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https://www.readbyqxmd.com/read/28052669/self-assembly-of-human-profilin-1-detected-by-cpmg-nmr-spectroscopy
#1
Enrico Rennella, Ashok Sekhar, Lewis E Kay
Protein oligomerization in the cell has important implications in both health and disease and an understanding of the mechanisms by which proteins can self-associate is, therefore, of critical interest. Initial stages of the oligomerization process can be hard to detect, as they often involve the formation of sparsely populated and transient states that are difficult to characterize by standard biophysical approaches. Using relaxation dispersion NMR spectroscopy we study the oligomerization of human profilin-1, a protein that regulates the polymerization of actin...
January 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/28049727/allosteric-transmission-along-a-loosely-structured-backbone-allows-a-cardiac-troponin-c-mutant-to-function-with-only-one-ca2-ion
#2
Mayra de A Marques, Jose Renato Pinto, Adolfo H Moraes, Anwar Iqbal, Mariana T Q de Magalhães, Jamila Monteiro, Murilo M Pedrote, Martha M Sorenson, Jerson L Silva, Guilherme A P de Oliveira
Hypertrophic cardiomyopathy (HCM) is one of the most common cardiomyopathies, and a major cause of sudden death in young athletes. The Ca2+ sensor of the sarcomere, cardiac troponin C (cTnC), plays an important role in regulating muscle contraction. Although several cardiomyopathy-causing mutations have been identified in cTnC, limited information about their structural defects has been mapped to the HCM phenotype. Here, we use high-resolution electron-spray ionization mass spectrometry (ESI-MS), Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG-RD) and affinity measurements of cTnC for the thin filament in reconstituted papillary muscles to provide evidence of an allosteric mechanism in mutant cTnC that may play a role to the HCM phenotype...
January 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28024258/phase-incremented-echo-train-acquisition-applied-to-magnetic-resonance-pore-imaging
#3
S A Hertel, P Galvosas
Efficient phase cycling schemes remain a challenge for NMR techniques if the pulse sequences involve a large number of rf-pulses. Especially complex is the Carr Purcell Meiboom Gill (CPMG) pulse sequence where the number of rf-pulses can range from hundreds to several thousands. Our recent implementation of Magnetic Resonance Pore Imaging (MRPI) is based on a CPMG rf-pulse sequence in order to refocus the effect of internal gradients inherent in porous media. While the spin dynamics for spin-1/2 systems in CPMG like experiments are well understood it is still not straight forward to separate the desired pathway from the spectrum of unwanted coherence pathways...
December 16, 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27993533/transverse-water-relaxation-in-whole-blood-and-erythrocytes-at-3t-7t-9-4t-11-7t-and-16-4t-determination-of-intracellular-hemoglobin-and-extracellular-albumin-relaxivities
#4
Ksenija Grgac, Wenbo Li, Alan Huang, Qin Qin, Peter C M van Zijl
Blood is a physiological substance with multiple water compartments, which contain water-binding proteins such as hemoglobin in erythrocytes and albumin in plasma. Knowing the water transverse (R2) relaxation rates from these different blood compartments is a prerequisite for quantifying the blood oxygenation level-dependent (BOLD) effect. Here, we report the Carr-Purcell-Meiboom-Gill (CPMG) based transverse (R2CPMG) relaxation rates of water in bovine blood samples circulated in a perfusion system at physiological temperature in order to mimic blood perfusion in humans...
December 16, 2016: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/27966496/recent-excitements-in-protein-nmr-large-proteins-and-biologically-relevant-dynamics
#5
Sai Chaitanya Chiliveri, Mandar V Deshmukh
The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecular NMR spectroscopists to overcome the size limitation barrier (approx. 20 kDa) in de novo structure determination of proteins. The utility of these techniques was immediately demonstrated on large proteins and protein complexes (e.g. GroELGroES, ClpP protease, Hsp90-p53, 20S proteasome, etc.). Further, recent methodological developments such as Residual Dipolar Couplings and Paramagnetic Relaxation Enhancement allowed accurate measurement of long-range structural restraints...
December 2016: Journal of Biosciences
https://www.readbyqxmd.com/read/27936313/knight-shift-in-13-c%C3%A2-nmr-resonances-confirms-the-coordination-of-n-heterocyclic-carbene-ligands-to-water-soluble-palladium-nanoparticles
#6
Juan M Asensio, Simon Tricard, Yannick Coppel, Román Andrés, Bruno Chaudret, Ernesto de Jesús
The coordination of N-heterocyclic carbene (NHC) ligands to the surface of 3.7 nm palladium nanoparticles (PdNPs) can be unambiguously established by observation of Knight shift (KS) in the (13) C resonance of the carbenic carbon. In order to validate this coordination, PdNPs with sizes ranging from 1.3 to 4.8 nm were prepared by thermal decomposition or reduction with CO of a dimethyl NHC Pd(II) complex. NMR studies after (13) CO adsorption established that the KS shifts the (13) C resonances of the chemisorbed molecules several hundreds of ppm to high frequencies only when the particle exceeds a critical size of around 2 nm...
December 9, 2016: Angewandte Chemie
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
#7
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...
December 19, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27810802/body-diffusion-weighted-imaging-using-non-cpmg-fast-spin-echo
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
December 2, 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
#17
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...
November 18, 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
#18
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
#19
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
#20
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
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