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Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNA(Ser3)
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Number of Authors: 42019 (English)In: Biomolecules, E-ISSN 2218-273X, Vol. 9, no 11, article id 745Article in journal (Refereed) Published
Abstract [en]

In-frame decoding in the ribosome occurs through canonical or wobble Watson-Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet-triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to -1 frameshifting. In E. coli, tRNA(GCU)(Ser3) can induce -1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon's GC could pair with the tRNA(Ser3 ')s GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce -1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNA(Ser3), as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for -1 frameshifting by tRNA(Ser3) at Ala codons.

Place, publisher, year, edition, pages
2019. Vol. 9, no 11, article id 745
Keywords [en]
ribosome, -1 frameshifting, S13, doublet decoding
National Category
Biophysics
Identifiers
URN: urn:nbn:se:su:diva-177503DOI: 10.3390/biom9110745ISI: 000502267900106PubMedID: 31752208Scopus ID: 2-s2.0-85075241444OAI: oai:DiVA.org:su-177503DiVA, id: diva2:1385529
Funder
The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), IG2012-5157Available from: 2020-01-14 Created: 2020-01-14 Last updated: 2025-02-20Bibliographically approved

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Caulfield, ThomasCoban, MattCoulbourn Flores, Samuel

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