Browse
Submit Data
Databases
API
Help

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanostructure of Materials Determined by Relayed Paramagnetic Relaxation Enhancement.

ABSTRACT: Particle and domain sizes strongly influence the properties of materials. Here we present an NMR approach based on paramagnetic relaxation enhancement (PRE) relayed by spin diffusion (SD), which allows us to determine lengths in the nm-?m range. We demonstrate the method on multicomponent organic polymer mixtures by selectively doping one component with a paramagnetic center in order to measure the domain size in a second component. Using this approach we determine domain sizes in ethyl cellulose/hydroxypropyl cellulose film coatings in pharmaceutical controlled release formulations. Here we measure particle sizes ranging from around 50 to 200 nm.

SUBMITTER: Schlagnitweit J

PROVIDER: S-EPMC4598824 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nanostructure of Materials Determined by Relayed Paramagnetic Relaxation Enhancement.

Schlagnitweit Judith J Tang Mingxue M Baias Maria M Richardson Sara S Schantz Staffan S Emsley Lyndon L

Journal of the American Chemical Society 20150928 39

Particle and domain sizes strongly influence the properties of materials. Here we present an NMR approach based on paramagnetic relaxation enhancement (PRE) relayed by spin diffusion (SD), which allows us to determine lengths in the nm-μm range. We demonstrate the method on multicomponent organic polymer mixtures by selectively doping one component with a paramagnetic center in order to measure the domain size in a second component. Using this approach we determine domain sizes in ethyl cellulos ...[more]

PMID: 26397956

Similar Datasets

Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement.

Project description:Challenges for structural characterization of membrane-bound glycosphingolipids include their high internal dynamic motions and their physical proximity to membrane surfaces. Here we demonstrate that NMR paramagnetic relaxation enhancement can be used, alongside independent molecular dynamics simulations and an outer-sphere relaxation model, to quantitatively characterize the presentation (insertion depth and orientation relative to a membrane surface) of ganglioside GM1 in biologically relevant membrane environments. Longitudinal and transverse paramagnetic relaxation enhancement effects were measured for GM1, anchored to phospholipid bicelles, using both water-soluble and membrane-anchored paramagnetic probes, respectively. A method was developed to rapidly calculate paramagnetic relaxation enhancement effects from thousands of structures taken from a simulation of GM1 in a phospholipid bilayer. The combined computational and experimental approach yielded experimentally verified atomic-resolution 3D models of a highly plastic membrane-bound biomolecule.

| S-EPMC2824572 | biostudies-literature

Enhancement of Paramagnetic Relaxation by Photoexcited Gold Nanorods.

Project description:Electron spin resonance (ESR) spectroscopy was used to investigate the switchable, light-dependent effects of gold nanorods (GNRs) on paramagnetic properties of nitroxide spin probes. The photoexcited GNRs enhanced the spin-spin and spin-lattice relaxations of nitroxide spin probes. It was shown that molecular oxygen plays the key role in this process. Our results demonstrate that ESR is a powerful tool for investigating the events following photoexcitation of GNRs. The novel light-controlled effects observed for GNRs on paramagnetic properties and activities of surrounding molecules have a number of significant applications where oxygen sensing and oxygen activity is important.

| S-EPMC4829829 | biostudies-literature

Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement.

Project description:Transient structures in unfolded proteins are important in elucidating the molecular details of initiation of protein folding. Recently, native and non-native secondary structure have been discovered in unfolded A. vinelandii flavodoxin. These structured elements transiently interact and subsequently form the ordered core of an off-pathway folding intermediate, which is extensively formed during folding of this alpha-beta parallel protein. Here, site-directed spin-labelling and paramagnetic relaxation enhancement are used to investigate long-range interactions in unfolded apoflavodoxin. For this purpose, glutamine-48, which resides in a non-native alpha-helix of unfolded apoflavodoxin, is replaced by cysteine. This replacement enables covalent attachment of nitroxide spin-labels MTSL and CMTSL. Substitution of Gln-48 by Cys-48 destabilises native apoflavodoxin and reduces flexibility of the ordered regions in unfolded apoflavodoxin in 3.4 M: GuHCl, because of increased hydrophobic interactions in the unfolded protein. Here, we report that in the study of the conformational and dynamic properties of unfolded proteins interpretation of spin-label data can be complicated. The covalently attached spin-label to Cys-48 (or Cys-69 of wild-type apoflavodoxin) perturbs the unfolded protein, because hydrophobic interactions occur between the label and hydrophobic patches of unfolded apoflavodoxin. Concomitant hydrophobic free energy changes of the unfolded protein (and possibly of the off-pathway intermediate) reduce the stability of native spin-labelled protein against unfolding. In addition, attachment of MTSL or CMTSL to Cys-48 induces the presence of distinct states in unfolded apoflavodoxin. Despite these difficulties, the spin-label data obtained here show that non-native contacts exist between transiently ordered structured elements in unfolded apoflavodoxin.

| S-EPMC2841281 | biostudies-literature

Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE).

