A new approach to distance measurements between two spin labels in the >10 nm range

2017 ◽  
Vol 19 (7) ◽  
pp. 5222-5229 ◽  
Author(s):  
A. Blank
Keyword(s):  
Esr Spectroscopy ◽  
Dipolar Interaction ◽  
Spin Labels ◽  
Interaction Frequency ◽  
Distance Measurements ◽  
New Approach ◽  
Nm Range

ESR spectroscopy can be efficiently used to acquire the distance between two spin labels placed on a macromolecule by measuring their mutual dipolar interaction frequency, as long as the distance is not greater than ∼10 nm.

Gd(iii)–Gd(iii) EPR distance measurements – the range of accessible distances and the impact of zero field splitting

2015 ◽  
Vol 17 (28) ◽  
pp. 18464-18476 ◽  
Author(s):  
Arina Dalaloyan ◽  
Mian Qi ◽  
Sharon Ruthstein ◽  
Shimon Vega ◽  
Adelheid Godt ◽  
...  
Keyword(s):  
Spin Labels ◽  
Zero Field ◽  
Zero Field Splitting ◽  
Distance Measurements ◽  
Field Splitting ◽  
The Impact ◽  
Nm Range

Gd rulers were designed in the 2–8 nm range for in-depth evaluation of Gd(iii) complexes as spin labels for EPR distance measurements.

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

Nucleotide-Independent Copper(II)-Based Distance Measurements in DNA by Pulsed ESR Spectroscopy

2017 ◽  
Vol 129 (8) ◽  
pp. 2147-2149 ◽  
Author(s):  
Matthew J. Lawless ◽  
Jessica L. Sarver ◽  
Sunil Saxena
Keyword(s):  
Esr Spectroscopy ◽  
Distance Measurements

Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells

2016 ◽  
Vol 56 (1) ◽  
pp. 177-181 ◽  
Author(s):  
J. Jacques Jassoy ◽  
Andreas Berndhäuser ◽  
Fraser Duthie ◽  
Sebastian P. Kühn ◽  
Gregor Hagelueken ◽  
...  
Keyword(s):  
Spin Labels ◽  
Distance Measurements

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy

2019 ◽  
Vol 131 (38) ◽  
pp. 13405-13409 ◽  
Author(s):  
Olesya A. Krumkacheva ◽  
Ivan O. Timofeev ◽  
Larisa V. Politanskaya ◽  
Yuliya F. Polienko ◽  
Evgeny V. Tretyakov ◽  
...  
Keyword(s):  
Epr Spectroscopy ◽  
Spin Labels ◽  
Distance Measurements

scholarly journals Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Eliane H. Yardeni ◽  
Thorsten Bahrenberg ◽  
Richard A. Stein ◽  
Smriti Mishra ◽  
Elia Zomot ◽  
...  
Keyword(s):  
Solution Structure ◽  
Spin Labels ◽  
Multidrug Transporter ◽  
Distance Measurements ◽  
E Coli

Pulsed electron–electron double resonance: beyond nanometre distance measurements on biomacromolecules

2011 ◽  
Vol 434 (3) ◽  
pp. 353-363 ◽  
Author(s):  
Gunnar W. Reginsson ◽  
Olav Schiemann
Keyword(s):  
Protein Complexes ◽  
Double Resonance ◽  
Resonance Method ◽  
Spin Labels ◽  
Coupling Mechanism ◽  
Distance Measurements ◽  
Paramagnetic Resonance ◽  
Distance Distributions ◽  
Nitroxide Spin Labels ◽  
Amino Acid Radicals

PELDOR (or DEER; pulsed electron–electron double resonance) is an EPR (electron paramagnetic resonance) method that measures via the dipolar electron–electron coupling distances in the nanometre range, currently 1.5–8 nm, with high precision and reliability. Depending on the quality of the data, the error can be as small as 0.1 nm. Beyond mere mean distances, PELDOR yields distance distributions, which provide access to conformational distributions and dynamics. It can also be used to count the number of monomers in a complex and allows determination of the orientations of spin centres with respect to each other. If, in addition to the dipolar through-space coupling, a through-bond exchange coupling mechanism contributes to the overall coupling both mechanisms can be separated and quantified. Over the last 10 years PELDOR has emerged as a powerful new biophysical method without size restriction to the biomolecule to be studied, and has been applied to a large variety of nucleic acids as well as proteins and protein complexes in solution or within membranes. Small nitroxide spin labels, paramagnetic metal ions, amino acid radicals or intrinsic clusters and cofactor radicals have been used as spin centres.

Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins

2017 ◽  
Vol 19 (39) ◽  
pp. 26944-26956 ◽  
Author(s):  
Yin Yang ◽  
Yan-Jun Gong ◽  
Aleksei Litvinov ◽  
Hong-Kai Liu ◽  
Feng Yang ◽  
...  
Keyword(s):  
Spin Label ◽  
Metal Ion ◽  
Coordination Mode ◽  
Distance Distribution ◽  
Spin Labels ◽  
Distance Measurements

The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.

scholarly journals A General Model to Optimise Copper(II) Labelling Efficiency of Double-Histidine Motifs for Pulse Dipolar EPR Applications

2020 ◽  
Author(s):  
Joshua L. Wort ◽  
Katrin Ackermann ◽  
David G. Norman ◽  
Bela E. Bode
Keyword(s):  
Conformational Changes ◽  
Dissociation Constants ◽  
Modulation Depth ◽  
Nitrilotriacetic Acid ◽  
Geometric Constraints ◽  
Spin Labels ◽  
Labelling Efficiency ◽  
Distance Measurements ◽  
Paramagnetic Resonance ◽  
Model Protein

<div> <p>Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with Cu<sup>II</sup> spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for Cu<sup>II</sup>-nitrilotriacetic acid were previously investigated <i>via </i>relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the double histidine motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in Cu<sup>II</sup>-Cu<sup>II </sup>RIDME to simultaneously estimate a pair of non-identical independent <i>K<sub>D</sub></i> values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise Cu<sup>II </sup>labelling efficiency, in dependence of pairs of identical or disparate <i>K<sub>D</sub></i> values and total Cu<sup>II</sup> label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model. </p> </div> <br>

scholarly journals Two closed ATP- and ADP-dependent conformations in yeast Hsp90 chaperone detected by Mn(II) EPR spectroscopic techniques

2019 ◽  
Vol 117 (1) ◽  
pp. 395-404 ◽  
Author(s):  
Angeliki Giannoulis ◽  
Akiva Feintuch ◽  
Yoav Barak ◽  
Hisham Mazal ◽  
Shira Albeck ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Close Contact ◽  
Energy State ◽  
Bound State ◽  
High Energy ◽  
Distance Distribution ◽  
Spin Labels ◽  
Atp Binding ◽  
Spectroscopic Techniques ◽  
Distance Measurements

Hsp90 plays a central role in cell homeostasis by assisting folding and maturation of a large variety of clients. It is a homo-dimer, which functions via hydrolysis of ATP-coupled to conformational changes. Hsp90’s conformational cycle in the absence of cochaperones is currently postulated as apo-Hsp90 being an ensemble of “open”/“closed” conformations. Upon ATP binding, Hsp90 adopts an active ATP-bound closed conformation where the N-terminal domains, which comprise the ATP binding site, are in close contact. However, there is no consensus regarding the conformation of the ADP-bound Hsp90, which is considered important for client release. In this work, we tracked the conformational states of yeast Hsp90 at various stages of ATP hydrolysis in frozen solutions employing electron paramagnetic resonance (EPR) techniques, particularly double electron–electron resonance (DEER) distance measurements. Using rigid Gd(III) spin labels, we found the C domains to be dimerized with same distance distribution at all hydrolysis states. Then, we substituted the ATPase Mg(II) cofactor with paramagnetic Mn(II) and followed the hydrolysis state using hyperfine spectroscopy and measured the inter–N-domain distance distributions via Mn(II)–Mn(II) DEER. The point character of the Mn(II) spin label allowed us resolve 2 different closed states: The ATP-bound (prehydrolysis) characterized by a distance distribution having a maximum of 4.3 nm, which broadened and shortened, shifting the mean to 3.8 nm at the ADP-bound state (posthydrolysis). This provides experimental evidence to a second closed conformational state of Hsp90 in solution, referred to as “compact.” Finally, the so-called high-energy state, trapped by addition of vanadate, was found structurally similar to the posthydrolysis state.

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