Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules

Olav Schiemann*, Caspar Heubach, Dinar Abdullin, Katrin Ackermann, Mykhailo Azarkh, Elena Bagryanskaya, Malte Drescher, Burkhard Endeward, Jack Freed, Laura Galazzo, Daniella Goldfarb, Tobias Hett, Laura Esteban Hofer, Luis Fábregas Ibáñez, Eric Hustedt, Svetlana Kucher, Ilya Kuprov, Janet Eleanor Lovett, Andreas Meyer, Sharon RuthsteinSunil Saxena, Stefan Stoll, Christiane Timmel, Marilena Di Valentin, Hassane Mchaourab*, Thomas Prisner*, Bela Ernest Bode*, Enrica Bordignon*, Marina Bennati*, Gunnar Jeschke*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

113 Citations (Scopus)
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Abstract

Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole–dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron–electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.
Original languageEnglish
Number of pages16
JournalJournal of the American Chemical Society
VolumeArticles ASAP
Early online date19 Oct 2021
DOIs
Publication statusE-pub ahead of print - 19 Oct 2021

Keywords

  • EPR
  • PELDOR
  • DEER
  • Benchmark study
  • Proteins
  • Integrated structural biology
  • Spin label
  • Nitroxide
  • Good practice

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