Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simple high-resolution NMR spectroscopy as a tool in molecular biology.

ABSTRACT: NMR is one of the major techniques for investigating the structure, dynamics and interactions between biomolecules. However, non-experts often experience NMR experimentation and data analysis as intimidating. We discuss a simple yet powerful NMR technique, the so-called chemical shift perturbation (CSP) analysis, as a tool to elucidate macromolecular interactions in small- and medium-sized complexes, including protein-protein, protein-drug, and protein-DNA/RNA interactions. We discuss current software packages for NMR data analysis and present a new interactive graphical tool implemented in CcpNmr AnalysisAssign version-3, which can drastically reduce the time required for the CSP analysis. Lastly, we illustrate the usefulness of a protein three-dimensional structure for interpretation of the CSP data.

SUBMITTER: Mureddu L

PROVIDER: S-EPMC6563160 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

High Resolution NMR Spectroscopy as a Structural and Analytical Tool for Unsaturated Lipids in Solution.

Project description:Mono- and polyunsaturated lipids are widely distributed in Nature, and are structurally and functionally a diverse class of molecules with a variety of physicochemical, biological, medicinal and nutritional properties. High resolution NMR spectroscopic techniques including 1H-, 13C- and 31P-NMR have been successfully employed as a structural and analytical tool for unsaturated lipids. The objective of this review article is to provide: (i) an overview of the critical 1H-, 13C- and 31P-NMR parameters for structural and analytical investigations; (ii) an overview of various 1D and 2D NMR techniques that have been used for resonance assignments; (iii) selected analytical and structural studies with emphasis in the identification of major and minor unsaturated fatty acids in complex lipid extracts without the need for the isolation of the individual components; (iv) selected investigations of oxidation products of lipids; (v) applications in the emerging field of lipidomics; (vi) studies of protein-lipid interactions at a molecular level; (vii) practical considerations and (viii) an overview of future developments in the field.

| S-EPMC6151582 | biostudies-literature

High-Resolution 17O NMR Spectroscopy of Structural Water.

Project description:The importance of studying site-specific interactions of structurally similar water molecules in complex systems is well known. We demonstrate the ability to resolve four distinct bound water environments within the crystal structure of lanthanum magnesium nitrate hydrate via 17O solid state nuclear magnetic resonance (NMR) spectroscopy. Using high-resolution multidimensional experiments at high magnetic fields (18.8-35.2 T), each individual water environment was resolved. The quadrupole coupling constants and asymmetry parameters of the 17O of each water were determined to be between 6.6 and 7.1 MHz, 0.83 and 0.90, respectively. The resolution of the four unique, yet similar, structural waters within a hydrated crystal via 17O NMR spectroscopy demonstrates the ability to decipher the unique electronic environment of structural water within a single hydrated crystal structure.

| S-EPMC6689193 | biostudies-literature

Ultrahigh-resolution NMR spectroscopy.

Project description: Not available

| S-EPMC4320760 | biostudies-literature

High-resolution NMR spectroscopy of a GPCR in aligned bicelles.

Project description:Solid-state NMR spectra with single-site resolution of CXCR1, a G protein-coupled receptor (GPCR), were obtained in magnetically aligned phospholipid bicelles. These results demonstrate that GPCRs in phospholipid bilayers are suitable samples for structure determination by solid-state NMR. The spectra also enable studies of drug-receptor interactions.

| S-EPMC3236030 | biostudies-literature

Looking at microbial metabolism by high-resolution (2)H-NMR spectroscopy.

Project description:We analyzed the applicability of high-resolution (2)H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.

| S-EPMC3709107 | biostudies-literature

Analysis and Authentication of Avocado Oil Using High Resolution NMR Spectroscopy.

Project description:Avocado oil is a food product of high commercial and nutritional value. As a result, it can be a subject of adulteration similar to other high-value edible oils, such as olive oil. For olive oil and many other foods products, NMR spectroscopy has been successfully used for authentication and quality assessment. In this study, we apply NMR analysis to avocado oil to differentiate it from other oils including olive, canola, high-oleic (HO) safflower, HO sunflower and soybean oil using commercial and lab-made samples of avocado oils. NMR allowed the rapid analysis of the fatty acid profile and detection of minor compounds, such as sterols, oxidation products, and hydrolysis products, which can be used to assess oil quality and authenticity. The NMR assignment was conducted using traditional 2D NMR and the novel NOAH super-sequences. Combining chemometrics with NMR enabled us to differentiate between avocado oil and other oils. Avocado oil has compositional similarities with other vegetable oils, such as HO sunflower and HO safflower oil, which can be used as potential adulterants. Despite these similarities, NMR-based metabolomics captured differences in the levels of certain compounds including fatty acids, terpenes, sterols, and oxidation products to detect adulteration and for quality control purposes.

| S-EPMC7828049 | biostudies-literature

High-resolution magic angle spinning NMR spectroscopy of human osteoarthritic cartilage.

