EPR spectroscopy in the study of ribosomal complexes

EPR spectroscopy in the study of ribosomal complexes Review

Journal

Biophysical Reviews
ISSN: 1867-2469

Output data

Year: 2025, Volume: 17, Pages: 1215–1231 Pages count : 17 DOI: 10.1007/s12551-025-01348-0

Authors

Krumkacheva Olesya ^1,2 , Malygin Alexey ³ , Graifer Dmitri ³ , Kolokolov Mikhail ^1,2 , Bagryanskaya Elena ⁴

Affiliations

1	International Tomography Center SB RAS, Institutskaya 3A, Novosibirsk, 630090, Russian Federation
2	Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russian Federation
3	Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
4	N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation

Protein synthesis is a fundamental biological process universally mediated by ribosomes—complex ribonucleoprotein assemblies responsible for translating genetic information into functional proteins. Despite significant structural information provided by X-ray crystallography and cryo-electron microscopy (cryo-EM), certain dynamic features of ribosomal function, particularly those involving RNA conformational flexibility and transient interactions, remain challenging to characterize. Electron Paramagnetic Resonance (EPR) spectroscopy, combined with site-directed spin labeling (SDSL), has emerged as a robust complementary approach for probing structural dynamics and conformational heterogeneity in ribosomal complexes. This review summarizes recent advances in applying EPR spectroscopy, particularly pulse dipolar EPR (DEER/PELDOR), to investigate human ribosomal complexes. We discuss methodological aspects of spin-labeling strategies for mRNA, comparing various nitroxide-based labels and highlighting their specific advantages for probing ribosomal interactions. Through representative examples, we illustrate how different EPR techniques yield complementary structural information in studying ribosome-RNA interactions. Key findings include the identification of alternative mRNA conformations within ribosomal complexes, characterization of labile RNA binding sites near the mRNA entry channel, and elucidation of stabilization effects mediated by tRNA interactions. Furthermore, we demonstrate how the integration of EPR data with molecular modeling facilitates accurate interpretation of distance distributions, enabling the correlation of experimental findings with atomic-level structural models. Finally, we address current methodological limitations of EPR spectroscopy, outlining promising perspectives and anticipated advancements in this evolving field.

Krumkacheva O. , Malygin A. , Graifer D. , Kolokolov M. , Bagryanskaya E.
EPR spectroscopy in the study of ribosomal complexes
Biophysical Reviews. 2025. V.17. P.1215–1231. DOI: 10.1007/s12551-025-01348-0 Scopus

Submitted:	Jun 30, 2025
Accepted:	Jul 21, 2025
Published online:	Aug 6, 2025
Published print:	Oct 1, 2025

Scopus:

2-s2.0-105012858290

DB	Citing
Scopus	1