Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules

Olav Schiemann; Caspar A. Heubach; Dinar Abdullin; Katrin Ackermann; Mykhailo Azarkh; Elena G. Bagryanskaya; Malte Drescher; Burkhard Endeward; Jack H. Freed; Laura Galazzo; Daniella Goldfarb; Tobias Hett; Laura Esteban Hofer; Luis Fábregas Ibáñez; Eric J. Hustedt; Svetlana Kucher; Ilya Kuprov; Janet Eleanor Lovett; Andreas Meyer; Sharon Ruthstein; Sunil Saxena; Stefan Stoll; Christiane R. Timmel; Marilena Di Valentin; Hassane S. McHaourab; Thomas F. 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 A. Heubach
, Dinar Abdullin
, Katrin Ackermann
, Mykhailo Azarkh
, Elena G. Bagryanskaya
, Malte Drescher
, Burkhard Endeward
, Jack H. Freed
, Laura Galazzo
, Daniella Goldfarb
, Tobias Hett
, Laura Esteban Hofer
, Luis Fábregas Ibáñez
, Eric J. Hustedt
, Svetlana Kucher
, Ilya Kuprov
, Janet Eleanor Lovett
, Andreas Meyer
, Sharon Ruthstein

Sunil Saxena, Stefan Stoll, Christiane R. Timmel, Marilena Di Valentin, Hassane S. McHaourab, Thomas F. Prisner, Bela Ernest Bode, Enrica Bordignon, Marina Bennati, Gunnar Jeschke

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

175 Scopus citations

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
Pages (from-to)	17875-17890
Number of pages	16
Journal	Journal of the American Chemical Society
Volume	143
Issue number	43
DOIs	https://doi.org/10.1021/jacs.1c07371
State	Published - 3 Nov 2021

Bibliographical note

Publisher Copyright:
© 2021 American Chemical Society.

Funding

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.

Funders	Funder number
National Science Foundation
National Institute of General Medical Sciences	R01GM125753
Biotechnology and Biological Sciences Research Council	BB/T017740/1, BB/R013780/1
Leverhulme Trust	RPG-2018-397
Royal Society
Deutsche Forschungsgemeinschaft

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10.1021/jacs.1c07371

Cite this

Schiemann, O., Heubach, C. A., Abdullin, D., Ackermann, K., Azarkh, M., Bagryanskaya, E. G., Drescher, M., Endeward, B., Freed, J. H., Galazzo, L., Goldfarb, D., Hett, T., Esteban Hofer, L., Fábregas Ibáñez, L., Hustedt, E. J., 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, 143(43), 17875-17890. https://doi.org/10.1021/jacs.1c07371

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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.",

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

note = "Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

month = nov,

day = "3",

doi = "10.1021/jacs.1c07371",

language = "אנגלית",

volume = "143",

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Schiemann, O, Heubach, CA, Abdullin, D, Ackermann, K, Azarkh, M, Bagryanskaya, EG, Drescher, M, Endeward, B, Freed, JH, Galazzo, L, Goldfarb, D, Hett, T, Esteban Hofer, L, Fábregas Ibáñez, L, Hustedt, EJ, Kucher, S, Kuprov, I, Lovett, JE, Meyer, A, Ruthstein, S, Saxena, S, Stoll, S, Timmel, CR, Di Valentin, M, McHaourab, HS, Prisner, TF, 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. 143, no. 43, pp. 17875-17890. https://doi.org/10.1021/jacs.1c07371

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T1 - Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules

AU - Schiemann, Olav

AU - Heubach, Caspar A.

AU - Abdullin, Dinar

AU - Ackermann, Katrin

AU - Azarkh, Mykhailo

AU - Bagryanskaya, Elena G.

AU - Drescher, Malte

AU - Endeward, Burkhard

AU - Freed, Jack H.

AU - Galazzo, Laura

AU - Goldfarb, Daniella

AU - Hett, Tobias

AU - Esteban Hofer, Laura

AU - Fábregas Ibáñez, Luis

AU - Hustedt, Eric J.

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 R.

AU - Di Valentin, Marilena

AU - McHaourab, Hassane S.

AU - Prisner, Thomas F.

AU - Bode, Bela Ernest

AU - Bordignon, Enrica

AU - Bennati, Marina

AU - Jeschke, Gunnar

PY - 2021/11/3

Y1 - 2021/11/3

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.

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U2 - 10.1021/jacs.1c07371

DO - 10.1021/jacs.1c07371

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C2 - 34664948

AN - SCOPUS:85118623024

SN - 0002-7863

VL - 143

SP - 17875

EP - 17890

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

IS - 43

ER -

Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules

Abstract

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