uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Why base tautomerization does not cause errors in mRNA decoding on the ribosome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2014 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 20, 12876-12884 p.Article in journal (Refereed) Published
Abstract [en]

The structure of the genetic code implies strict Watson-Crick base pairing in the first two codon positions, while the third position is known to be degenerate, thus allowing wobble base pairing. Recent crystal structures of near-cognate tRNAs accommodated into the ribosomal A-site, however, show canonical geometry even with first and second position mismatches. This immediately raises the question of whether these structures correspond to tautomerization of the base pairs. Further, if unusual tautomers are indeed trapped why do they not cause errors in decoding? Here, we use molecular dynamics free energy calculations of ribosomal complexes with cognate and near-cognate tRNAs to analyze the structures and energetics of G-U mismatches in the first two codon positions. We find that the enol tautomer of G is almost isoenergetic with the corresponding ketone in the first position, while it is actually more stable in the second position. Tautomerization of U, on the other hand is highly penalized. The presence of the unusual enol form of G thus explains the crystallographic observations. However, the calculations also show that this tautomer does not cause high codon reading error frequencies, as the resulting tRNA binding free energies are significantly higher than for the cognate complex.

Place, publisher, year, edition, pages
2014. Vol. 42, no 20, 12876-12884 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-245555DOI: 10.1093/nar/gku1044ISI: 000347693200048PubMedID: 25352546OAI: oai:DiVA.org:uu-245555DiVA: diva2:791420
Funder
Swedish Research Council, 2010-5264Knut and Alice Wallenberg Foundation
Available from: 2015-02-27 Created: 2015-02-26 Last updated: 2017-12-04Bibliographically approved

Open Access in DiVA

fulltext(2511 kB)185 downloads
File information
File name FULLTEXT01.pdfFile size 2511 kBChecksum SHA-512
2c749ae5757a23aa093b6f7f19229ab06ad7b66386afb25e0f293e6719d2d7fb6c243a60a234ca9061a124c2a76c2259eb2a6f65458b6226d733f3df3a3f3bd9
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Satpati, PriyadarshiÅqvist, Johan

Search in DiVA

By author/editor
Satpati, PriyadarshiÅqvist, Johan
By organisation
Computational and Systems Biology
In the same journal
Nucleic Acids Research
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 185 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 613 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf