Speaker
Description
We have been studying protein synthesis on ribosomes for many years. One of the open questions concerns the translocation of the nascent protein through the ribosome during synthesis (1). It is still unclear what forces drive the peptide from the catalytic center, buried deep within the ribosome, toward the ribosome surface.
To address this, we performed a series of non-equilibrium molecular dynamics simulations on a simplified system (2). Specifically, we examined how a peptide moves through a carbon nanotube under an applied mechanical force. We were particularly interested in the difference between pulling the peptide and pushing it in the same direction. Does it matter where the force probe is attached? And would that choice affect the conformational ensemble of the peptide?
Highlights
• It's fairly easy to move a peptide through a narrow channel when an external force is applied.
• Pulling the peptide makes its movement smoother than pushing, though in both cases the peptide's own flexibility adds complexity.
• Where the force is applied matters less than the peptide's sequence or how quickly the force is applied.
(1) Kolář et al.: Three stages of nascent protein translocation through the ribosome exit tunnel, WIREs RNA, 2024.
(2) Nepomuceno, Kolář: Sensitivity of peptide conformational dynamics in carbon nanotubes to directional mechanical forces, Phys. Chem. Chem. Phys., 2025.
