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 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.

Spin Label Study of Apomembranes and Purple Membranes

1993 ◽  
Vol 48 (5-6) ◽  
pp. 500-503
Author(s):  
Tzvetana R. Lazarova ◽  
Maya Y. Velitchkova
Keyword(s):  
Fatty Acids ◽  
Lipid Bilayer ◽  
Spin Label ◽  
Hyperfine Splitting ◽  
Esr Spectra ◽  
Spin Labels ◽  
Label Study ◽  
Splitting Parameter ◽  
Induced Changes ◽  
Purple Membranes

Abstract Three spin-labelled fatty acids were used to detect the dynamics of lipid bilayer of apomem branes and purple membranes. It was found that ESR spectra of spin labels bound to apo­ membranes showed a temperature-induced changes rather similar to those seen with purple membranes. At the same time, however, the values of hyperfine splitting parameter 2Tm were lower as compared to purple membranes. The results pointed out that the removal of the retinal from purple membranes affects the dynamics of lipid bilayer and apomembranes were more rigid structure than those of purple membranes.

Tetranuclear MnII /ZnII and Novel Azido-Bridged Chair-Shaped Heptanuclear CdII Compounds: The Effect of Metal Ion and Coordination Mode of the Azide Group on the Structure of the Products

2018 ◽  
Vol 2019 (2) ◽  
pp. 262-270 ◽  
Author(s):  
Farhad Akbari Afkhami ◽  
Ghodrat Mahmoudi ◽  
Ali Akbar Khandar ◽  
Antonio Franconetti ◽  
Ennio Zangrando ◽  
...  
Keyword(s):  
Metal Ion ◽  
Coordination Mode ◽  
Azide Group

Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides

2019 ◽  
Vol 25 (9) ◽  
pp. 2203-2207 ◽  
Author(s):  
Janine Wegner ◽  
Gabriele Valora ◽  
Karin Halbmair ◽  
Annemarie Kehl ◽  
Brigitte Worbs ◽  
...  
Keyword(s):  
Lipid Bilayer ◽  
Long Range ◽  
Spin Label ◽  
Distance Measurements

High Sensitivity In-Cell EPR Distance Measurements on Proteins using an Optimized Gd(III) Spin Label

2018 ◽  
Vol 9 (20) ◽  
pp. 6119-6123 ◽  
Author(s):  
Yin Yang ◽  
Feng Yang ◽  
Yan-Jun Gong ◽  
Thorsten Bahrenberg ◽  
Akiva Feintuch ◽  
...  
Keyword(s):  
Spin Label ◽  
High Sensitivity ◽  
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

scholarly journals High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label

2019 ◽  
Vol 48 (2) ◽  
pp. 924-933 ◽  
Author(s):  
Marcel Heinz ◽  
Nicole Erlenbach ◽  
Lukas S Stelzl ◽  
Grace Thierolf ◽  
Nilesh R Kamble ◽  
...  
Keyword(s):  
High Resolution ◽  
Nucleic Acids ◽  
Spin Label ◽  
Double Resonance ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Spin Labels ◽  
Abasic Site ◽  
Abasic Sites ◽  
Rna And Dna

Abstract Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.

Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements

2019 ◽  
Vol 21 (20) ◽  
pp. 10238-10243 ◽  
Author(s):  
Austin Gamble Jarvi ◽  
Timothy F. Cunningham ◽  
Sunil Saxena
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Metal Binding ◽  
Metal Ion ◽  
Native Metal ◽  
Distance Measurements ◽  
Metal Binding Site ◽  
Paramagnetic Metal

A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.

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