logo nioch.ru


N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry
Siberian Branch of Russian Academy of Science

The paper of NIOCh's researchers (international collaboration) is published in the journal  Nucleic Acids Research (IF 11,147I

Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy

Alexey A Malygin, Olesya A Krumkacheva, Dmitri M Graifer, Ivan O Timofeev, Anastasia S Ochkasova, Maria I Meschaninova, Alya G Venyaminova, Matvey V Fedin, Michael Bowman, Galina G Karpova, Elena G Bagryanskaya

Nucleic Acids Research, Volume 47, Issue 22, 16 December 2019, Pages 11850–11860
First published: 14 Nov 2019


 https://doi.org/10.1093/nar/gkz1039


Abstract

The features of previously unexplored labile complexes of human 40S ribosomal subunits with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of RNAs to the ribosomal protein uS3 through its peptide 55–64 located outside the mRNA channel, were studied by EPR spectroscopy methods. Analysis of subatomic 40S subunit models showed that a likely site for labile RNA binding is a cluster of positively charged amino acid residues between the mRNA entry site and uS3 peptide 55–64. This is consistent with our finding that the 3′-terminal mRNA fragment hanging outside the 40S subunit prevents the cross-linking of an RNA derivative to this peptide. To detect labile complexes of 40S subunits with RNA by DEER/PELDOR spectroscopy, an undecaribonucleotide derivative with nitroxide spin labels at terminal nucleotides was utilized. We demonstrated that the 40S subunit channel occupancy with mRNA does not affect the RNA derivative binding and that uS3 peptide 55–64 is not involved in binding interactions. Replacing the RNA derivative with a DNA one revealed the importance of ribose 2′-OH groups for the complex formation. Using the single-label RNA derivatives, the distance between the mRNA entry site and the loosely bound RNA site on the 40S subunit was estimated.

Altmetrics: