Evidence for multiple conformational changes in the active center of thrombin induced by complex formation with thrombomodulin: an analysis employing nitroxide spin-labels

Biochemistry ◽  
1988 ◽  
Vol 27 (2) ◽  
pp. 769-773 ◽  
Author(s):  
Giovanni Musci ◽  
Lawrence J. Berliner ◽  
Charles T. Esmon
Keyword(s):  
Complex Formation ◽  
Active Center ◽  
Conformational Changes ◽  
Spin Labels ◽  
Nitroxide Spin Labels

scholarly journals DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

2019 ◽  
Vol 47 (15) ◽  
pp. 7767-7780 ◽  
Author(s):  
Olesya A Krumkacheva ◽  
Georgiy Yu Shevelev ◽  
Alexander A Lomzov ◽  
Nadezhda S Dyrkheeva ◽  
Andrey A Kuzhelev ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Md Simulations ◽  
Dna Lesions ◽  
Spin Labels ◽  
Paramagnetic Resonance ◽  
Applied Pulse ◽  
Oligonucleotide Duplex ◽  
Nitroxide Spin Labels ◽  
Ap Sites ◽  
Electron Paramagnetic

Abstract A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5′ ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.

scholarly journals DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis

2021 ◽  
Author(s):  
Hannah Russell ◽  
Rachel Stewart ◽  
Christopher Prior ◽  
Vasily S. Oganesyan ◽  
Thembaninkosi G. Gaule ◽  
...  
Keyword(s):  
Dipolar Coupling ◽  
Amine Oxidase ◽  
Spin Labels ◽  
Arthrobacter Globiformis ◽  
Copper Amine Oxidase ◽  
Dipole Interactions ◽  
Nitroxide Spin Labels ◽  
Double Electron Electron Resonance ◽  
Dipolar Modulation ◽  
Paramagnetic Centres

AbstractIn the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin–spin distances at nanometre-scale by measuring dipole–dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO.

Comparison of Ionic and Non-Ionic Nitroxide Spin Labels for Urographic Enhancement in Magnetic Resonance Imaging

1987 ◽  
Vol 28 (5) ◽  
pp. 593-600 ◽  
Author(s):  
Wolfgang Grodd ◽  
H. Paajanen ◽  
U. G. Eriksson ◽  
D. Revel ◽  
F. Terrier ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Spin Labels ◽  
Resonance Imaging ◽  
Nitroxide Spin Labels

Conformational Changes in ι- and κ-Carrageenans Induced by Complex Formation with Bovine β-Casein

2007 ◽  
Vol 8 (2) ◽  
pp. 368-375 ◽  
Author(s):  
Tatiana V. Burova ◽  
Natalia V. Grinberg ◽  
Valerij Ya. Grinberg ◽  
Anatoly I. Usov ◽  
Vladimir B. Tolstoguzov ◽  
...  
Keyword(s):  
Complex Formation ◽  
Conformational Changes
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