cpmg

Nuclear magnetic resonance (NMR) spectroscopy is the method of choice for studying the dynamics of biological macromolecules in solution. By exploiting the intricate interplay between the effects of protein motion (both overall rotational diffusion and internal mobility) and nuclear spin relaxation, NMR allows molecular motion to be probed at atomic resolution over a wide range of timescales, including picosecond (bond vibrations and methyl-group rotations), nanosecond (loop motions and rotational diffusion), and microsecond-millisecond (ligand binding, allostery)...

Efficient acquisition of wideline solid-state nuclear magnetic resonance (NMR) spectra with patterns affected by large inhomogeneous broadening is accomplished with the use of broadband pulse sequences. These specialized pulse sequences often use frequency-swept pulses, which feature time-dependent phase and amplitude modulations that in turn deliver broad and uniform excitation across large spectral bandwidths. However, the resulting NMR spectra are often affected by complex frequency-dependent phase dispersions, owing to the interplay between the frequency-swept excitations and anisotropic resonance frequencies...

14-3-3σ plays an important role in controlling tumor metabolic reprogramming and cancer cell growth. However, its function is often compromised in many cancers due to its downregulation. Previous studies found that homodimerization of 14-3-3σ is critical for its activity. However, to date, it is not known if stabilization of 14-3-3σ homodimers can improve its activity or prevent its degradation. In our previous work, we have showed that GCP-Lys-OMe is a potential 14-3-3σ homodimer stabilizer...

The purpose of the current study was to develop a novel single-voxel MR spectroscopy acquisition scheme to simultaneously determine metabolite-specific concentrations and transverse relaxation times within realistic clinical scan times. Partly truncated multi-TE data are acquired as an echo train in a single acquisition (multi-echo single-shot [MESS]). A 2D multiparametric model fitting approach combines truncated, low-resolved short TE data with fully sampled, highly resolved, longer TE data to yield concentration and T2 estimates for major brain metabolites simultaneously...

The promyelocytic leukemia protein, PML, plays a vital role in the cellular response to oxidative stress; however, the molecular mechanism of its action remains poorly understood. Here, we identify redox-sensitive sites of PML. A molecule of PML is cysteine-rich and contains three zinc-binding domains including RING, B-box1, and B-box2. Using in vitro assays, we have compared the sensitivity of the isolated RING and B-box1 domains and shown that B-box1 is more sensitive to oxidation. NMR studies of PML dynamics showed that one of the Zn-coordination sites within the B-box1 undergoes significant conformational exchange, revealing a hotspot for exposure of reactive cysteines...

O-GlcNAcylation is a specific type of post-translational glycosylation modification, which is regulated by two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). Aberrant overexpression of OGT is associated with the development of many solid tumors. In this study, we have developed and optimized a sensitive Homogeneous Time-Resolved Fluorescence (HTRF) assay then identified a novel OGT inhibitor CDDO (also called Bardoxolone) through a high-throughput screening (HTS) based on HTRF assay. Further characterization suggested that CDDO is an effective OGT inhibitor with an IC50 value of 6...

NMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) 1 H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T 2 filter to suppress macromolecule signals and reduce the humped curve in the spectrum...

In this study, an optimized unilateral magnetic resonance sensor with a three-magnet array is presented for assessing the aging of composite insulators in power grids. The sensor's optimization involved enhancing the static magnetic field strength and the homogeneity of the RF field while maintaining a constant gradient in the direction of the vertical sensor surface and maximizing homogeneity in the horizontal direction. The center layer of the target area was positioned 4 mm from the coil's upper surface, resulting in a magnetic field strength of 139...

In this paper, we present a portable NMR relaxometry system optimized for the point-of-care analysis of body liquids such as blood. The presented system is centered on an NMR-on-a-chip transceiver ASIC, a reference frequency generator with arbitrary phase control, and a custom-designed miniaturized NMR magnet with a field strength of 0.29 T and a total weight of 330 g. The NMR-ASIC co-integrates a low-IF receiver, a power amplifier, and a PLL-based frequency synthesizer on a total chip area of 1100 [Formula: see text] 900  μ m[Formula: see text]...

Introduction: There is evidence that sample treatment of blood-based biosamples may affect integral signals in nuclear magnetic resonance-based metabolomics. The presence of macromolecules in plasma/serum samples makes investigating low-molecular-weight metabolites challenging. It is particularly relevant in the targeted approach, in which absolute concentrations of selected metabolites are often quantified based on the area of integral signals. Since there are a few treatments of plasma/serum samples for quantitative analysis without a universally accepted method, this topic remains of interest for future research...

Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations...

