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Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

Publication ,  Journal Article
Zeng, X; Chugh, J; Casiano-Negroni, A; Al-Hashimi, HM; Brooks, CL
Published in: J Mol Biol
September 23, 2014

Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near-cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA.

Duke Scholars

Published In

J Mol Biol

DOI

EISSN

1089-8638

Publication Date

September 23, 2014

Volume

426

Issue

19

Start / End Page

3201 / 3213

Location

Netherlands

Related Subject Headings

  • Thermus
  • Ribosomes
  • RNA, Transfer
  • Protein Structure, Tertiary
  • Protein Biosynthesis
  • Peptide Elongation Factor Tu
  • Paromomycin
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Mutation, Missense
 

Citation

APA
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ICMJE
MLA
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Zeng, X., Chugh, J., Casiano-Negroni, A., Al-Hashimi, H. M., & Brooks, C. L. (2014). Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol, 426(19), 3201–3213. https://doi.org/10.1016/j.jmb.2014.04.029
Zeng, Xiancheng, Jeetender Chugh, Anette Casiano-Negroni, Hashim M. Al-Hashimi, and Charles L. Brooks. “Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.J Mol Biol 426, no. 19 (September 23, 2014): 3201–13. https://doi.org/10.1016/j.jmb.2014.04.029.
Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol. 2014 Sep 23;426(19):3201–13.
Zeng, Xiancheng, et al. “Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.J Mol Biol, vol. 426, no. 19, Sept. 2014, pp. 3201–13. Pubmed, doi:10.1016/j.jmb.2014.04.029.
Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol. 2014 Sep 23;426(19):3201–3213.
Journal cover image

Published In

J Mol Biol

DOI

EISSN

1089-8638

Publication Date

September 23, 2014

Volume

426

Issue

19

Start / End Page

3201 / 3213

Location

Netherlands

Related Subject Headings

  • Thermus
  • Ribosomes
  • RNA, Transfer
  • Protein Structure, Tertiary
  • Protein Biosynthesis
  • Peptide Elongation Factor Tu
  • Paromomycin
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Mutation, Missense