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https://www.readbyqxmd.com/read/29240977/broadband-homonuclear-decoupled-hsqmbc-methods
#1
István Timári, Katalin E Kövér
Long-range heteronuclear coupling constants convey invaluable information for stereochemical and conformational analysis of molecules from synthetic and natural origin. Here we report a real-time Zangger-Sterk CPMG-HSQMBC method for the precise and direct measurement of multiple-bond heteronuclear couplings. It is demonstrated that the real-time acquisition strategy combined with multiple slice selective excitation can provide substantial improvement in sensitivity (or reduction of experimental time) as compared to other variants of broadband homonuclear decoupled HSQMBC methods published previously...
December 14, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/29219218/rotator-cuff-tendon-assessment-using-magic-angle-insensitive-3d-ultrashort-echo-time-cones-magnetization-transfer-ute-cones-mt-imaging-and-modeling-with-histological-correlation
#2
Yanchun Zhu, Xin Cheng, Yajun Ma, Jonathan H Wong, Yaoqin Xie, Jiang Du, Eric Y Chang
BACKGROUND: Rotator cuff tendons (RCTs) are challenging to image due to the "magic angle effect" and their short T2 . PURPOSE: To assess the degree of magic angle sensitivity of human RCTs and to utilize a 3D ultrashort echo time Cones sequence with magnetization transfer preparation (UTE-Cones-MT) and two-pool quantitative MT modeling with histological correlation. We hypothesized that MT parameters would be less sensitive to the magic angle compared with conventional T2 measurements...
December 8, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29188417/simultaneous-determination-of-fast-and-slow-dynamics-in-molecules-using-extreme-cpmg-relaxation-dispersion-experiments
#3
Jithender G Reddy, Supriya Pratihar, David Ban, Sebastian Frischkorn, Stefan Becker, Christian Griesinger, Donghan Lee
Molecular dynamics play a significant role in how molecules perform their function. A critical method that provides information on dynamics, at the atomic level, is NMR-based relaxation dispersion (RD) experiments. RD experiments have been utilized for understanding multiple biological processes occurring at micro-to-millisecond time, such as enzyme catalysis, molecular recognition, ligand binding and protein folding. Here, we applied the recently developed high-power RD concept to the Carr-Purcell-Meiboom-Gill sequence (extreme CPMG; E-CPMG) for the simultaneous detection of fast and slow dynamics...
November 29, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29151212/cpmg-experiments-for-protein-minor-conformer-structure-determination
#4
Anusha B Gopalan, D Flemming Hansen, Pramodh Vallurupalli
CPMG relaxation dispersion NMR experiments have emerged as a powerful method to characterize protein minor states that are in exchange with a visible dominant conformation, and have lifetimes between ~0.5 and 5 milliseconds (ms) and populations greater than 0.5%. The structure of the minor state can, in favorable cases, be determined from the parameters provided by the CPMG relaxation dispersion experiments. Here, we go through the intricacies of setting up these powerful CPMG experiments.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29044721/body-diffusion-weighted-imaging-using-magnetization-prepared-single-shot-fast-spin-echo-and-extended-parallel-imaging-signal-averaging
#5
Eric K Gibbons, Shreyas S Vasanawala, John M Pauly, Adam B Kerr
PURPOSE: This work demonstrates a magnetization prepared diffusion-weighted single-shot fast spin echo (SS-FSE) pulse sequence for the application of body imaging to improve robustness to geometric distortion. This work also proposes a scan averaging technique that is superior to magnitude averaging and is not subject to artifacts due to object phase. THEORY AND METHODS: This single-shot sequence is robust against violation of the Carr-Purcell-Meiboom-Gill (CPMG) condition...
October 17, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28951313/utilizing-tagged-paramagnetic-shift-reagents-to-monitor-protein-dynamics-by-nmr
#6
Libin Ye, Ned Van Eps, Xiang Li, Oliver P Ernst, R Scott Prosser
Calmodulin is a ubiquitous calcium sensor protein, known to serve as a critical interaction hub with a wide range of signaling partners. While the holo form of calmodulin (CaM-4Ca(2+)) has a well-defined ground state structure, it has been shown to undergo exchange, on a millisecond timescale, to a conformation resembling that of the peptide bound state. Tagged paramagnetic relaxation agents have been previously used to identify long-range dipolar interactions through relaxation effects on nuclear spins of interest...
September 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28915495/impact-of-chemotherapy-on-metabolic-reprogramming-characterization-of-the-metabolic-profile-of-breast-cancer-mda-mb-231-cells-using-1-h-hr-mas-nmr-spectroscopy
#7
Roberta M Maria, Wanessa F Altei, Heloisa S Selistre-de-Araujo, Luiz A Colnago
Doxorubicin, cisplatin, and tamoxifen are part of many chemotherapeutic regimens. However, studies investigating the effect of chemotherapy on the metabolism of breast cancer cells are still limited. We used (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to study the metabolic profile of human breast cancer MDA-MB-231 cells either untreated (control) or treated with tamoxifen, cisplatin, and doxorubicin. (1)H HR-MAS NMR single pulse spectra evidenced signals from all mobile cell compounds, including fatty acids (membranes), water-soluble proteins, and metabolites...
