AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers
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Applied Magnetic Resonance
ORIGINAL PAPER
AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers Dinar Abdullin1 Received: 13 May 2020 / Revised: 6 July 2020 © The Author(s) 2020
Abstract Pulsed electron paramagnetic resonance dipolar spectroscopy (PDS) allows to measure the distances between electron spin centers and, in favorable cases, their relative orientation. This data is frequently used in structural biology for studying biomolecular structures, following their conformational changes and localizing paramagnetic centers within them. In order to extract the inter-spin distances and the relative orientation of spin centers from the primary, time-domain PDS signals, a specialized data analysis is required. So far, the software to do such analysis was available only for isotropic S = 1/2 spin centers, such as nitroxide and trityl radicals, as well as for high-spin Gd3+ and Mn2+ ions. Here, a new data analysis program, called AnisoDipFit, was introduced for spin systems consisting of one isotropic and one anisotropic S = 1/2 spin centers. The program was successfully tested on the PDS data corresponding to the spin systems Cu2+/organic radical, low-spin Fe3+/organic radical, and high-spin Fe3+/organic radical. For all tested spin systems, AnisoDipFit allowed determining the inter-spin distance distribution with a sub-angstrom precision. In addition, the spatial orientation of the inter-spin vector with respect to the g-frame of the metal center was determined for the last two spin systems. Thus, this study expands the arsenal of the PDS data analysis programs and facilitates the PDS-based distance and angle measurements on the highly relevant class of metolloproteins.
1 Introduction Electron paramagnetic resonance spectroscopy (EPR) offers several pulsed techniques to measure nanometer-scale distances in condensed matter. These techniques include pulsed electron–electron double resonance (PELDOR or DEER) [1, 2], double quantum coherence EPR (DQC) [3], single-frequency technique for refocusing dipolar couplings (SIFTER) [4], and relaxation induced dipolar modulation enhancement (RIDME) [5, 6]. Altogether, they are often denoted as pulsed * Dinar Abdullin [email protected]‑bonn.de 1
Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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EPR dipolar spectroscopy or, shortly, PDS [7, 8]. In the last decade, PDS distance restraints were used for numerous tasks arising from structural biology, such as studying the structure of biomolecules and biomolecular complexes [9–11], following the conformational changes of proteins during their function [12–14], and localization of metal ions within biomolecules [15–17]. The idea behind PDS is the measurement of the dipolar coupling between electron spin centers, which has a 1/r3 dependence on the distance r between these centers. In order to be applicable, PDS requires that a biomolecule or a biomolecular complex contains at least two electron spin cen
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