Refining Spin–Spin Distance Distributions in Complex Biological Systems Using Multi-Gaussian Monte Carlo Analysis
- Authors: Timofeev I.O.1,2, Krumkacheva O.A.1,2, Fedin M.V.1,2, Karpova G.G.2,3, Bagryanskaya E.G.4,2
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Affiliations:
- International Tomography Center SB RAS
- Novosibirsk State University
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- N. N. Vorozhtsov, Novosibirsk Institute of Organic Chemistry SB RAS
- Issue: Vol 49, No 3 (2018)
- Pages: 265-276
- Section: Original Paper
- URL: https://journals.rcsi.science/0937-9347/article/view/248026
- DOI: https://doi.org/10.1007/s00723-017-0965-y
- ID: 248026
Cite item
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.
About the authors
Ivan O. Timofeev
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Russian Federation, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Olesya A. Krumkacheva
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Russian Federation, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Matvey V. Fedin
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Russian Federation, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Galina G. Karpova
Novosibirsk State University; Institute of Chemical Biology and Fundamental Medicine SB RAS
Email: egbagryanskaya@nioch.nsc.ru
Russian Federation, Pirogova Str. 2, Novosibirsk, 630090; pr. Lavrentjeva 8, Novosibirsk, 630090
Elena G. Bagryanskaya
N. N. Vorozhtsov, Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk State University
Author for correspondence.
Email: egbagryanskaya@nioch.nsc.ru
Russian Federation, pr. Lavrentjeva 9, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090