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

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

Journal

Applied Magnetic Resonance
ISSN: 0937-9347 , E-ISSN: 1613-7507

Output data

Year: 2018, Volume: 49, Number: 3, Pages: 265-276 Pages count : 12 DOI: 10.1007/s00723-017-0965-y

Authors

Timofeev Ivan O. ^1,3 , Krumkacheva Olesya A. ^1,3 , Fedin Matvey V. ^1,3 , Karpova Galina G. ^3,4 , Bagryanskaya Elena G. ^2,3

Affiliations

1	(Данные Web of science) Int Tomog Ctr SB RAS, Inst Skaya Str 3a, Novosibirsk 630090, Russia
2	(Данные Web of science) NN Vorozhtsov Novosibirsk Inst Organ Chem SB RAS, Pr Lavrentjeva 9, Novosibirsk 630090, Russia
3	(Данные Web of science) Novosibirsk State Univ, Pirogova Str 2, Novosibirsk 630090, Russia
4	(Данные Web of science) Inst Chem Biol & Fundamental Med SB RAS, Pr Lavrentjeva 8, Novosibirsk 630090, Russia

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.

Timofeev I.O. , Krumkacheva O.A. , Fedin M.V. , Karpova G.G. , Bagryanskaya E.G.
Refining Spin-Spin Distance Distributions in Complex Biological Systems Using Multi-Gaussian Monte Carlo Analysis
Applied Magnetic Resonance. 2018. V.49. N3. P.265-276. DOI: 10.1007/s00723-017-0965-y WOS Scopus РИНЦ OpenAlex

Published online:	Nov 10, 2017
Published print:	Mar 1, 2018

Web of science:	WOS:000425002600004
Scopus:	2-s2.0-85033493451
Elibrary:	35515483
OpenAlex:	W2767772952

DB	Citing
Web of science	2
Scopus	3
Elibrary	2
OpenAlex	4