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https://www.readbyqxmd.com/read/29564579/measuring-the-signs-of-the-methyl-1-h-chemical-shift-differences-between-major-and-invisible-minor-protein-conformational-states-using-methyl-1-h-multi-quantum-spectroscopy
#1
Anusha B Gopalan, Pramodh Vallurupalli
Carr-Purcell-Meiboom-Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and 'invisible' minor states. The exchange rate(s) ([Formula: see text]), population(s) of the minor state(s) and the absolute value of the chemical shift difference [Formula: see text] (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of [Formula: see text] that is required to reconstruct the spectrum of the 'invisible' minor state(s) cannot be obtained from CPMG data alone...
March 21, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29498093/phase-encoded-xspen-a-novel-high-resolution-volumetric-alternative-to-rare-mri
#2
Zhiyong Zhang, Michael Lustig, Lucio Frydman
PURPOSE: To develop a rapid, non-CPMG high-resolution volumetric imaging approach, exhibiting a speed and in-plane resilience to field inhomogeneities comparable to RARE/turbo-spin-echo (TSE) while endowed with unique downsampling characteristics. METHODS: A multi-scan extension of cross-term spatiotemporal encoding (xSPEN) is introduced and analyzed. The method simultaneously yields ky /kz data containing low and high frequency components, as well as transposed, low-resolution z/y images...
March 1, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29480470/applications-of-nmr-and-itc-for-the-study-of-the-kinetics-of-carbohydrate-binding-by-ampk-%C3%AE-subunit-carbohydrate-binding-modules
#3
Paul R Gooley, Ann Koay, Jesse I Mobbs
Understanding the kinetics of proteins interacting with their ligands is important for characterizing molecular mechanism. However, it can be difficult to determine the extent and nature of these interactions for weakly formed protein-ligand complexes that have lifetimes of micro- to milliseconds. Nuclear magnetic resonance (NMR) spectroscopy is a powerful solution-based method for the atomic-level analysis of molecular interactions on a wide range of timescales, including micro- to milliseconds. Recently the combination of thermodynamic experiments using isothermal titration calorimetry (ITC) with kinetic measurements using ZZ-exchange and CPMG relaxation dispersion NMR spectroscopy have been used to determine the kinetics of weakly interacting protein systems...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29471276/optimized-phases-for-the-acquisition-of-j-spectra-in-coupled-spin-systems-for-thermally-and-phip-polarized-molecules
#4
S Bussandri, I Prina, R H Acosta, L Buljubasich
We demonstrate that the relative phases in the refocusing pulses of multipulse sequences can compensate for pulse errors and off-resonant effects, which are commonly encountered in J-spectroscopy when CPMG is used for acquisition. The use of supercycles has been considered many times in the past, but always from the view point of time-domain NMR, that is, in an effort to lengthen the decay of the magnetization. Here we use simple spin-coupled systems, in which the quantum evolution of the system can be simulated and contrasted to experimental results...
January 31, 2018: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29468164/glutamine-hydrolysis-by-imidazole-glycerol-phosphate-synthase-displays-temperature-dependent-allosteric-activation
#5
George P Lisi, Allen A Currier, J Patrick Loria
The enzyme imidazole glycerol phosphate synthase (IGPS) is a model for studies of long-range allosteric regulation in enzymes. Binding of the allosteric effector ligand N'-[5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) stimulates millisecond (ms) timescale motions in IGPS that enhance its catalytic function. We studied the effect of temperature on these critical conformational motions and the catalytic mechanism of IGPS from the hyperthermophile Thermatoga maritima in an effort to understand temperature-dependent allostery...
2018: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29412477/residue-and-site-specific-labeling-of-ccr5-rna-pseudoknot-reveals-internal-motions-that-correlate-with-microrna-binding
#6
Bin Chen, Andrew P Longhini, Felix Nußbaumer, Christoph Kreutz, Jonathan Dinman, T Kwaku Dayie
Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNAs' dynamic behaviour shed important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution NMR are difficult for large RNAs (>70 nt) due to severe spectral overlap, homonuclear 13C scalar couplings, and line-broadening. In this work, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites and enzymatic ligation is introduced...
February 7, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29386458/quantitative-t2-mapping-of-knee-cartilage-comparison-between-the-synthetic-mr-imaging-and-the-cpmg-sequence
#7
Seung Hyun Lee, Young Han Lee, Ho-Taek Song, Jin-Suck Suh
The purpose was to evaluate the feasibility of quantitative MRI T2 mapping based on the quantitative MRI (QRAPMASTER) sequence for the quantitative assessment of knee cartilage. The T2 values from the phantom study showed excellent correlation between the two techniques (r2 = 0.998). The cartilage T2 values exhibited strong correlations (r2 = 0.867-0.982). Quantitative MRI (qMRI) T2 mapping can be used as an alternative to multi-echo T2 mapping, with relatively short scan time.
February 1, 2018: Magnetic Resonance in Medical Sciences: MRMS
https://www.readbyqxmd.com/read/29335164/local-t-1-t-2-distribution-measurements-in-porous-media
#8
S Vashaee, M Li, B Newling, B MacMillan, F Marica, H T Kwak, J Gao, A M Al-Harbi, B J Balcom
A novel slice-selective T1 -T2 measurement is proposed to measure spatially resolved T1 -T2 distributions. An adiabatic inversion pulse is employed for slice-selection. The slice-selective pulse is able to select a quasi-rectangular slice, on the order of 1 mm, at an arbitrary position within the sample.The method does not employ conventional selective excitation in which selective excitation is often accomplished by rotation of the longitudinal magnetization in the slice of interest into the transverse plane, but rather a subtraction based on CPMG data acquired with and without adiabatic inversion slice selection...
February 2018: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29323890/high-resolution-magic-angle-spinning-nmr-and-magnetic-resonance-imaging-spectroscopies-distinguish-metabolome-and-structural-properties-of-maize-seeds-from-plants-treated-with-different-fertilizers-and-arbuscular-mycorrhizal-fungi
#9
Pierluigi Mazzei, Vincenza Cozzolino, Alessandro Piccolo
Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI...
March 21, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29276882/deciphering-the-dynamic-interaction-profile-of-an-intrinsically-disordered-protein-by-nmr-exchange-spectroscopy
#10
Elise Delaforge, Jaka Kragelj, Laura Tengo, Andrés Palencia, Sigrid Milles, Guillaume Bouvignies, Nicola Salvi, Martin Blackledge, Malene Ringkjøbing Jensen
Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state...
January 24, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29240977/broadband-homonuclear-decoupled-hsqmbc-methods
#11
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
#12
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
#13
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...
January 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29151212/cpmg-experiments-for-protein-minor-conformer-structure-determination
#14
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
#15
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
#16
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-4Ca2+ ) 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...
November 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
#17
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
#18
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
#19
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
#20
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
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