Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Broadband Tunable Electron Paramagnetic Resonance Spectroscopy of Dilute Metal Complexes.

ABSTRACT: Analysis of the electron paramagnetic resonance (EPR) of transition ion complexes requires data taken at different microwave frequencies because the spin Hamiltonian contains operators linear in the frequency as well as operators independent of the frequency. In practice, data collection is hampered by the fact that conventional EPR spectrometers have always been designed to operate at a single frequency. Here, a broadband instrument is described and tested that operates from 0.5 to 12 GHz and whose sensitivity approaches that of single-frequency spectrometers. Multifrequency EPR from triclinic substitutional (0.5%) Cu(II) in ZnSO4 is globally analyzed to illustrate a novel approach to reliable determination of the molecular electronic structure of transition ion complexes from field-frequency 2D data sets.

SUBMITTER: Hagen WR

PROVIDER: S-EPMC6750836 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Broadband Tunable Electron Paramagnetic Resonance Spectroscopy of Dilute Metal Complexes.

Hagen Wilfred R WR

The journal of physical chemistry. A 20190801 32

Analysis of the electron paramagnetic resonance (EPR) of transition ion complexes requires data taken at different microwave frequencies because the spin Hamiltonian contains operators linear in the frequency as well as operators independent of the frequency. In practice, data collection is hampered by the fact that conventional EPR spectrometers have always been designed to operate at a single frequency. Here, a broadband instrument is described and tested that operates from 0.5 to 12 GHz and w ...[more]

PMID: 31319028

Similar Datasets

Very Low-Frequency Broadband Electron Paramagnetic Resonance Spectroscopy of Metalloproteins.

Project description:A previously developed spectrometer for broadband electron paramagnetic resonance (EPR) spectroscopy of dilute randomly oriented systems has been considerably modified to extend the frequency reach down to the hundred MHz range and to boost concentration sensitivity by 1 to 2 orders of magnitude. The instrument is now suitable for the study of biological systems in particular metalloproteins. As a proof of concept, examples from the class of low-spin ferric hemoproteins are studied in terms of frequency-dependent changes in their EPR spectra. Mono-heme cytochrome c EPR is determined by g-strain over a wide frequency range, whereas a combination of unresolved ligand hyperfine interaction and concentration-dependent intermolecular dipolar interaction becomes dominant at very low frequencies. In the four heme containing cytochrome c3, g-strain combines with intramolecular dipolar interaction over the full-studied frequency range of 0.23-12.0 GHz. It is concluded that the point-dipole approach is inappropriate to describe magnetic interactions between low-spin ferric heme systems and that a body of literature on redox interactions in multi-heme proteins will be affected by this conclusion.

| S-EPMC8154605 | biostudies-literature

Electron paramagnetic resonance spectroscopy of nitroxide-labeled calmodulin.

Project description:Calmodulin (CaM) is a highly conserved calcium-binding protein consisting of two homologous domains, each of which contains two EF-hands, that is known to bind well over 300 proteins and peptides. In most cases the (Ca(2+))(4-)form of CaM leads to the activation of a key regulatory enzyme or protein in a myriad of biological processes. Using the nitroxide spin-labeling reagent, 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyl oxyl, bovine brain CaM was modified at 2-3 methionines with retention of activity as judged by the activation of cyclic nucleotide phosphodiesterase. X-band electron paramagnetic resonance (EPR) spectroscopy was used to measure the spectral changes upon addition of Ca(2+) to the apo-form of spin-labeled protein. A significant loss of spectral intensity, arising primarily from reductions in the heights of the low, intermediate, and high field peaks, accompanied Ca(2+) binding. The midpoint of the Ca(2+)-mediated transition determined by EPR occurred at a higher Ca(2+) concentration than that measured with circular dichroic spectroscopy and enzyme activation. Recent data have indicated that the transition from the apo-state of CaM to the fully saturated form, [(Ca(2+))(4-)CaM], contains a compact intermediate corresponding to [(Ca(2+))(2-)CaM], and the present results suggest that the spin probes are reporting on Ca(2+) binding to the last two sites in the N-terminal domain, i.e. for the [(Ca(2+))(2)-CaM] ? [(Ca(2+))(4-)CaM] transition in which the compact structure becomes more extended. EPR of CaM, spin-labeled at methionines, offers a different approach for studying Ca(2+)-mediated conformational changes and may emerge as a useful technique for monitoring interactions with target proteins.

| S-EPMC4096354 | biostudies-literature

Spin hamiltonian parameters for Cu(II)-prion peptide complexes from L-band electron paramagnetic resonance spectroscopy.