The relaxation dispersion (rd) of nuclear magnetic resonance provides thermodynamic and kinetic information regarding molecules for which the conformations are exchanging in equilibrium. Experiments have often been implemented with Carr-Purcell-Meiboom-Gill (CPMG) pulse sequences for heteronuclear S-spin in SI and SI3 spin systems. One of the most common CPMG sequences contains a sequence called a P-element in the middle to average the different relaxation rates of anti-phase and in-phase coherences; however, its drawback is that the artifacts that can be compensated for are only those in one of the two S-spin doublet magnetization components, for example, SIα or SIβ in an SI spin system...

'Tonda Gentile Romana' and 'Tonda di Giffoni' ( Corylus avellana L.) are two Italian hazelnut cultivars, recognized under the quality labels "Protected Designation of Origin" (PDO) and "Protected Geographical Indication" (PGI), respectively. Hazelnut seeds are characterized by a complex microstructure and the presence of different physical compartments. This peculiarity has been studied and evidenced by Time Domain (TD) Nuclear Magnetic Resonance (NMR) experiments. This technique allowed the assessment of the presence of different diffusion compartments, or domains, by evaluating the distribution of the spin-spin relaxation time (T2 )...

Caseous lymphadenitis (CLA), an infectious disease caused by Corynebacterium pseudotuberculosis in small ruminants, is highly prevalent worldwide. Economic losses have already been associated with the disease, and little is known about the host-pathogen relationship associated with the disease. The present study aimed to perform a metabolomic study of the C. pseudotuberculosis infection in goats. Serum samples were collected from a herd of 173 goats. The animals were classified as controls (not infected), asymptomatic (seropositives but without detectable CLA clinical signs), and symptomatic (seropositive animals presenting CLA lesions), according to microbiological isolation and immunodiagnosis...

Methods of multi-pulse sequences are widely used in magnetic resonance to study the local properties of magnetic particles and to increase the lifetime of spin coherence. Imperfect refocusing pulses lead to non-exponential signal decay due to the contribution of the coherence pathways in which T1 and T2 relaxation segments are mixed. Here, we present analytical approximations for echoes generated in the Carr-Purcell-Meiboom-Gill (CPMG) sequence. They provide simple expressions for the leading terms of the echo train decay and allow the relaxation times to be estimated for sequences with a relatively small number of pulses...

A methyl Transverse Relaxation Optimized Spectroscopy (methyl-TROSY) based, multiple quantum (MQ) 13 C Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiment is described. The experiment is derived from the previously developed MQ 13 C-1 H CPMG scheme (Korzhnev in J Am Chem Soc 126: 3964-73, 2004) supplemented with a CPMG train of refocusing 1 H pulses applied with constant frequency and synchronized with the 13 C CPMG pulse train. The optimal 1 H 'decoupling' scheme that minimizes the amount of fast-relaxing methyl MQ magnetization present during CPMG intervals, makes use of an XY-4 phase cycling of the refocusing composite 1 H pulses...

As global environmental sustainability becomes increasingly emphasized, the development of eco-friendly materials, including solutions to the issue of marine plastics, is thriving. However, the material parameter space is vast, making efficient search a challenge. Time-domain nuclear magnetic resonance offers material property information through the complex T2 relaxation curves resulting from multiple mobilities. In this research, we used the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence to evaluate the binding state of water (water affinity) in polymers synthesized with various monomer compositions, which were immersed in seawater...

Photo-excited triplet states represent a new class of spin labels in pulse electron paramagnetic resonance (EPR), attracting increasing attention because of their unique spectroscopic properties. Despite certain advantages, the use of photo-labels has also some challenges, e.g. low repetition rates due to technical laser-related limitations and intrinsic properties of the labels. The application of additional pulse trains for multiple refocusing of the electron spin echo and integration of all observed echoes can significantly enhance sensitivity at a given repetition rate...

Primary Sjögren's Syndrome (pSS) is a multi-system autoimmune disease that involves the exocrine glands. Lymphocytes infiltrate the gland tissue, leading to anatomical modification and hypofunction. Even if the prognosis of pSS is favorable, quality of life is typically reduced due to the diverse manifestations of the disease. The aim of this study is to compare the salivary metabolomes of pSS with healthy controls (HCs). Seven cases were selected from a cohort of pSS patients, and six age- and sex-matched HCs were recruited from a cohort of volunteers...

Post-translationally modified (PTM) amyloid-β (Aβ) species can play an important role in modulating Alzheimer's disease pathology. These relatively less populated modifications can cross-seed the wild-type Aβ peptides to produce fibrils that retain many structural and functional features of the original PTM variants. We focus on studies of internal flexibility in the cross-seeded Aβ1-40 fibrils originating from seeding with two PTM variants with modifications in the disordered N-terminal domain: Δ E 3 truncation and S8-phosphorylation...