseudo-2-d-relaxation-model
#19
Nathan H Williamson, Magnus Röding, Petrik Galvosas, Stanley J Miklavcic, Magnus Nydén
We present the pseudo 2-D relaxation model (P2DRM), a method to estimate multidimensional probability distributions of material parameters from independent 1-D measurements. We illustrate its use on 1-D T1 and T2 relaxation measurements of saturated rock and evaluate it on both simulated and experimental T1-T2 correlation measurement data sets. Results were in excellent agreement with the actual, known 2-D distribution in the case of the simulated data set. In both the simulated and experimental case, the functional relationships between T1 and T2 were in good agreement with the T1-T2 correlation maps from the 2-D inverse Laplace transform of the full 2-D data sets...
August 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27331118/absolute-nutrient-concentration-measurements-in-cell-culture-media-1-h-q-nmr-spectra-and-data-to-compare-the-efficiency-of-ph-controlled-protein-precipitation-versus-cpmg-or-post-processing-filtering-approaches
#20
Luca Goldoni, Tiziana Beringhelli, Walter Rocchia, Natalia Realini, Daniele Piomelli
The NMR spectra and data reported in this article refer to the research article titled "A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR" [1]. We provide the (1)H q-NMR spectra of cell culture media (DMEM) after removal of serum proteins, which show the different efficiency of various precipitating solvents, the solvent/DMEM ratios, and pH of the solution. We compare the data of the absolute nutrient concentrations, measured by PULCON external standard method, before and after precipitation of serum proteins and those obtained using CPMG (Carr-Purcell-Meiboom-Gill) sequence or applying post-processing filtering algorithms to remove, from the (1)H q-NMR spectra, the proteins signal contribution...
September 2016: Data in Brief
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