Journal of the American Chemical Society

, volume 143 , issue 43 , pages 17875-17890

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

Olav Schiemann ¹

Caspar A Heubach ¹

Dinar Abdullin ¹

Katrin Ackermann ²

Mykhailo Azarkh ³

Elena G. Bagryanskaya ⁴

M. Drescher ³

Burkhard Endeward ⁵

Jack H. Freed ⁶

Laura Galazzo ⁷

D. A. Goldfarb ⁸

Tobias Hett ¹

Laura Esteban Hofer ⁹

Luis Fábregas Ibáñez ⁹

Eric J Hustedt ¹⁰

Svetlana Kucher ⁷

Ilya Kuprov ¹¹

Janet E. Lovett ¹²

Andreas Meyer ¹³

Sharon Ruthstein ¹⁴

Sunil Saxena ¹⁵

Stefan Stoll ¹⁶

Christiane R. Timmel ¹⁷

Marilena Di Valentin ¹⁸

Hassane S. Mchaourab ¹⁰

Thomas F. Prisner ⁵

Bela Bode ²

Enrica Bordignon ⁷

M. Bennati ¹³

Gunnar Jeschke ⁹

Hide authors affiliations Show authors affiliations: 18 affiliations

Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany |

EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K. |

Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany |

⁴

N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Lavrentieva aven 9, 630090 Novosibirsk, Russia |

⁵

Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany |

⁶

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 States |

⁷

Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany |

⁸

Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel |

⁹

Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland |

¹⁰

Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States |

¹¹

School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, U.K. |

¹²

SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K. |

¹³

Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany |

¹⁴

Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel |

¹⁵

Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States |

¹⁶

Department of Chemistry, University of Washington, Seattle, Washington 98195, United States |

¹⁷

Department of Chemistry, Centre for Advanced Electron Spin Resonance, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K. |

¹⁸

Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy |

Publication type: Journal Article

Publication date: 2021-10-19

American Chemical Society (ACS)

Journal of the American Chemical Society

scimago Q1

wos Q1

SJR: 5.554

CiteScore: 22.5

Impact factor: 15.6

ISSN: 00027863, 15205126

DOI: 10.1021/jacs.1c07371

Copy DOI

PubMed ID: 34664948

General Chemistry

Catalysis

Biochemistry

Colloid and Surface Chemistry

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.

Found

4 citations

Krumkacheva Olesya

🥼 🤝

DSc in Physics and Mathematics

53 publications, 1 193 citations, 2 reviews

h-index: 21

International Tomography Center of the Siberian Branch of the Russian Academy of Sciences

Photodynamic Therapy (PDT)

RNA

Ribosomal complexes

Structural Biology

3 citations

Novopashina Daria

77 publications, 730 citations, 11 reviews

h-index: 13

Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences

3 citations

Sannikova Natalya

7 publications, 74 citations

h-index: 3

International Tomography Center of the Siberian Branch of the Russian Academy of Sciences

Novosibirsk State University

2 citations

Kuznetsov Nikita

DSc in Biological/biomedical sciences

126 publications, 1 741 citations, 3 reviews

h-index: 25

Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences

1 citation

Sukhanov Andrey

🥼 🤝

PhD in Physics and Mathematics

109 publications, 1 396 citations

h-index: 18

Kazan E.K. Zavoisky Physical-Technical Institute of the Kazan Scientific Center of the Russian Academy of Sciences

Kazan Scientific Center of the Russian Academy of Sciences

1 citation

Zhdanova Kseniya

🥼 🤝

PhD in Chemistry

43 publications, 543 citations, 1 review

h-index: 11

MIREA — Russian Technological University

Research interests

Bioorganic chemistry

Coordination Chemistry

Photodynamic Therapy (PDT)

1 citation

Bulygin Anatoliy

9 publications, 37 citations

h-index: 3

Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences

Novosibirsk State University

Research interests

Enzymology

Molecular modeling

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211

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Schiemann O. et al. Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules // Journal of the American Chemical Society. 2021. Vol. 143. No. 43. pp. 17875-17890.

GOST all authors (up to 50) Copy

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. A., Hett T., Esteban Hofer L., Fábregas Ibáñez L., Hustedt E. J., Kucher S., Kuprov I., Lovett J. E., Meyer A., Ruthstein S., Saxena S., Stoll S., Timmel C. R., Di Valentin M., Mchaourab H. S., Prisner T. F., Bode B., Bordignon E., Bennati M., Jeschke G. Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules // Journal of the American Chemical Society. 2021. Vol. 143. No. 43. pp. 17875-17890.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1021/jacs.1c07371

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

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

T2 - Journal of the American Chemical Society

AU - Schiemann, Olav

AU - Heubach, Caspar A

AU - Abdullin, Dinar

AU - Ackermann, Katrin

AU - Azarkh, Mykhailo

AU - Bagryanskaya, Elena G.

AU - Drescher, M.

AU - Endeward, Burkhard

AU - Freed, Jack H.

AU - Galazzo, Laura

AU - Goldfarb, D. A.

AU - Hett, Tobias

AU - Esteban Hofer, Laura

AU - Fábregas Ibáñez, Luis

AU - Hustedt, Eric J

AU - Kucher, Svetlana

AU - Kuprov, Ilya

AU - Lovett, Janet E.

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

AU - Bordignon, Enrica

AU - Bennati, M.

AU - Jeschke, Gunnar

PY - 2021

DA - 2021/10/19

PB - American Chemical Society (ACS)

SP - 17875-17890

IS - 43

VL - 143

PMID - 34664948

SN - 0002-7863

SN - 1520-5126

ER -

BibTex |

Cite this

BibTex (up to 50 authors) Copy

@article{2021_Schiemann,

author = {Olav Schiemann and Caspar A Heubach and Dinar Abdullin and Katrin Ackermann and Mykhailo Azarkh and Elena G. Bagryanskaya and M. Drescher and Burkhard Endeward and Jack H. Freed and Laura Galazzo and D. A. Goldfarb and Tobias Hett and Laura Esteban Hofer and Luis Fábregas Ibáñez and Eric J Hustedt and Svetlana Kucher and Ilya Kuprov and Janet E. Lovett and Andreas Meyer and Sharon Ruthstein and Sunil Saxena and Stefan Stoll and Christiane R. Timmel and Marilena Di Valentin and Hassane S. Mchaourab and Thomas F. Prisner and Bela Bode and Enrica Bordignon and M. Bennati and Gunnar Jeschke},

title = {Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules},

journal = {Journal of the American Chemical Society},

year = {2021},

volume = {143},

publisher = {American Chemical Society (ACS)},

month = {oct},

url = {https://doi.org/10.1021/jacs.1c07371},

number = {43},

pages = {17875--17890},

doi = {10.1021/jacs.1c07371}

}

MLA

Cite this

MLA Copy

Schiemann, Olav, et al. “Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.” Journal of the American Chemical Society, vol. 143, no. 43, Oct. 2021, pp. 17875-17890. https://doi.org/10.1021/jacs.1c07371.

Publisher

American Chemical Society (ACS)

Journal

Journal of the American Chemical Society

scimago Q1

wos Q1

SJR

5.554

CiteScore

22.5

Impact factor

15.6

ISSN

00027863 (Print)

15205126 (Electronic)