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Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules

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Abstract

Paramagnetic relaxation enhancement (PRE) can be used to determine long-range distance restraints in biomolecules. The PREs are typically determined by analysis of intensity differences in HSQC experiments of paramagnetic and diamagnetic spin labels. However, this approach requires both isotope- and spin-labelling. Herein, we report a novel method to evaluate NOESY intensities in the presence of a paramagnetic moiety to determine PRE restraints. The advantage of our approach over HSQC-based approaches is the increased number of available signals without the need for isotope labelling. NOESY intensities affected by a paramagnetic center were evaluated during a structure calculation within the paramagnetic iterative relaxation matrix approach (P-IRMA). We applied P-IRMA to a 14-mer RNA with a known NMR solution structure, which allowed us to assess the quality of the PRE restraints. To this end, three different spin labels have been attached at different positions of the 14-mer to test the influence of flexibility on the structure calculation. Structural disturbances introduced by the spin label have been evaluated by chemical shift analysis. Furthermore, the impact of P-IRMA on the quality of the structure bundles were tested by intentionally leaving out available diamagnetic restraints. Our analyses show that P-IRMA is a powerful tool to refine RNA structures for systems that are insufficiently described by using only diamagnetic restraints.

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Acknowledgements

E.C.C. gratefully acknowledges a MainCampus scholarship provided by the Stiftung Polytechnische Gesellschaft (Frankfurt). We would like to thank E. Stirnal, M. Gränz and E. Jaumann for help with experiments. The work was supported by DFG through CRC902 and by the state of Hesse through institutional funding to BMRZ.

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Authors and Affiliations

  1. Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe Universität Frankfurt am Main, Max-von-Laue Straße 7, 60438, Frankfurt am Main, Germany

    E. C. Cetiner, H. R. A. Jonker, C. Helmling, C. Grünewald & H. Schwalbe

  2. Department of Chemistry Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland

    D. B. Gophane & S. Th. Sigurdsson

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  1. E. C. Cetiner
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  2. H. R. A. Jonker
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  3. C. Helmling
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  4. D. B. Gophane
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  5. C. Grünewald
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  6. S. Th. Sigurdsson
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  7. H. Schwalbe
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Correspondence to H. Schwalbe.

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Cetiner, E.C., Jonker, H.R.A., Helmling, C. et al. Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules. J Biomol NMR 73, 699–712 (2019). https://doi.org/10.1007/s10858-019-00282-0

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