Project description:Characterization of the conformational ensemble of disordered proteins is highly important for understanding protein folding and aggregation mechanisms, but remains a computational and experimental challenge owing to the dynamic nature of these proteins. New observables that can provide unique insights into transient residual structures in disordered proteins are needed. Here using denatured ubiquitin as a model system, NMR solvent paramagnetic relaxation enhancement (sPRE) measurements provide an accurate and highly sensitive probe for detecting low populations of residual structure in a disordered protein. Furthermore, a new ensemble calculation approach based on sPRE restraints in conjunction with residual dipolar couplings (RDCs) and small-angle X-ray scattering (SAXS) is used to define the conformational ensemble of disordered proteins at atomic resolution. The approach presented should be applicable to a wide range of dynamic macromolecules.

| S-EPMC6396310 | biostudies-literature

(19)F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins.

Project description:Fluorine NMR paramagnetic relaxation enhancement was evaluated as a versatile approach for extracting distance information in selectively F-labeled proteins. Proof of concept and initial applications are presented for the HIV-inactivating lectin cyanovirin-N. Single F?atoms were introduced at the 4-, 5-, 6- or 7 positions of Trp49 and the 4-position of Phe4, Phe54, and Phe80. The paramagnetic nitroxide spin label was attached to Cys residues that were placed into the protein at positions 50 or 52. (19)F-T2 ?NMR spectra with different relaxation delays were recorded and the transverse (19)F-PRE rate, (19)F-?2 , was used to determine the average distance between the F nucleus and the paramagnetic center. Our data show that experimental (19)F?PRE-based distances correspond to 0.93 of the (1)HN-PRE distances, in perfect agreement with the gyromagnetic ?(19)F/?(1)H ratio, thereby demonstrating that (19)F PREs are excellent alternative parameters for quantitative distance measurements in selectively F-labeled proteins.

| S-EPMC4715678 | biostudies-literature

Quantifying Dissolved Transition Metals in Battery Electrolyte Solutions with NMR Paramagnetic Relaxation Enhancement.

Project description:Transition metal dissolution is an important contributor to capacity fade in lithium-ion cells. NMR relaxation rates are proportional to the concentration of paramagnetic species, making them suitable to quantify dissolved transition metals in battery electrolytes. In this work, 7Li, 31P, 19F, and 1H longitudinal and transverse relaxation rates were measured to study LiPF6 electrolyte solutions containing Ni2+, Mn2+, Co2+, or Cu2+ salts and Mn dissolved from LiMn2O4. Sensitivities were found to vary by nuclide and by transition metal. 19F (PF6-) and 1H (solvent) measurements were more sensitive than 7Li and 31P measurements due to the higher likelihood that the observed species are in closer proximity to the metal center. Mn2+ induced the greatest relaxation enhancement, yielding a limit of detection of ∼0.005 mM for 19F and 1H measurements. Relaxometric analysis of a sample containing Mn dissolved from LiMn2O4 at ∼20 °C showed good sensitivity and accuracy (suggesting dissolution of Mn2+), but analysis of a sample stored at 60 °C showed that the relaxometric quantification is less accurate for heat-degraded LiPF6 electrolytes. This is attributed to degradation processes causing changes to the metal solvation shell (changing the fractions of PF6-, EC, and EMC coordinated to Mn2+), such that calibration measurements performed with pristine electrolyte solutions are not applicable to degraded solutions-a potential complication for efforts to quantify metal dissolution during operando NMR studies of batteries employing widely-used LiPF6 electrolytes. Ex situ nondestructive quantification of transition metals in lithium-ion battery electrolytes is shown to be possible by NMR relaxometry; further, the method's sensitivity to the metal solvation shell also suggests potential use in assessing the coordination spheres of dissolved transition metals.

| S-EPMC10226131 | biostudies-literature

Paramagnetic relaxation enhancement-assisted structural characterization of a partially disordered conformation of ubiquitin.

Project description:Nuclear magnetic resonance (NMR) is a powerful tool to study three-dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N1 and N2 and plus another folded conformation, I, in which some amide group signals of residues 33-41 almost disappeared above 3 kbar at pH 4.5 and 273 K. Thus, well-converged structural models could not be obtained for this region owing to the absence of distance restraints. Here, we reexamine the problem using the ubiquitin Q41N variant as a model for this locally disordered conformation, I. We demonstrate that the variant shows pressure-induced loss of backbone amide group signals at residues 28, 33, 36, and 39-41 like the wild-type, with a similar but smaller effect on CαH and CβH signals. In order to characterize this I structure, we measured paramagnetic relaxation enhancement (PRE) under high pressure to obtain distance restraints, and calculated the structure assisted by Bayesian inference. We conclude that the more disordered I conformation observed at pH 4.0, 278 K, and 2.5 kbar largely retained the N2 conformation, although the amide groups at residues 33-41 have more heterogeneous conformations and more contact with water, which differ from the N1 and N2 states. The PRE-assisted strategy has the potential to improve structural characterization of proteins that lack NMR signals, especially for relatively more open and hydrated protein conformations.

| S-EPMC6798129 | biostudies-literature

Gadolinium-Based Paramagnetic Relaxation Enhancement Agent Enhances Sensitivity for NUS Multidimensional NMR-Based Metabolomics.

Project description:Gadolinium is a paramagnetic relaxation enhancement (PRE) agent that accelerates the relaxation of metabolite nuclei. In this study, we noted the ability of gadolinium to improve the sensitivity of two-dimensional, non-uniform sampled NMR spectral data collected from metabolomics samples. In time-equivalent experiments, the addition of gadolinium increased the mean signal intensity measurement and the signal-to-noise ratio for metabolite resonances in both standard and plasma samples. Gadolinium led to highly linear intensity measurements that correlated with metabolite concentrations. In the presence of gadolinium, we were able to detect a broad array of metabolites with a lower limit of detection and quantification in the low micromolar range. We also observed an increase in the repeatability of intensity measurements upon the addition of gadolinium. The results of this study suggest that the addition of a gadolinium-based PRE agent to metabolite samples can improve NMR-based metabolomics.

| S-EPMC8433644 | biostudies-literature

Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.

Project description:Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides with the protein, and the resulting sPRE manifests the relative solvent exposure of protein nuclei. To make the back-calculated sPRE values most consistent with the observed values, the protein structure is either refined against the sPRE, or an ensemble of conformers is selected from a pre-generated library using a Monte Carlo algorithm. The ensemble structure comprises either N conformers of equal occupancy, or two conformers with different relative populations. We demonstrate the sPRE method using GB1, a structurally rigid protein, and calmodulin, a protein comprising two domains and existing in open and closed states. The sPRE can be computed with a stand-alone program for rapid evaluation, or with the invocation of a module in the latest release of the structure calculation software Xplor-NIH. As a label-free method, the sPRE measurement can be readily integrated with other biophysical techniques. The current limitations of the sPRE method are also discussed, regarding accurate measurement and theoretical calculation, model selection and suitable timescale.

| S-EPMC6133729 | biostudies-literature

Paramagnetic relaxation enhancement NMR as a tool to probe guest binding and exchange in metallohosts.

Project description:Paramagnetic metallohost systems can bind guest molecules and find application as biomimetic catalysts. Due to the presence of the paramagnetic metal center, rigorous characterization of these systems by NMR spectroscopy can be very difficult. We report here that metallohost-guest systems can be studied by using the paramagnetic relaxation enhancement (PRE) effect. Manganese(III) porphyrin cage compounds are shown through their PRE to thread and bind viologen guests, including a polymeric one. The binding constants and dethreading activation parameters are lower than those of the metal-free porphyrin cage compounds, which is proposed to be a result of charge repulsion of the trivalent metal center and dicationic viologen guest. The threading rate of the manganese(III) porphyrin cage onto the polymer is more than 10 times faster than that of the non-metallated one, which is ascribed to initial binding of the cage to the polymer chain prior to threading, and to an entron effect.

| S-EPMC8986849 | 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