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Two alternative conformations of mRNA in the human ribosome during elongation and termination of translation as revealed by EPR spectroscopy

Authors
  • Bulygin, Konstantin N.1
  • Timofeev, Ivan O.2
  • Malygin, Alexey A.1
  • Graifer, Dmitri M.1
  • Meschaninova, Maria I.1
  • Venyaminova, Alya G.1
  • Krumkacheva, Olesya A.2
  • Fedin, Matvey V.2
  • Yu. Frolova, Ludmila3
  • Karpova, Galina G.1
  • Bagryanskaya, Elena G.4
  • 1 Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
  • 2 International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
  • 3 Engelhardt Institute of Molecular Biology RAS, Vavilova Str. 32, Moscow 119991, Russia
  • 4 N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
Type
Published Article
Journal
Computational and Structural Biotechnology Journal
Publisher
Elsevier
Publication Date
Aug 19, 2021
Volume
19
Pages
4702–4710
Identifiers
DOI: 10.1016/j.csbj.2021.08.024
PMID: 34504663
PMCID: PMC8390954
Source
PubMed Central
Disciplines
  • Research Article
License
Unknown

Abstract

The conformation of mRNA in the region of the human 80S ribosome decoding site was monitored using 11-mer mRNA analogues that bore nitroxide spin labels attached to the terminal nucleotide bases. Intramolecular spin–spin distances were measured by DEER/PELDOR spectroscopy in model complexes mimicking different states of the 80S ribosome during elongation and termination of translation. The measurements revealed that in all studied complexes, mRNA exists in two alternative conformations, whose ratios are different in post-translocation, pre-translocation and termination complexes. We found that the presence of a tRNA molecule at the ribosomal A site decreases the relative share of the more extended mRNA conformation, whereas the binding of eRF1 (alone or in a complex with eRF3) results in the opposite effect. In the termination complexes, the ratios of mRNA conformations are practically the same, indicating that a part of mRNA bound in the ribosome channel does not undergo significant structural alterations in the course of completion of the translation. Our results contribute to the understanding of mRNA molecular dynamics in the mammalian ribosome channel during translation.

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