Project description:Osteoarthritis (OA) is a degenerative disease of the joints and results in changes in the biochemical composition of cartilage. Previous studies have been undertaken that have used high-resolution NMR spectroscopy to study the biochemical composition of porcine, canine and bovine cartilage. In the present study, high-resolution magical angle spinning (HR-MAS) NMR spectroscopy at 11.7 T has been used to characterize metabolites and detect differences in the spectral signature of human knee articular cartilage from non-OA healthy cadaver knees and samples acquired from severe OA patients at the time of total knee replacement surgery. A statistically significant difference in the alanine (1.47 p.p.m.), N-acetyl (2.04 p.p.m.), choline (3.25 p.p.m.) and glycine (3.55 p.p.m.) metabolite levels was observed between healthy and OA specimens. The results of the present study indicate that a decrease in the intensity of N-acetyl resonance occurs in the later stages of OA. A positive correlation of the N-acetyl levels as measured by (1)H HR-MAS NMR spectroscopy with the total proteoglycan content in the same cartilage specimens as measured by the glycosaminoglycan (GAG) assay was observed. This indicates that N-acetyl can serve as an important bio-marker of OA disease progression. A decrease in the alanine concentration in OA may be attributed to the degradation of the collagen framework with disease progression and eventual loss of the degradation products that are transported from cartilage into the synovial cavity.

| S-EPMC3299852 | biostudies-other

High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy.

Project description:Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible spongiform encephalopathies. Despite the immense medical importance of amyloid fibrils, no atomic-resolution structures are available for these materials, because the intact fibrils are insoluble and do not form diffraction-quality 3D crystals. Here we report the high-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105-115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves not only the backbone fold but also the precise conformation of the side chains. Nearly complete (13)C and (15)N resonance assignments for TTR(105-115) formed the basis for the extraction of a set of distance and dihedral angle restraints. A total of 76 self-consistent experimental measurements, including 41 restraints on 19 backbone dihedral angles and 35 (13)C-(15)N distances between 3 and 6 A were obtained from 2D and 3D NMR spectra recorded on three fibril samples uniformly (13)C, (15)N-labeled in consecutive stretches of four amino acids and used to calculate an ensemble of peptide structures. Our results indicate that TTR(105-115) adopts an extended beta-strand conformation in the amyloid fibrils such that both the main- and side-chain torsion angles are close to their optimal values. Moreover, the structure of this peptide in the fibrillar form has a degree of long-range order that is generally associated only with crystalline materials. These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly.

| S-EPMC321745 | biostudies-literature

High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids.

Project description:High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (<25kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the 'slow tumbling problem' can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics.

| S-EPMC4127067 | biostudies-literature

Mapping oxygen accessibility to ribonuclease a using high-resolution NMR relaxation spectroscopy.

Project description:Paramagnetic contributions to nuclear magnetic spin-lattice relaxation rate constant induced by freely diffusing molecular oxygen measured at hundreds of different protein proton sites provide a direct means for characterizing the exploration of the protein by oxygen. This report focuses on regions of ribonuclease A where the rate constant enhancements are either quite large or quite small. We find that there are several regions of enhanced oxygen affinity for the protein both on the surface and in interior pockets where sufficient free volume permits. Oxygen has weak associative interactions with a number of surface crevices that are generally between secondary structural elements of the protein fold. Several regions near the surface have higher than expected accessibility to oxygen indicating that structural fluctuations in the protein provide intermolecular access. Oxygen penetrates part of the hydrophobic interior, but affinity does not correlate simply with hydrophobicity indices. Oxygen is excluded from regions of high interior packing density and a few surface sites where x-ray diffraction data have indicated the presence of specific hydration with high occupancy.

| S-EPMC1304007 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data