contributed talk given on XX Discussions in Structural Molecular Biology, Nové Hrady, Czechia
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Three epochs of nascent protein translocation through the ribosome exit tunnel
Michal H. Kolář
michal@mhko.science
30–40 residues of the nascent polypeptide are protected from protease cleavage
Rate of translation
10–20 residues per second in bacteria
4–5 residues per second in eukaryotes
Epoch I
Translocation of the N-terminus from the catalytic center to the tunnel exit.
About 4 seconds on average in E. coli.
Epoch II
N-terminus outside the ribosome, C-terminus still attached to the tRNA.
In bacteria, a few dozen seconds depending on the protein lenght.
Epoch III
Ejection of the nascent polypeptide after its release from the tRNA.
A few milliseconds.
Is the constriction site flexible?
Yes, is seems so from both PDB survey and MD simulations. The flexibility is especially high for certain side chains of uL4 and uL22.
Can the constriction get closed?
Temporarily yes, at least for certain lengths of the nascent peptide.
After all, why does the constriction exist and is evolutionary conserved?
All-atom MD simulations of a ribosome cutout.
Metadynamics simulations with two collective variables describing the constriction width.
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Three epochs of nascent protein translocation through the ribosome exit tunnel
