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:https://doi.org/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 RuthsteinSunil Saxena, Stefan Stoll, Christiane R. Timmel, Marilena Di Valentin, Hassane S. McHaourab, Thomas F. Prisner, Bela Ernest Bode, Enrica Bordignon, Marina Bennati, Gunnar Jeschke

Bar-Ilan University, Weizmann Institute of Science

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
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

All Science Journal Classification (ASJC) codes

General Chemistry
Biochemistry
Catalysis
Colloid and Surface Chemistry

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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

@article{3042074606bd4537a8af9c9fb269fffc,

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 = "https://doi.org/10.1021/jacs.1c07371",

language = "الإنجليزيّة",

volume = "143",

pages = "17875--17890",

journal = "Journal of the American Chemical Society",

issn = "0002-7863",

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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

TY - JOUR

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.

UR - http://www.scopus.com/inward/record.url?scp=85118623024&partnerID=8YFLogxK

U2 - https://doi.org/10.1021/jacs.1c07371

DO - https://doi.org/10.1021/jacs.1c07371

M3 - مقالة

C2 - 34664948

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

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