scholarly journals Dependence of Distance Distributions Derived from Double Electron-Electron Resonance Pulsed EPR Spectroscopy on Pulse-Sequence Time

2015 ◽  
Vol 54 (18) ◽  
pp. 5336-5339 ◽  
Author(s):  
James L. Baber ◽  
John M. Louis ◽  
G. Marius Clore
Keyword(s):  
Epr Spectroscopy ◽  
Pulse Sequence ◽  
Electron Resonance ◽  
Pulsed Epr ◽  
Distance Distributions ◽  
Double Electron ◽  
Double Electron Electron Resonance

scholarly journals Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts

2016 ◽  
Vol 18 (8) ◽  
pp. 5819-5831 ◽  
Author(s):  
Zhanglong Liu ◽  
Thomas M. Casey ◽  
Mandy E. Blackburn ◽  
Xi Huang ◽  
Linh Pham ◽  
...  
Keyword(s):  
Spin Labeling ◽  
Conformational Sampling ◽  
Electron Resonance ◽  
Pulsed Epr ◽  
Double Electron ◽  
Conformational Landscape ◽  
Double Electron Electron Resonance ◽  
Hiv 1

The conformational landscape of HIV-1 protease can be characterized by double electron–electron resonance (DEER) spin-labeling.

scholarly journals Protein conformation by EPR spectroscopy using gadolinium tags clicked to genetically encoded p-azido-l-phenylalanine

2015 ◽  
Vol 51 (88) ◽  
pp. 15898-15901 ◽  
Author(s):  
E. H. Abdelkader ◽  
A. Feintuch ◽  
X. Yao ◽  
L. A. Adams ◽  
L. Aurelio ◽  
...  
Keyword(s):  
Amino Acids ◽  
Epr Spectroscopy ◽  
Protein Conformation ◽  
Unnatural Amino Acids ◽  
Distance Measurements ◽  
Electron Resonance ◽  
Double Electron ◽  
Double Electron Electron Resonance

First example of gadolinium tags attached to a pair of unnatural amino acids for distance measurements by double electron–electron resonance.

scholarly journals Strategies to identify and suppress crosstalk signals in double electron–electron resonance (DEER) experiments with gadolinium<sup>III</sup> and nitroxide spin-labeled compounds

2020 ◽  
Vol 1 (2) ◽  
pp. 285-299
Author(s):  
Markus Teucher ◽  
Mian Qi ◽  
Ninive Cati ◽  
Henrik Hintz ◽  
Adelheid Godt ◽  
...  
Keyword(s):  
Relaxation Times ◽  
Molecular Complexes ◽  
Spin Labels ◽  
Electron Resonance ◽  
Molecular Rulers ◽  
Distance Distributions ◽  
Double Electron ◽  
Biomolecular Complexes ◽  
Double Electron Electron Resonance ◽  
Intermolecular Distances

Abstract. Double electron–electron resonance (DEER) spectroscopy applied to orthogonally spin-labeled biomolecular complexes simplifies the assignment of intra- and intermolecular distances, thereby increasing the information content per sample. In fact, various spin labels can be addressed independently in DEER experiments due to spectroscopically nonoverlapping central transitions, distinct relaxation times, and/or transition moments; hence, they are referred to as spectroscopically orthogonal. Molecular complexes which are, for example, orthogonally spin-labeled with nitroxide (NO) and gadolinium (Gd) labels give access to three distinct DEER channels that are optimized to selectively probe NO–NO, NO–Gd, and Gd–Gd distances. Nevertheless, it has been previously recognized that crosstalk signals between individual DEER channels can occur, for example, when a Gd–Gd distance appears in a DEER channel optimized to detect NO–Gd distances. This is caused by residual spectral overlap between NO and Gd spins which, therefore, cannot be considered as perfectly orthogonal. Here, we present a systematic study on how to identify and suppress crosstalk signals that can appear in DEER experiments using mixtures of NO–NO, NO–Gd, and Gd–Gd molecular rulers characterized by distinct, nonoverlapping distance distributions. This study will help to correctly assign the distance peaks in homo- and heterocomplexes of biomolecules carrying not perfectly orthogonal spin labels.

scholarly journals The decay of the refocused Hahn echo in double electron–electron resonance (DEER) experiments

2021 ◽  
Vol 2 (1) ◽  
pp. 161-173
Author(s):  
Thorsten Bahrenberg ◽  
Samuel M. Jahn ◽  
Akiva Feintuch ◽  
Stefan Stoll ◽  
Daniella Goldfarb
Keyword(s):  
Electron Spin ◽  
Large Scale ◽  
Pulse Sequence ◽  
Spin Dynamics ◽  
Spin Echo ◽  
Sequence Length ◽  
Flip Flop ◽  
Electron Resonance ◽  
Double Electron ◽  
Double Electron Electron Resonance

Abstract. Double electron–electron resonance (DEER) is a pulse electron paramagnetic resonance (EPR) technique that measures distances between paramagnetic centres. It utilizes a four-pulse sequence based on the refocused Hahn spin echo. The echo decays with increasing pulse sequence length 2(τ1+τ2), where τ1 and τ2 are the two time delays. In DEER, the value of τ2 is determined by the longest inter-spin distance that needs to be resolved, and τ1 is adjusted to maximize the echo amplitude and, thus, sensitivity. We show experimentally that, for typical spin centres (nitroxyl, trityl, and Gd(III)) diluted in frozen protonated solvents, the largest refocused echo amplitude for a given τ2 is obtained neither at very short τ1 (which minimizes the pulse sequence length) nor at τ1=τ2 (which maximizes dynamic decoupling for a given total sequence length) but rather at τ1 values smaller than τ2. Large-scale spin dynamics simulations based on the coupled cluster expansion (CCE), including the electron spin and several hundred neighbouring protons, reproduce the experimentally observed behaviour almost quantitatively. They show that electron spin dephasing is driven by solvent protons via the flip-flop coupling among themselves and their hyperfine couplings to the electron spin.

Reliable nanometre-range distance distributions from 5-pulse double electron electron resonance

2017 ◽  
Vol 19 (24) ◽  
pp. 15754-15765 ◽  
Author(s):  
Frauke D. Breitgoff ◽  
Yevhen O. Polyhach ◽  
Gunnar Jeschke
Keyword(s):  
Signal Processing ◽  
Electron Resonance ◽  
Experimental Time ◽  
Distance Distributions ◽  
Double Electron ◽  
Double Electron Electron Resonance

The partial excitation artefact in 5-pulse DEER data can be eliminated by experimental time shifting and signal processing.

scholarly journals Tm filtering by 1H-methyl labeling in a deuterated protein for pulsed double electron–electron resonance EPR

2020 ◽  
Vol 56 (74) ◽  
pp. 10890-10893
Author(s):  
Thomas Schmidt ◽  
G. Marius Clore
Keyword(s):  
Relaxation Time ◽  
Electron Resonance ◽  
Methyl Labeling ◽  
Distance Distributions ◽  
Deuterated Protein ◽  
Double Electron ◽  
Phase Memory ◽  
Double Electron Electron Resonance ◽  
Methyl Protonation

Methyl protonation in a deuterated protein background is used to assign DEER-derived multimodal distance distributions by phase-memory relaxation time filtering.

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