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Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET

Author

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  • Martin F. Peter

    (University of Bonn)

  • Christian Gebhardt

    (Faculty of Biology, Ludwig-Maximilians-Universität München)

  • Rebecca Mächtel

    (Faculty of Biology, Ludwig-Maximilians-Universität München)

  • Gabriel G. Moya Muñoz

    (Faculty of Biology, Ludwig-Maximilians-Universität München)

  • Janin Glaenzer

    (University of Bonn)

  • Alessandra Narducci

    (Faculty of Biology, Ludwig-Maximilians-Universität München)

  • Gavin H. Thomas

    (University of York)

  • Thorben Cordes

    (Faculty of Biology, Ludwig-Maximilians-Universität München)

  • Gregor Hagelueken

    (University of Bonn)

Abstract

Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.

Suggested Citation

  • Martin F. Peter & Christian Gebhardt & Rebecca Mächtel & Gabriel G. Moya Muñoz & Janin Glaenzer & Alessandra Narducci & Gavin H. Thomas & Thorben Cordes & Gregor Hagelueken, 2022. "Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31945-6
    DOI: 10.1038/s41467-022-31945-6
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    1. Martin F. Peter & Jan A. Ruland & Yeojin Kim & Philipp Hendricks & Niels Schneberger & Jan Peter Siebrasse & Gavin H. Thomas & Ulrich Kubitscheck & Gregor Hagelueken, 2024. "Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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