Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel

The geometry of the ribosomal polypeptide exit tunnel.

The geometry of the polypeptide exit tunnel has been determined using the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The tunnel is a component of a much larger, interconnected system of channels accessible to solvent that permeates the subunit and is connected to the exterior at many points. Since water and other small molecules can diffuse into and out of the...

Folding and escape of nascent proteins at ribosomal exit tunnel.

We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or near the temperature of the fastest folding, folding proceeds concomitantly with the escape process, resulting in vectorial folding and enhancement of foldabili...

Antibiotics at the Ribosomal Exit Tunnel – Selected Structural Aspects

Ribosomes, which are the target of many antibiotics [1, 2] possess spectacular architecture and inherentmobility, allowing their smooth performance in decoding the genetic information as well as in the formation of the peptide bond and the elongation of the newly synthesized proteins. The site for peptide bond formation (peptidyl transferase center, PTC, is located within a highly conserved pse...

Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.

Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.

Molecular Dynamics Simulations of the Nascent Peptide Chain in the Ribosomal Exit Tunnel