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Ribosomes are large ribonucleoprotein complexes that drive protein synthesis, a fundamental process for all living systems. During translation, the nascent polypeptide traverses the ribosomal exit tunnel, a narrow passage shaped by both ribosomal RNA and proteins. The tunnel's architecture influences nascent chain folding, interactions, and even stalling (Kolář et al., 2024). The narrowest region of the tunnel, the constriction site (CS), is formed by the extended loops of proteins uL4 and uL22. We focus on the earliest stages of translation, when the nascent peptide has not yet passed the CS. The molecular details of how the peptide interacts with the CS and how the CS responds remain unclear. To address this, we performed all-atom molecular dynamics simulations of the entire ribosome with polyalanine and polyglycine peptides of varying lengths, as well as without a peptide. Our results show that the CS is highly flexible and can close to about 0.4 nm. It is narrowest in the absence of a peptide and, when a peptide is present, exhibits a preference for interaction with uL22. These findings provide new insight into the earliest events of protein biogenesis.
Kolář, M. H., McGrath, H., Nepomuceno, F. C., & Černeková, M. (2024). Three stages of nascent protein translocation through the ribosome exit tunnel. Wiley Interdisciplinary Reviews - RNA, 15(6). https://doi.org/10.1002/wrna.1873