September 12, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28822305/an-optimal-control-approach-to-design-entire-relaxation-dispersion-experiments
#8
Thoa T Nguyen, Steffen J Glaser
A general approach is introduced to optimize experiments for the analysis of spin systems in the presence of chemical exchange. Rather than optimizing individual pulse sequence elements, such as refocusing pulses, entire relaxation dispersion sequences are optimized in the form of a single shaped pulse. This is achieved by defining a performance index that is only based on the remaining signal after the relaxation dispersion sequence for a range of exchange, relaxation, offset, and rf inhomogeneity parameters...
July 31, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28771339/specific-acetylation-patterns-of-h2a-z-form-transient-interactions-with-the-bptf-bromodomain
#9
Gabriella T Perell, Neeraj K Mishra, Babu Sudhamalla, Peter D Ycas, Kabirul Islam, William C K Pomerantz
Post-translational lysine acetylation of histone tails affects both chromatin accessibility and recruitment of multifunctional bromodomain-containing proteins for modulating transcription. The bromodomain- and PHD finger-containing transcription factor (BPTF) regulates transcription but has also been implicated in high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for its affinity for BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region...
September 5, 2017: Biochemistry
https://www.readbyqxmd.com/read/28737383/alternatives-to-nuclear-overhauser-enhancement-spectroscopy-presat-and-carr-purcell-meiboom-gill-presat-for-nmr-based-metabolomics
#10
Adrien Le Guennec, Fariba Tayyari, Arthur S Edison
NMR metabolomics are primarily conducted with 1D nuclear Overhauser enhancement spectroscopy (NOESY) presat for water suppression and Carr-Purcell-Meiboom-Gill (CPMG) presat as a T2 filter to remove macromolecule signals. Others pulse sequences exist for these two objectives but are not often used in metabolomics studies, because they are less robust or unknown to the NMR metabolomics community. However, recent improvements on alternative pulse sequences provide attractive alternatives to 1D NOESY presat and CPMG presat...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28647789/probing-slow-timescale-dynamics-in-proteins-using-methyl-1-h-cest
#11
Tairan Yuwen, Rui Huang, Lewis E Kay
Although (15)N- and (13)C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, (1)H CEST experiments are only beginning to emerge. We present a methyl-TROSY (1)H CEST experiment that eliminates deleterious (1)H-(1)H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for (13)CHD2 labeled proteins, is established through studies of exchanging protein systems...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28625405/metabolomic-analysis-with-1-h-nmr-for-non-invasive-diagnosis-of-hepatic-fibrosis-degree-in-patients-with-chronic-hepatitis-c
#12
Tommaso Gabbani, Maria Marsico, Patrizia Bernini, Elisabetta Lorefice, Cecilia Grappone, Maria Rosa Biagini, Stefano Milani, Vito Annese
BACKGROUND: The assessment of fibrosis degree in liver diseases is based on several non-invasive techniques, but none has been accurate. AIM: This study employed proton nuclear magnetic resonance spectroscopy to identify metabolic profiles in serum and urine, specific for different fibrosis degree in chronic hepatitis C patients. METHOD: 71 plasma, 73 serum, and 578 urine samples were collected. All samples were analyzed using (1)H-NMR spectroscopy technique and three different NMR spectra were acquired for each serum/plasma sample...
June 13, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28576318/automated-quantification-of-metabolites-in-blood-derived-samples-by-nmr
#13
Aswin Verhoeven, Eline Slagboom, Manfred Wuhrer, Martin Giera, Oleg A Mayboroda
NMR is widely applied in the field of metabolomics due to the quantitative nature of the technology and the reproducible data generated. However, because of severe spectral crowding, quantifying individual metabolites in body fluids such as serum and plasma remains a challenge. In this study, a method to automatically annotate and quantify a number of small metabolites in human serum and EDTA plasma is introduced. It combines the superior signal-to-noise ratio of the commonly applied CPMG and NOESY1D pulse sequences with the superior resolution of the 2D JRES experiment to construct a model that extracts the metabolite concentrations directly from the 1D spectra without tedious deconvolution...
July 11, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28546889/tuning-the-spin-coherence-time-of-cu-ii-bis-oxamato-and-cu-ii-bis-oxamidato-complexes-by-advanced-esr-pulse-protocols
#14
Ruslan Zaripov, Evgeniya Vavilova, Iskander Khairuzhdinov, Kev Salikhov, Violeta Voronkova, Mohammad A Abdulmalic, Francois E Meva, Saddam Weheabby, Tobias Rüffer, Bernd Büchner, Vladislav Kataev
We have investigated with the pulsed ESR technique at X- and Q-band frequencies the coherence and relaxation of Cu spins S = 1/2 in single crystals of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opba)] (1%) in the host lattice of [n-Bu4N]2[Ni(opba)] (99%, opba = o-phenylenebis(oxamato)) and of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opbon-Pr2)] (1%) in the host lattice of [n-Bu4N]2[Ni(opbon-Pr2)] (99%, opbon-Pr2 = o-phenylenebis(N(propyl)oxamidato)). For that we have measured the electron spin dephasing time Tm at different temperatures with the two-pulse primary echo and with the special Carr-Purcell-Meiboom-Gill (CPMG) multiple microwave pulse sequence...
