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Published (Version of record)CC BY-NC-ND V4.0, Open Access
Journal article
Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules
Journal of the American Chemical Society, Vol.143(43), pp.17875-17890
03/Nov/2021
PMID: 34664948
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.
Details
- Title
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules
- Creators
- Olav Schiemann - Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, GermanyCaspar A Heubach - Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, GermanyDinar Abdullin - Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, GermanyKatrin Ackermann - EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.KMykhailo Azarkh - Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, GermanyElena G Bagryanskaya - N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Lavrentieva aven 9, 630090 Novosibirsk, RussiaMalte Drescher - Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, GermanyBurkhard Endeward - Goethe University FrankfurtJack H Freed - Department of Chemistry and Chemical Biology, and ACERT, National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York 14853-1301, United StatesLaura Galazzo - Ruhr University BochumDaniella Goldfarb - 972WIS_INST___136Tobias Hett - University of BonnLaura Esteban Hofer - ETH ZurichLuis Fábregas Ibáñez - ETH ZurichEric J Hustedt - Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United StatesSvetlana Kucher - Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, GermanyIlya Kuprov - School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, U.KJanet Eleanor Lovett - SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.KAndreas Meyer - Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, GermanySharon Ruthstein - Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, IsraelSunil Saxena - Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United StatesStefan Stoll - University of WashingtonChristiane R Timmel - Department of Chemistry, Centre for Advanced Electron Spin Resonance, University of Oxford, South Parks Road, Oxford OX1 3QR, U.KMarilena Di Valentin - University of PaduaHassane S Mchaourab - Vanderbilt UniversityThomas F Prisner - Goethe University FrankfurtBela Ernest Bode - EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.KEnrica Bordignon - Ruhr University BochumMarina Bennati - Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, GermanyGunnar Jeschke - ETH Zurich
- Resource Type
- Journal article
- Publication Details
- Journal of the American Chemical Society, Vol.143(43), pp.17875-17890; 03/Nov/2021
- Number of pages
- 16
- Language
- English
- DOI
- https://doi.org/10.1021/jacs.1c07371
- PMID
- 34664948
- Grant note
- We acknowledge the DFG (German Research Foundation) priority program SPP 1601 for funding multiple projects (O.S., G.J., E.B., M.D., T.F.P., and M.B.) related to the present work together with the funding of many collaborations outside Germany, particularly the NSF (National Science Foundation)-funded SharedEPR. J.E.L. thanks The Royal Society for a University Research Fellowship. We thank the Leverhulme Trust (RPG-2018-397) and the BBSRC (BB/R013780/1 and BB/T017740/1) for funding.R01 GM125753 / NIGMS NIH HHS
- Record Identifier
- 993330748103596
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