Effects of Protein Subunits Removal on the Computed Motions of Partial 30S Structures of the Ribosome

The Anisotropic Network Model (ANM) is used to study motions of the 30S small ribosomal subunit. The effect of the absence of certain subunits on the motions of the remaining partial structures was investigated by removing one protein, pairs of proteins, and selected sets of proteins at a time. Our results show that the removal of some proteins does not change the large-scale dynamics of the partial structures, but the removal of certain subunits does cause significant changes in motion of the remaining structure, and these changes can be reverted by the removal of other subunits, which indicates interdependence between motions of various parts of the 30S ribosomal structure. We further found that the subunits showing such interdependence have strong positive correlation of their motions, which indicates that these subunits function as a unit block in the 30S small ribosomal subunit. Dynamically interdependent subunit pairs identified in this paper are consistent with previous experimental observations that suggested dimerization of those subunits.