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

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 spectrosco...

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Autores principales: Malygin, Alexey A, Krumkacheva, Olesya A, Graifer, Dmitri M, Timofeev, Ivan O, Ochkasova, Anastasia S, Meschaninova, Maria I, Venyaminova, Alya G, Fedin, Matvey V, Bowman, Michael, Karpova, Galina G, Bagryanskaya, Elena G
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145563/
https://www.ncbi.nlm.nih.gov/pubmed/31724718
http://dx.doi.org/10.1093/nar/gkz1039
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author Malygin, Alexey A
Krumkacheva, Olesya A
Graifer, Dmitri M
Timofeev, Ivan O
Ochkasova, Anastasia S
Meschaninova, Maria I
Venyaminova, Alya G
Fedin, Matvey V
Bowman, Michael
Karpova, Galina G
Bagryanskaya, Elena G
author_facet Malygin, Alexey A
Krumkacheva, Olesya A
Graifer, Dmitri M
Timofeev, Ivan O
Ochkasova, Anastasia S
Meschaninova, Maria I
Venyaminova, Alya G
Fedin, Matvey V
Bowman, Michael
Karpova, Galina G
Bagryanskaya, Elena G
author_sort Malygin, Alexey A
collection PubMed
description 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.
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spelling pubmed-71455632020-04-13 Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy Malygin, Alexey A Krumkacheva, Olesya A Graifer, Dmitri M Timofeev, Ivan O Ochkasova, Anastasia S Meschaninova, Maria I Venyaminova, Alya G Fedin, Matvey V Bowman, Michael Karpova, Galina G Bagryanskaya, Elena G Nucleic Acids Res RNA and RNA-Protein Complexes 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. Oxford University Press 2019-12-16 2019-11-14 /pmc/articles/PMC7145563/ /pubmed/31724718 http://dx.doi.org/10.1093/nar/gkz1039 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA and RNA-Protein Complexes
Malygin, Alexey A
Krumkacheva, Olesya A
Graifer, Dmitri M
Timofeev, Ivan O
Ochkasova, Anastasia S
Meschaninova, Maria I
Venyaminova, Alya G
Fedin, Matvey V
Bowman, Michael
Karpova, Galina G
Bagryanskaya, Elena G
Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title_full Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title_fullStr Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title_full_unstemmed Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title_short Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
title_sort exploring the interactions of short rnas with the human 40s ribosomal subunit near the mrna entry site by epr spectroscopy
topic RNA and RNA-Protein Complexes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145563/
https://www.ncbi.nlm.nih.gov/pubmed/31724718
http://dx.doi.org/10.1093/nar/gkz1039
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