Refining Spin–Spin Distance Distributions in Complex Biological Systems Using Multi-Gaussian Monte Carlo Analysis
- Авторлар: Timofeev I.1,2, Krumkacheva O.1,2, Fedin M.1,2, Karpova G.2,3, Bagryanskaya E.4,2
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Мекемелер:
- 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
- Шығарылым: Том 49, № 3 (2018)
- Беттер: 265-276
- Бөлім: Original Paper
- URL: https://journals.rcsi.science/0937-9347/article/view/248026
- DOI: https://doi.org/10.1007/s00723-017-0965-y
- ID: 248026
Дәйексөз келтіру
Аннотация
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.
Авторлар туралы
Ivan Timofeev
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Ресей, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Olesya Krumkacheva
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Ресей, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Matvey Fedin
International Tomography Center SB RAS; Novosibirsk State University
Email: egbagryanskaya@nioch.nsc.ru
Ресей, Institutskaya str. 3a, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090
Galina Karpova
Novosibirsk State University; Institute of Chemical Biology and Fundamental Medicine SB RAS
Email: egbagryanskaya@nioch.nsc.ru
Ресей, Pirogova Str. 2, Novosibirsk, 630090; pr. Lavrentjeva 8, Novosibirsk, 630090
Elena Bagryanskaya
N. N. Vorozhtsov, Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk State University
Хат алмасуға жауапты Автор.
Email: egbagryanskaya@nioch.nsc.ru
Ресей, pr. Lavrentjeva 9, Novosibirsk, 630090; Pirogova Str. 2, Novosibirsk, 630090