  We study the post-translational escape of nascent proteins at the ribosomal
exit tunnel with the consideration of a real shape atomistic tunnel based on
the Protein Data Bank (PDB) structure of the large ribosome subunit of archeon
Haloarcula marismortui. Molecular dynamics simulations employing the Go-like
model for the proteins show that at intermediate and high temperatures,
including a presumable physiological temperature, the protein escape process at
the atomistic tunnel is quantitatively similar to that at a cylinder tunnel of
length L = 72 {\AA} and diameter d = 16 {\AA}. At low temperatures, the
atomistic tunnel, however, yields an increased probability of protein trapping
inside the tunnel while the cylinder tunnel does not cause the trapping.
All-$\beta$ proteins tend to escape faster than all-$\alpha$ proteins but this
difference is blurred on increasing the protein's chain length. A 29-residue
zinc-finger domain is shown to be severely trapped inside the tunnel. Most of
the single-domain proteins considered, however, can escape efficiently at the
physiological temperature with the escape time distribution following the
diffusion model proposed in our previous works. An extrapolation of the
simulation data to a realistic value of the friction coefficient for amino
acids indicates that the escape times of globular proteins are at the
sub-millisecond scale. It is argued that this time scale is short enough for
the smooth functioning of the ribosome by not allowing nascent proteins to jam
the ribosome tunnel.