2017: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/28495594/elevated-%C3%AE-s-ms-timescale-backbone-dynamics-in-the-transition-state-analog-form-of-arginine-kinase
#15
Omar Davulcu, Yu Peng, Rafael Brüschweiler, Jack J Skalicky, Michael S Chapman
Arginine kinase catalyzes reversible phosphoryl transfer between arginine and ATP. Crystal structures of arginine kinase in an open, substrate-free form and closed, transition state analog (TSA) complex indicate that the enzyme undergoes substantial domain and loop rearrangements required for substrate binding, catalysis, and product release. Nuclear magnetic resonance (NMR) has shown that substrate-free arginine kinase is rigid on the ps-ns timescale (average S(2)=0.84±0.08) yet quite dynamic on the µs-ms timescale (35 residues with Rex, 12%), and that movements of the N-terminal domain and the loop comprising residues I182-G209 are rate-limiting on catalysis...
May 8, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28480603/a-single-shot-t2-mapping-protocol-based-on-echo-split-gradient-spin-echo-acquisition-and-parametric-multiplexed-sensitivity-encoding-based-on-projection-onto-convex-sets-reconstruction
#16
Mei-Lan Chu, Hing-Chiu Chang, Koichi Oshio, Nan-Kuei Chen
PURPOSE: To develop a high-speed T2 mapping protocol that is capable of accurately measuring T2 relaxation time constants from a single-shot acquisition. THEORY: A new echo-split single-shot gradient-spin-echo (GRASE) pulse sequence is developed to acquire multicontrast data while suppressing signals from most nonprimary echo pathways in Carr-Purcell-Meiboom-Gill (CPMG) echoes. Residual nonprimary pathway signals are taken into consideration when performing T2 mapping using a parametric multiplexed sensitivity encoding based on projection onto convex sets (parametric-POCSMUSE) reconstruction method that incorporates extended phase graph modeling of GRASE signals...
May 7, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28396388/altering-the-allosteric-pathway-in-igps-suppresses-millisecond-motions-and-catalytic-activity
#17
George P Lisi, Kyle W East, Victor S Batista, J Patrick Loria
Imidazole glycerol phosphate synthase (IGPS) is a V-type allosteric enzyme, meaning that its catalytic rate is critically dependent on activation by its allosteric ligand, N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR). The allosteric mechanism of IGPS is reliant on millisecond conformational motions for efficient catalysis. We engineered four mutants of IGPS designed to disrupt millisecond motions and allosteric coupling to identify regions that are critical to IGPS function...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28388495/local-diffusion-and-diffusion-t2-distribution-measurements-in-porous-media
#18
S Vashaee, B Newling, B MacMillan, F Marica, M Li, B J Balcom
Slice-selective pulsed field gradient (PFG) and PFG-T2 measurements are developed to measure spatially-resolved molecular diffusion and diffusion-T2 distributions. A spatially selective adiabatic inversion pulse was employed for slice-selection. The slice-selective pulse is able to select a coarse slice, on the order of 1cm, at an arbitrary position in the sample. The new method can be employed to characterize oil-water mixtures in porous media. The new technique has an inherent sensitivity advantage over phase encoding imaging based methods due to signal being localized from a thick slice...
May 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28379688/effects-of-doxorubicin-cisplatin-and-tamoxifen-on-the-metabolic-profile-of-human-breast-cancer-mcf-7-cells-as-determined-by-1-h-high-resolution-magic-angle-spinning-nuclear-magnetic-resonance
#19
Roberta M Maria, Wanessa F Altei, Heloisa S Selistre-de-Araujo, Luiz A Colnago
Doxorubicin (Doxo), cisplatin (Cis), and tamoxifen (Tamo) are part of many chemotherapeutic regimens. However, there have been limited studies of the way metabolism in breast cancer is affected by chemotherapy. We studied, through (1)H high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, the metabolic profile of human breast cancer MCF-7 control (Con) cells as well as MCF-7 cells treated with Tamo, Cis, and Doxo. (1)H HR-MAS NMR single-pulse spectra evidenced signals from the cell compounds, including fatty acids (membranes), water-soluble proteins, and metabolites...
April 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28351813/1d-and-2d-diffusion-pore-imaging-on-a-preclinical-mr-system-using-adaptive-rephasing-feasibility-and-pulse-sequence-comparison
#20
Marco Bertleff, Sebastian Domsch, Frederik B Laun, Tristan A Kuder, Lothar R Schad
Diffusion pore imaging (DPI) has recently been proposed as a means to acquire images of the average pore shape in an image voxel or region of interest. The highly asymmetric gradient scheme of its sequence makes it substantially demanding in terms of the hardware of the NMR system. The aim of this work is to show the feasibility of DPI on a preclinical 9.4T animal scanner. Using water-filled capillaries with an inner radius of 10μm, four different variants of the DPI sequence were compared in 1D and 2D measurements...
May 2017: Journal of Magnetic Resonance
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