[Molecular modeling of positioning of human release factor eRF1 relative to mRNA stop-codon explains a proximity of the eRF1 C-domain to stop-codon in ribosomal complex].

Abstract

A properties of atomic models of structure of eukaryotic triple complex eRF1 . mRNA . tRNAPhe containing human class-1 polypeptide release factor eRF1 at the A-site of human 80S ribosome, mRNA and P-site tRNAPhe, obtained before, are considered. The stricture of the complex is described using high resolution NMR structure of eRF1 M-domain. The structural properties of distribution of chemical cross-links are investigated, which allows us to choose correct model of positioning of the eRF1 molecule in ribosome A-site relative to stop codon of mRNA. A distributions of crosslinks between photoactivatable perfluoroaryl azide group of modified nucleotides of mRNA analogues and eRF1 molecule are modeled via molecular dynamics method. Twelve different mRNA analogues with modified nucleotides of stop signal in positions +4 to +9 with respect to the first nucleotide of the P-site codon are modeled. It was shown that only one of the two models of complex eRFI . mRNA . tRNA gives cross-link distribution in a good agreement with experimental data. A new features of the final structure of triple complex eRF1 . mRNA . tRNA is spatial proximity of stop-codon nucleotides to the C-domain of the eRF1, which explains previously obtained cross-link experimental data.

Cite this paper

@article{Vorobev2008MolecularMO, title={[Molecular modeling of positioning of human release factor eRF1 relative to mRNA stop-codon explains a proximity of the eRF1 C-domain to stop-codon in ribosomal complex].}, author={Iu N Vorob'ev and L. L. Kiselev}, journal={Molekuliarnaia biologiia}, year={2008}, volume={42 2}, pages={341-51} }