ArticleScientific reports2021
Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Decoding the molecular script of 2'-O-ribomethylation: Implications across CNS disorders.Heliyon · 2024Review
- N-Terminal Amino Acid Affects the Translation Efficiency at Lower Temperatures in a Reconstituted Protein Synthesis System.International journal of molecular sciences · 2024Article
- Development of label-free light-controlled gene expression technologies using mid-IR and terahertz light.Frontiers in bioengineering and biotechnology · 2024Review
- Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.ACS central science · 2023Article
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Authors and funding
3 authors.
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Abstract
Peptide bond formation on the ribosome requires that aminoacyl-tRNAs and peptidyl-tRNAs are properly positioned on the A site and the P site of the peptidyl transferase center (PTC) so that nucleophilic attack can occur. Here we analyse some constraints associated with the induced-fit mechanism of the PTC, that promotes this positioning through a compaction around the aminoacyl ester orchestrated by U2506. The physical basis of PTC decompaction, that allows the elongated peptidyl-tRNA to free itself from that state and move to the P site of the PTC, is still unclear. From thermodynamics considerations and an analysis of published ribosome structures, the present work highlights the rational of this mechanism, in which the free-energy released by the new peptide bond is used to kick U2506 away from the reaction center. Furthermore, we show the evidence that decompaction is impaired when the nascent peptide is not yet anchored inside the exit tunnel, which may contribute to explain why the first rounds of elongation are inefficient, an issue that has attracted much interest for about two decades. Results in this field are examined in the light of the present analysis and a physico-chemical correlation in the genetic code, which suggest that elementary constraints associated with the size of the side-chain of the amino acids penalize early elongation events.
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