Project description:Cu(II) is an essential element for life but is also associated with numerous and serious medical conditions, particularly neurodegeneration. Structural modeling of crystallization-resistant biological Cu(II) species relies on detailed spectroscopic analysis. Electron paramagnetic resonance (EPR) can, in principle, provide spin hamiltonian parameters that contain information on the geometry and ligand atom complement of Cu(II). Unfortunately, EPR spectra of Cu(II) recorded at the traditional X-band frequency are complicated by (i) strains in the region of the spectrum corresponding to the g(?) orientation and (ii) potentially very many overlapping transitions in the g(?) region. The rapid progress of density functional theory computation as a means to correlate EPR and structure, and the increasing need to study Cu(II) associated with biomolecules in more biologically and biomedically relevant environments such as cells and tissue, have spurred the development of a technique for the extraction of a more complete set of spin hamiltonian parameters that is relatively straightforward and widely applicable. EPR at L-band (1-2 GHz) provides much enhanced spectral resolution and straightforward analysis via computer simulation methods. Herein, the anisotropic spin hamiltonian parameters and the nitrogen coordination numbers for two hitherto incompletely characterized Cu(II)-bound species of a prion peptide complex are determined by analysis of their L-band EPR spectra.

| S-EPMC3150385 | biostudies-literature

Electron-paramagnetic-resonance spectroscopy of complexes of xanthine oxidase with xanthine and uric acid.

Project description:Molybdenum(V) e.p.r. signals from reduced functional milk xanthine oxidase molecules (the Rapid signals), obtained in the presence of purine substrates and products, were further investigated [cf. Bray & Vänngård, (1969) Biochem. J. 114, 725-734; Pick & Bray (1969) Biochem. J. 114, 735-742]. Xanthine forms two complexes with the enzyme that are believed to correspond to different orientations of the substrate molecule in the active site. Only one complex appears to undergo the catalytic reaction. Non-productive complexes, analogous to theone with xanthine, are not formed by 1-methylxanthine or purine. Uric acid forms more than one e.p.r.-detectable complex, one of which is analogous to the non-productive xanthine complex. The computer program used for handing the e.p.r. data is described briefly.

| S-EPMC1184010 | biostudies-other

Study of nanostructural organization of ionic liquids by electron paramagnetic resonance spectroscopy.

Project description:The X-band electron paramagnetic resonance spectroscopy (EPR) of a stable, spherical nitroxide spin probe, perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (pDTO) has been used to study the nanostructural organization of a series of 1-alkyl-3-methylimidazolium tetrafluoroborate ionic liquids (ILs) with alkyl chain lengths from two to eight carbons. By employing nonlinear least-squares fitting of the EPR spectra, we have obtained values of the rotational correlation time and hyperfine coupling splitting of pDTO to high precision. The rotational correlation time of pDTO in ILs and squalane, a viscous alkane, can be fit very well to a power law functionality with a singular temperature, which often describes a number of physical quantities measured in supercooled liquids. The viscosity of the ILs and squalane, taken from the literature, can also be fit to the same power law expression, which means that the rotational correlation times and the ionic liquid viscosities have similar functional dependence on temperature. The apparent activation energy of both the rotational correlation time of pDTO and the viscous flow of ILs and squalane increases with decreasing temperature; in other words, they exhibit strong non-Arrhenius behavior. The rotational correlation time of pDTO as a function of ?/T, where ? is the shear viscosity and T is the temperature, is well described by the Stokes-Einstein-Debye (SED) law, while the hydrodynamic probe radii are solvent dependent and are smaller than the geometric radius of the probe. The temperature dependence of hyperfine coupling splitting is the same in all four ionic liquids. The value of the hyperfine coupling splitting starts decreasing with increasing alkyl chain length in the ionic liquids in which the number of carbons in the alkyl chain is greater than four. This decrease together with the decrease in the hydrodynamic radius of the probe indicates a possible existence of nonpolar nanodomains.

| S-EPMC4871252 | biostudies-literature

Exploring intrinsically disordered proteins using site-directed spin labeling electron paramagnetic resonance spectroscopy.

Project description:Proteins are highly variable biological systems, not only in their structures but also in their dynamics. The most extreme example of dynamics is encountered within the family of Intrinsically Disordered Proteins (IDPs), which are proteins lacking a well-defined 3D structure under physiological conditions. Among the biophysical techniques well-suited to study such highly flexible proteins, Site-Directed Spin Labeling combined with EPR spectroscopy (SDSL-EPR) is one of the most powerful, being able to reveal, at the residue level, structural transitions such as folding events. SDSL-EPR is based on selective grafting of a paramagnetic label on the protein under study and is limited neither by the size nor by the complexity of the system. The objective of this mini-review is to describe the basic strategy of SDSL-EPR and to illustrate how it can be successfully applied to characterize the structural behavior of IDPs. Recent developments aimed at enlarging the panoply of SDSL-EPR approaches are presented in particular newly synthesized spin labels that allow the limitations of the classical ones to be overcome. The potentialities of these new spin labels will be demonstrated on different examples of IDPs.

| S-EPMC4436889 | biostudies-literature

DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data.

Project description:Dipolar EPR spectroscopy (DEER and other techniques) enables the structural characterization of macromolecular and biological systems by measurement of distance distributions between unpaired electrons on a nanometer scale. The inference of these distributions from the measured signals is challenging due to the ill-posed nature of the inverse problem. Existing analysis tools are scattered over several applications with specialized graphical user interfaces. This renders comparison, reproducibility, and method development difficult. To remedy this situation, we present DeerLab, an open-source software package for analyzing dipolar EPR data that is modular and implements a wide range of methods. We show that DeerLab can perform one-step analysis based on separable non-linear least squares, fit dipolar multi-pathway models to multi-pulse DEER data, run global analysis with non-parametric distributions, and use a bootstrapping approach to fully quantify the uncertainty in the analysis.

| S-EPMC8462493 | biostudies-literature

Kilohertz electron paramagnetic resonance spectroscopy of single nitrogen centers at zero magnetic field.

Project description:Electron paramagnetic resonance (EPR) spectroscopy is among the most important analytical tools in physics, chemistry, and biology. The emergence of nitrogen-vacancy (NV) centers in diamond, serving as an atomic-sized magnetometer, has promoted this technique to single-spin level, even under ambient conditions. Despite the enormous progress in spatial resolution, the current megahertz spectral resolution is still insufficient to resolve key heterogeneous molecular information. A major challenge is the short coherence times of the sample electron spins. Here, we address this challenge by using a magnetic noise-insensitive transition between states of different symmetry. We demonstrate a 27-fold narrower spectrum of single substitutional nitrogen (P1) centers in diamond with a linewidth of several kilohertz, and then some weak couplings can be resolved. Those results show both spatial and spectral advances of NV center-based EPR and provide a route toward analytical (EPR) spectroscopy at the single-molecule level.

| S-EPMC7385428 | biostudies-literature

Characterization of monomeric Mn(II/III/IV)-hydroxo complexes from X- and Q-band dual mode electron paramagnetic resonance (EPR) spectroscopy.

Project description:Manganese-hydroxo species have been implicated in C-H bond activation performed by metalloenzymes, but the electronic properties of many of these intermediates are not well characterized. The present work presents a detailed characterization of three Mn(n)-OH complexes (where n = II, III, and IV) of the tris[(N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea](3-)) ligand using X- and Q-band dual mode electron paramagnetic resonance (EPR). Quantitative simulations for the [Mn(II)H3buea(OH)](2-) complex demonstrated the ability to characterize similar Mn(II) species commonly present in the resting states of manganese-containing enzymes. The spin states of the Mn(III) and Mn(IV) complexes determined from EPR spectroscopy are S = 2 and 3/2, respectively, as expected for the C3 symmetry imposed by the [H3buea](3-) ligand. Simulations of the spectra indicated the constant presence of two Mn(IV) species in solutions of [Mn(IV)H3buea(OH)] complex. The simulations of perpendicular- and parallel-mode EPR spectra allow determination of zero-field splitting and hyperfine parameters for all complexes. For the Mn(III) and Mn(IV) complexes, density functional theory calculations are used to determine the isotropic Mn hyperfine values, to compare the excited electronic state energies, and to give theoretical estimates of the zero-field energy.

| S-EPMC3878184 | biostudies-literature

Hyperbolic-cosine waveguide tapers and oversize rectangular waveguide for reduced broadband insertion loss in W-band electron paramagnetic resonance spectroscopy.

Project description:The two-way insertion loss of a 1 m length of waveguide was reduced by nearly 5 dB over a 4% bandwidth at W-band (94 GHz) for an electron paramagnetic resonance (EPR) spectrometer relative to WR10 waveguide. The waveguide has an oversize section of commercially available rectangular WR28 and a novel pair of tapers that vary in cross section with axial position according to a hyperbolic-cosine (HC) function. The tapers connect conventional rectangular WR10 waveguide to the WR28. For minimum loss, the main mode electric field is parallel to the long side of the WR28. Using mode coupling theory, the position of maximum flare (inflection point) in the taper was optimized with respect to the coupling to higher order modes and the reflection of the main mode. The optimum inflection point position is about one-tenth of the taper length from the small end of the taper. Reflection and coupling were reduced by about 20 dB relative to a pyramidal (linear) taper of the same length. Comb-like dips in the transmission coefficient produced by resonances of the higher order modes in the oversize section were about 0.03 dB. Specially designed high-precision, adjustable WR28 flanges with alignment to about 5 μm were required to keep higher order mode amplitudes arising from the flanges comparable to those from the HC tapers. Minimum return loss was about 30 dB. This paper provides a foundation for further optimization, if needed. Methods are not specific to EPR or the microwave frequency band.

| S-EPMC3155584 | biostudies-other

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