scholarly journals The contribution of modern EPR to structural biology

2018 ◽  
Vol 2 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Gunnar Jeschke
Keyword(s):  
System Size ◽  
Native Conformation ◽  
Paramagnetic Resonance ◽  
Building Models ◽  
Distance Distributions ◽  
Double Electron ◽  
The Mean ◽  
Structural Restraints ◽  
Double Electron Electron Resonance ◽  
Electron Paramagnetic

Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron–electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

Dipolar pathways in dipolar EPR spectroscopy

2022 ◽  
Author(s):  
Luis Fábregas-Ibáñez ◽  
Maxx H. Tessmer ◽  
Gunnar Jeschke ◽  
Stefan Stoll
Keyword(s):  
Electron Paramagnetic Resonance ◽  
Structural Characterization ◽  
Epr Spectroscopy ◽  
Nanometer Scale ◽  
Paramagnetic Resonance ◽  
Double Electron ◽  
Double Electron Electron Resonance ◽  
Electron Paramagnetic ◽  
Epr Experiments

Dipolar electron paramagnetic resonance (EPR) experiments such as double electron--electron resonance (DEER) measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and...

scholarly journals Characterization of Aqueous Lower Polarity Solvation Shells Around Amphiphilic TEMPO Radicals in Water

2020 ◽  
Author(s):  
Johannes Hunold ◽  
Jana Eisermann ◽  
Martin Brehm ◽  
Dariush Hinderberger
Keyword(s):  
Organic Solvents ◽  
Pure Water ◽  
Paramagnetic Resonance ◽  
Double Electron ◽  
Spectral Simulations ◽  
Local Enrichment ◽  
Double Electron Electron Resonance ◽  
Electron Paramagnetic ◽  
Stable Nitroxide

Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.

Characterization of Aqueous Lower Polarity Solvation Shells Around Amphiphilic TEMPO Radicals in Water

2020 ◽  
Author(s):  
Johannes Hunold ◽  
Jana Eisermann ◽  
Martin Brehm ◽  
Dariush Hinderberger
Keyword(s):  
Organic Solvents ◽  
Pure Water ◽  
Paramagnetic Resonance ◽  
Double Electron ◽  
Spectral Simulations ◽  
Local Enrichment ◽  
Double Electron Electron Resonance ◽  
Electron Paramagnetic ◽  
Stable Nitroxide

Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.

scholarly journals Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels

2021 ◽  
Author(s):  
Igor Tkach ◽  
Ulf Diederichsen ◽  
Marina Bennati
Keyword(s):  
Molecular Level ◽  
Dipolar Interaction ◽  
Spin Labels ◽  
Paramagnetic Centers ◽  
Structural Adaptation ◽  
Paramagnetic Resonance ◽  
Transmembrane Peptides ◽  
Distance Distributions ◽  
Lipid Environment ◽  
Electron Paramagnetic

AbstractElectron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5–10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes. Graphical Abstract

scholarly journals DFT Protocol for EPR Prediction of Paramagnetic Cu(II) Complexes and Application to Protein Binding Sites

2018 ◽  
Vol 4 (4) ◽  
pp. 55 ◽  
Author(s):  
Giuseppe Sciortino ◽  
Giuseppe Lubinu ◽  
Jean-Didier Maréchal ◽  
Eugenio Garribba
Keyword(s):  
Binding Sites ◽  
Density Functional ◽  
Computational Procedure ◽  
Paramagnetic Resonance ◽  
Functional Theory ◽  
Protein Binding Sites ◽  
The Mean ◽  
Hamiltonian Parameters ◽  
Electron Paramagnetic

With the aim to provide a general protocol to interpret electron paramagnetic resonance (EPR) spectra of paramagnetic copper(II) coordination compounds, density functional theory (DFT) calculations of spin Hamiltonian parameters g and A for fourteen Cu(II) complexes with different charges, donor sets, and geometry were carried out using ORCA software. The performance of eleven functionals was tested, and on the basis of the mean absolute percent deviation (MAPD) and standard deviation (SD), the ranking of the functionals for Az is: B3LYP > B3PW91 ~ B3P86 > PBE0 > CAM-B3LYP > TPSSh > BH and HLYP > B2PLYP > MPW1PW91 > ω-B97x-D >> M06; and for gz is: PBE0 > BH and HLYP > B2PLYP > ω-B97x-D > B3PW91~B3LYP~B3P86 > CAM-B3LYP > TPSSh~MPW1PW91 >> M06. With B3LYP the MAPD with respect to A z exp t l is 8.6% with a SD of 4.2%, while with PBE0 the MAPD with respect to g z exp t l is 2.9% with a SD of 1.1%. The results of the validation confirm the fundamental role of the second order spin-orbit contribution to Az. The computational procedure was applied to predict the values of gz and Az of the adducts formed by Cu(II) with albumin and two fragments of prion protein, 106–126 and 180–193.

scholarly journals Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution

2020 ◽  
Vol 48 (9) ◽  
pp. e49-e49 ◽  
Author(s):  
Shreya Ghosh ◽  
Matthew J Lawless ◽  
Hanna J Brubaker ◽  
Kevin Singewald ◽  
Michael R Kurpiewski ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Conformational Changes ◽  
Continuous Wave ◽  
Md Simulations ◽  
Distance Measurements ◽  
Paramagnetic Resonance ◽  
Pulsed Epr ◽  
Distance Distributions ◽  
Dna Backbone ◽  
Double Electron Electron Resonance

Abstract Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2′dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules.

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