Nov 3 – 4, 2022
Europe/Prague timezone

Binding of Peptide Deformylase to the Ribosome Surface Modulates Exit Tunnel Interior

Not scheduled
atrium (IT4Innovations)



Studentská 6231/1B 708 00 Ostrava-Poruba
Poster Poster session Conference Dinner and Poster Session


Hugo McGrath (UCT Prague)


Ribosomes are the biomolecular factories in charge of protein synthesis and are thus essential for life as we know it. In order to better understand proteosynthesis it is important to understand the ways in which it is regulated. The regulatory mechanisms may involve conformational changes of the ribosome induced by external factors possibly transferred over large distances. The principles of this allosteric communication between distant ribosome parts are not fully understood yet. Here we investigate peptide deformylase, an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and modifies the emerging nascent chain, to understand how conformational motion of the ribosome is affected by external factors.
We have performed all-atom molecular dynamics simulations of the entire ribosome. The simulated system consists of about 2 million atoms and microsecond-scale simulations of such a system require the use of high-performance computing.
We analyzed these simulations using principal component regression, a form of supervised learning. The results indicate conformational changes of the ribosomal protein uL22 inside the ribosomal exit tunnel upon deformylase binding suggesting a possible effect of the deformylase on the nascent peptide transport through the tunnel.

Primary author

Hugo McGrath (UCT Prague)


Michaela Černeková (UCT Prague) Michal Kolář (UCT Prague)

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