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

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dc.contributor.authorMalygin, Alexey A.
dc.contributor.authorKrumkacheva, Olesya A.
dc.contributor.authorGraifer, Dmitry M.
dc.contributor.authorTimofeev, Ivan O.
dc.contributor.authorOchkasova, Anastasia S.
dc.contributor.authorMeschaninova, Mariya, I
dc.contributor.authorVenyaminova, Alya G.
dc.contributor.authorFedin, Matvey, V
dc.contributor.authorBowman, Michael
dc.contributor.authorKarpova, Galina G.
dc.contributor.authorBagryanskaya, Elena G.
dc.contributor.otherInstitute of Chemical Biology & Fundamental Medicine, Siberian Branch of the RAS
dc.contributor.otherRussian Academy of Sciences
dc.contributor.otherVorozhtsov Novosibirsk Institute of Organic Chemistry
dc.contributor.otherNovosibirsk State University
dc.contributor.otherInternational Tomography Center, Siberian Branch of Russian Academy of Sciences
dc.contributor.otherUniversity of Alabama Tuscaloosa
dc.date.accessioned2023-09-28T19:17:47Z
dc.date.available2023-09-28T19:17:47Z
dc.date.issued2019
dc.description.abstractThe 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.en_US
dc.format.mediumelectronic
dc.format.mimetypeapplication/pdf
dc.identifier.citationMalygin, A. A., Krumkacheva, O. A., Graifer, D. M., Timofeev, I. O., Ochkasova, A. S., Meschaninova, M. I., Venyaminova, A. G., Fedin, M. V., Bowman, M., Karpova, G. G., & Bagryanskaya, E. G. (2019). Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy. In Nucleic Acids Research. Oxford University Press (OUP). https://doi.org/10.1093/nar/gkz1039
dc.identifier.doi10.1093/nar/gkz1039
dc.identifier.orcidhttps://orcid.org/0000-0002-0777-5103
dc.identifier.orcidhttps://orcid.org/0000-0003-0057-383X
dc.identifier.orcidhttps://orcid.org/0000-0003-0045-2413
dc.identifier.orcidhttps://orcid.org/0000-0002-0537-5755
dc.identifier.orcidhttps://orcid.org/0000-0001-9177-4148
dc.identifier.orcidhttps://orcid.org/0000-0001-5439-2140
dc.identifier.urihttps://ir.ua.edu/handle/123456789/11258
dc.languageEnglish
dc.language.isoen_US
dc.publisherOxford University Press
dc.rights.licenseAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectABASIC SITE
dc.subjectPROTEIN
dc.subjectDNA
dc.subjectRECOGNITION
dc.subjectINITIATION
dc.subjectELEMENTS
dc.subjectBINDING
dc.subjectBiochemistry & Molecular Biology
dc.titleExploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopyen_US
dc.typeArticle
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