“Solvent Volumes in the Large Ribosomal Subunit: The Geometry of”
Neil Voss – Yale University, Peter Moore Lab
A representation of the surface of the polypeptide exit tunnel has been constructed from the crystal structure of the large ribosomal subunit from Haloarcula marismortui. It shows that tunnel is part of an interconnected system of solvent channels that permeates the large ribosomal subunit, the interior volume of which is 39% solvent. Water and small molecules having radii less than 3.0 should be able to diffuse into and out of the tunnel along many different paths. Thus, the ribosome cannot be the seal that prevents ions from diffusing through the ribosome-translocon complex. However, for objects the size of nascent polypeptides, which have linear dimensions greater than 6 , the tunnel is effectively an unbranched tube connecting the peptidyl transferase center of the large subunit to the site where nascent peptides emerge that contains only 4.4% of the total solvent volume. The average diameter of the exit tunnel is so small (~20 ) that it cannot accommodate folded polypeptides larger than alpha-helices.