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Durgesh Dubey, Smriti Chaurasia, Anupam Guleria, Sandeep Kumar, Dinesh Raj Modi, Ramnath Misra, Dinesh Kumar
Currently, there are no reliable clinical biomarkers available that can aid early differential diagnosis of reactive arthritis (ReA) from other inflammatory joint diseases. Metabolic profiling of synovial fluid (SF) -obtained from joints affected in ReA- holds great promise in this regard and will further aid monitoring treatment and improving our understanding about disease mechanism. As a first step in this direction, we report here the metabolite specific assignment of 1 H and 13 C resonances detected in the NMR spectra of SF samples extracted from human patients with established ReA...
June 15, 2018: Magnetic Resonance in Chemistry: MRC
Xiaogang Niu, Jienv Ding, Wenbo Zhang, Qianwen Li, Yunfei Hu, Changwen Jin
Proteins are intrinsically dynamic molecules and undergo exchanges among multiple conformations to perform biological functions. The CPMG relaxation dispersion and CEST experiments are two important solution NMR techniques for characterizing the conformational exchange processes on the millisecond timescale. Traditional pseudo 3D 15 N CEST and CPMG experiments have certain limitations in their applications. For example, both experiments have low sensitivity for broadened resonances, and the process of optimizing sample conditions and experimental parameters are often time consuming...
June 1, 2018: Journal of Magnetic Resonance
Yury G Kolyagin, Alexander Vyacheslavovich Yakimov, Søren Tolborg, Peter N R Vennestrøm, Irina I Ivanova
The direct and quantitative identification of active sites is crucial for the development of zeolite catalysts and their implementation in industry. Herein we report on the application of 1D 119Sn DP-CPMG, REDOR-CPMG and 2D 119Sn MAT-CPMG MAS NMR spectroscopy for the identification of different Sn-sites in fully dehydrated Sn-BEA zeolite. It is demonstrated that 119Sn MAS NMR techniques allows to resolve 3 groups of NMR signals which can be attributed to three groups of nonequivalent T-sites: I - T9, T4 and T3; II - T2, T1 and T8; III - T7, T5 and T6 based on the existing theoretical predictions...
June 6, 2018: Journal of Physical Chemistry Letters
Soumya Deep Chatterjee, Marcellus Ubbink, Hugo van Ingen
Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments are a powerful tool to investigate protein dynamics on a millisecond time scale...
June 2, 2018: Journal of Biomolecular NMR
Regan M LeBlanc, Andrew P Longhini, Vitali Tugarinov, T Kwaku Dayie
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are invaluable for probing sparsely and transiently populated biomolecular states that cannot be directly detected by traditional NMR experiments and that are invisible by other biophysical approaches. A notable gap for RNA is the absence of CPMG experiments for measurement of methine base 1 H and methylene C5' chemical shifts of ribose moieties in the excited state, partly because of complications from homonuclear 13 C-13 C scalar couplings...
June 1, 2018: Journal of Biomolecular NMR
Dan Nguyen, Junji Iwahara
NMR relaxation of arginine (Arg) 15 Nε nuclei is useful for studying side-chain dynamics of proteins. In this work, we studied the impact of two geminal 15 N-15 N scalar couplings on measurements of transverse relaxation rates (R 2 ) for Arg side-chain 15 Nε nuclei. For 12 Arg side chains of the DNA-binding domain of the Antp protein, we measured the geminal 15 N-15 N couplings ( 2 J NN ) of the 15 Nε nuclei and found that the magnitudes of the 2 J NN coupling constants were virtually uniform with an average of 1...
May 29, 2018: Journal of Biomolecular NMR
Abdullah Karaer, Gorkem Tuncay, Akın Mumcu, Berat Dogan
The purpose of this study was to investigate whether a change in the follicular fluid metabolomics profile due to endometrioma is identifiable. Twelve women with ovarian endometriosis (aged<40 years, with a body mass index [BMI] of <30 kg/m2 ) and 12 age- and BMI-matched controls (women with infertility purely due to a male factor) underwent ovarian stimulation for intracytoplasmic sperm injection (ICSI). Follicular fluid samples were collected from both of groups at the time of oocyte retrieval for ICSI...
May 28, 2018: Systems Biology in Reproductive Medicine
Elisabeth Strebitzer, Felix Nußbaumer, Johannes Kremser, Martin Tollinger, Christoph Kreutz
Using chemical synthesis and solution NMR spectroscopy, RNA structural ensembles including a major ground state and minor populated excited states can be studied at atomic resolution. In this work, atom-specific 13 C labeled RNA building blocks - a 5-13 C-uridine and a 2,8-13 C2 -adenosine building block - are used to introduce isolated 13 C-1 H-spin topologies into a target RNA to probe such structural ensembles via NMR spectroscopy. First, the 5-13 C-uridine 2'-O-TBDMS-phosphoramidite building block was introduced into a 21 nucleotide (nt) tP5c stem construct of the tP5abc subdomain of the Tetrahymena group I ribozyme...
May 10, 2018: Methods: a Companion to Methods in Enzymology
Eva Baranovicova, Marian Grendar, Dagmar Kalenska, Anna Tomascova, Daniel Cierny, Jan Lehotsky
Cardiac arrest is one of the leading causes of death among adults in older age. Understanding mechanisms how organism responds to ischemia at global level is essential for the prevention and ischemic patient's treatment. In this study, we used a global cerebral ischemia induced by four-vessel occlusion as an established animal model for ischemic stroke to investigate metabolic changes after 24 h reperfusion, when transitions occur due to the onset of delayed neuronal death. We also focused on the endogenous phenomenon known as ischemic tolerance by the pre-ischemic treatment...
May 11, 2018: Journal of Physiology and Biochemistry
Ronald Mooiweer, Alessandro Sbrizzi, Alexander J E Raaijmakers, Cornelis A T van den Berg, Peter R Luijten, Hans Hoogduin
A method is described to design parallel transmit (PTX) excitation pulses that are compatible with turbo spin echo (TSE) sequences, based on information available from conventional per-channel B1 + mapping. The excitation phase of PTX pulses that generate a reduced field of excitation (rFOX) is matched to the phase the quadrature mode of a PTX coil. This enables TSE imaging of a PTX-enabled rFOX excitation combined with standard nonselective refocusing pulses transmitted in the quadrature mode. In-vivo imaging experiments were performed at 7T using a dual channel parallel transmit head coil...
May 7, 2018: Magnetic Resonance Imaging
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 2018: Journal of Biomolecular NMR
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
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
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...
April 2018: Journal of Magnetic Resonance
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
Bin Chen, Andrew P Longhini, Felix Nußbaumer, Christoph Kreutz, Jonathan D Dinman, T Kwaku Dayie
Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced...
April 11, 2018: Chemistry: a European Journal
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
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
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
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
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