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 Ruthstein; Sunil Saxena; Stefan Stoll; Christiane Timmel; Marilena Di Valentin; Hassane Mchaourab; Thomas Prisner; Bela Ernest Bode; Enrica Bordignon; Marina Bennati; Gunnar Jeschke

doi:10.1021/jacs.1c07371

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 journal › Article › peer-review

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 language	English
Number of pages	16
Journal	Journal of the American Chemical Society
Volume	Articles ASAP
Early online date	19 Oct 2021
DOIs	https://doi.org/10.1021/jacs.1c07371
Publication status	E-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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10.1021/jacs.1c07371Licence: CC BY-NC-ND

Schiemann_2021_JACS_Benchmark-test-guidelines_CC
Copyright © 2021 The Authors. Published by American Chemical Society. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made
Final published version, 4.55 MBLicence: CC BY-NC-ND

Enabling Shaped Pulse Capability: Enabling Shaped Pulse Capability for Superior Biological Structural Determination Using EPR Spectroscopy.
Lovett, J. E. (PI), Bode, B. E. (CoI), Penedo, C. (CoI), Pitt, S. J. (CoI), Schwarz-Linek, U. (CoI), Smith, G. M. (CoI), Watson, A. J. B. (CoI) & White, M. (CoI)
BBSRC
1/10/20 → 30/09/21
Project: Standard
Understanding sensitivity gains in pulse: Understanding sensitivity gains in pulse EPR on multimeric membrane proteins
Bode, B. E. (PI) & Pliotas, C. (CoI)
The Leverhulme Trust
14/05/19 → 18/02/22
Project: Standard
Cryogen-free arbitrary waveform EPR: Cryogen-free arbitrary waveform EPR for structural Biology and Biophysics
Bode, B. E. (PI), Lovett, J. E. (CoI), Pliotas, C. (CoI), Schwarz-Linek, U. (CoI), Smith, G. M. (CoI), Stewart, A. J. (CoI) & White, M. (CoI)
1/05/18 → 30/04/19
Project: Standard

Cite this

Schiemann, O., Heubach, C., Abdullin, D., Ackermann, K., Azarkh, M., Bagryanskaya, E., Drescher, M., Endeward, B., Freed, J., Galazzo, L., Goldfarb, D., Hett, T., Esteban Hofer, L., Fábregas Ibáñez, L., Hustedt, E., Kucher, S., Kuprov, I., Lovett, J. E., Meyer, A., ... Jeschke, G. (2021). Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules. Journal of the American Chemical Society, Articles ASAP. Advance online publication. https://doi.org/10.1021/jacs.1c07371

@article{906a324d2c39495c87b517fd7b8c0e39,

title = "Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules",

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.",

keywords = "EPR, PELDOR, DEER, Benchmark study, Proteins, Integrated structural biology, Spin label, Nitroxide, Good practice",

author = "Olav Schiemann and Caspar Heubach and Dinar Abdullin and Katrin Ackermann and Mykhailo Azarkh and Elena Bagryanskaya and Malte Drescher and Burkhard Endeward and Jack Freed and Laura Galazzo and Daniella Goldfarb and Tobias Hett and {Esteban Hofer}, Laura and {F{\'a}bregas Ib{\'a}{\~n}ez}, Luis and Eric Hustedt and Svetlana Kucher and Ilya Kuprov and Lovett, {Janet Eleanor} and Andreas Meyer and Sharon Ruthstein and Sunil Saxena and Stefan Stoll and Christiane Timmel and {Di Valentin}, Marilena and Hassane Mchaourab and Thomas Prisner and Bode, {Bela Ernest} and Enrica Bordignon and Marina Bennati and Gunnar Jeschke",

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. JEL 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.",

year = "2021",

month = oct,

day = "19",

doi = "10.1021/jacs.1c07371",

language = "English",

volume = "Articles ASAP",

journal = "Journal of the American Chemical Society",

issn = "0002-7863",

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Schiemann, O, Heubach, C, Abdullin, D, Ackermann, K, Azarkh, M, Bagryanskaya, E, Drescher, M, Endeward, B, Freed, J, Galazzo, L, Goldfarb, D, Hett, T, Esteban Hofer, L, Fábregas Ibáñez, L, Hustedt, E, Kucher, S, Kuprov, I, Lovett, JE, Meyer, A, Ruthstein, S, Saxena, S, Stoll, S, Timmel, C, Di Valentin, M, Mchaourab, H, Prisner, T, Bode, BE, Bordignon, E, Bennati, M & Jeschke, G 2021, 'Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules', Journal of the American Chemical Society, vol. Articles ASAP. https://doi.org/10.1021/jacs.1c07371

TY - JOUR

T1 - Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules

AU - Schiemann, Olav

AU - Heubach, Caspar

AU - Abdullin, Dinar

AU - Ackermann, Katrin

AU - Azarkh, Mykhailo

AU - Bagryanskaya, Elena

AU - Drescher, Malte

AU - Endeward, Burkhard

AU - Freed, Jack

AU - Galazzo, Laura

AU - Goldfarb, Daniella

AU - Hett, Tobias

AU - Esteban Hofer, Laura

AU - Fábregas Ibáñez, Luis

AU - Hustedt, Eric

AU - Kucher, Svetlana

AU - Kuprov, Ilya

AU - Lovett, Janet Eleanor

AU - Meyer, Andreas

AU - Ruthstein, Sharon

AU - Saxena, Sunil

AU - Stoll, Stefan

AU - Timmel, Christiane

AU - Di Valentin, Marilena

AU - Mchaourab, Hassane

AU - Prisner, Thomas

AU - Bode, Bela Ernest

AU - Bordignon, Enrica

AU - Bennati, Marina

AU - Jeschke, Gunnar

N1 - 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. JEL 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.

PY - 2021/10/19

Y1 - 2021/10/19

N2 - 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.

AB - 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.

KW - EPR

KW - PELDOR

KW - DEER

KW - Benchmark study

KW - Proteins

KW - Integrated structural biology

KW - Spin label

KW - Nitroxide

KW - Good practice

U2 - 10.1021/jacs.1c07371

DO - 10.1021/jacs.1c07371

M3 - Article

SN - 0002-7863

VL - Articles ASAP

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

ER -

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

Abstract

Keywords

Access to Document

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Projects

Enabling Shaped Pulse Capability: Enabling Shaped Pulse Capability for Superior Biological Structural Determination Using EPR Spectroscopy.

Understanding sensitivity gains in pulse: Understanding sensitivity gains in pulse EPR on multimeric membrane proteins

Cryogen-free arbitrary waveform EPR: Cryogen-free arbitrary waveform EPR for structural Biology and Biophysics

Cite this