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Guidelines for the Simulations of Nitroxide X-Band cw EPR Spectra from Site-Directed Spin Labeling Experiments Using S imLabel.

Authors :
Etienne, Emilien
Pierro, Annalisa
Tamburrini, Ketty C.
Bonucci, Alessio
Mileo, Elisabetta
Martinho, Marlène
Belle, Valérie
Source :
Molecules. Feb2023, Vol. 28 Issue 3, p1348. 16p.
Publication Year :
2023

Abstract

Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the local level, the dynamics of structural transitions in proteins. Here, we consider SDSL-EPR based on the selective grafting of a nitroxide on the protein under study, followed by X-band cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give a reliable interpretation on biological system dynamics, a numerical simulation of the spectra is required. However, regardless of the numerical tool chosen to perform such simulations, the number of parameters is often too high to provide unambiguous results. In this study, we have chosen SimLabel to perform such simulations. SimLabel is a graphical user interface (GUI) of Matlab, using some functions of Easyspin. An exhaustive review of the parameters used in this GUI has enabled to define the adjustable parameters during the simulation fitting and to fix the others prior to the simulation fitting. Among them, some are set once and for all (gy, gz) and others are determined (Az, gx) thanks to a supplementary X-band spectrum recorded on a frozen solution. Finally, we propose guidelines to perform the simulation of X-band cw-EPR spectra of nitroxide labeled proteins at room temperature, with no need of uncommon higher frequency spectrometry and with the minimal number of variable parameters. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14203049
Volume :
28
Issue :
3
Database :
Academic Search Index
Journal :
Molecules
Publication Type :
Academic Journal
Accession number :
161858012
Full Text :
https://doi.org/10.3390/molecules28031348