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Refining Spin–Spin Distance Distributions in Complex Biological Systems Using Multi-Gaussian Monte Carlo Analysis

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Abstract

Pulse dipolar electron paramagnetic resonance spectroscopy provides means of distance measurements in the range of ~ 1.5–10 nm between two spin labels tethered to a biological system. However, the extraction of distance distribution between spin labels is an ill-posed mathematical problem. The most common approach for obtaining distance distribution employs Tikhonov regularization method, where a regularization parameter characterizing the smoothness of distribution is introduced. However, in case of multi-modal distance distributions with peaks of different widths, the use of a single regularization parameter might lead to certain distortions of actual distribution shapes. Recently, a multi-Gaussian Monte Carlo approach was proposed for eliminating this drawback and verified for model biradicals [1]. In the present work, we for the first time test this approach on complicated biological systems exhibiting multi-modal distance distributions. We apply multi-Gaussian analysis to pulsed electron–electron double resonance data of supramolecular ribosomal complexes, where the 11-mer oligoribonucleotide (MR) bearing two nitroxide labels at its termini is used as a reporter. Calculated distance distributions reveal the same conformations of MR as those obtained by Tikhonov regularization, but feature the peaks having different widths, which leads to a better resolution in several cases. The advantages, complications, and further perspectives of application of Monte-Carlo-based multi-Gaussian approach to real biological systems are discussed.

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Acknowledgements

This work was supported by Russian Science Foundation (project no. 14-14-00922).

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Authors and Affiliations

  1. International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia

    Ivan O. Timofeev, Olesya A. Krumkacheva & Matvey V. Fedin

  2. N. N. Vorozhtsov, Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk, 630090, Russia

    Elena G. Bagryanskaya

  3. Novosibirsk State University, Pirogova Str. 2, Novosibirsk, 630090, Russia

    Ivan O. Timofeev, Olesya A. Krumkacheva, Matvey V. Fedin, Galina G. Karpova & Elena G. Bagryanskaya

  4. Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk, 630090, Russia

    Galina G. Karpova

Authors
  1. Ivan O. Timofeev
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  2. Olesya A. Krumkacheva
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  3. Matvey V. Fedin
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  4. Galina G. Karpova
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  5. Elena G. Bagryanskaya
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Correspondence to Elena G. Bagryanskaya.

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Timofeev, I.O., Krumkacheva, O.A., Fedin, M.V. et al. Refining Spin–Spin Distance Distributions in Complex Biological Systems Using Multi-Gaussian Monte Carlo Analysis. Appl Magn Reson 49, 265–276 (2018). https://doi.org/10.1007/s00723-017-0965-y

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  • DOI: https://doi.org/10.1007/s00723-017-0965-y

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