Computing the Structure of Large Complexes: Modeling the 16S Ribosoma RNA

Abstract

Ribosomes are the sites of messenger RNA (mRNA) translation to protein, and thus are crucial to the normal functioning of all cells. These ribonucleoprotein particles are composed of a small (30S) subunit and a large (50S) subunit. The 30S subunit, in turn, is composed of a strand of RNA (16S rRNA) and 21 proteins ranging in molecular weight from 9 kD to 61 kD. Studies have demonstrated that ribosomal RNA is necessary for normal ribosome function and protein production (Dahlberg, 1989; Noller, 1991). In particular, 16S rRNA is essential for normal assembly and function of the 30S subunit, which is responsible for translation initiation (Hardestyand Kramer, 1985). Elucidating the structure of 16S rRNA could greatly aid our understanding of the molecular mechanisms for protein translation, and such basic structural information could ultimately have wide-ranging importance in fields such as pharmacology and drug design. Because of the difficulties associated with X-ray analysis of large complexes such as the ribosome (Eisenstein et al., 1991), high-resolution structural data for the 16S rRNA remain sparse. However, neutron diffraction studies have determined the relative positions of the 30S proteins (Capel et al., 1988), which, along with the reported 16S rRNA-protein interactions (Noller, 1991, Noller et al., unpublished; Brimacombe, 1991), enable low-resolution structural models—showing how the RNA associates with the protein components—to be built. Several studies have sought to take advantage of these structural data for the 308 subunit. Stern et al. have used interactive model building to produce a three-dimensional 16S rRNA structure (Stern et al., 1988). This method can produce viable models, but is hindered somewhat by subjectivity intrinsic to the process and by the nonexhaustive nature of its conformation search. Hubbard and Hearst have used distance geometry techniques to model the RNA structure, but did not incorporate neutron diffraction data on the protein positions (Hubbard and Hearst, 1991). Malhotra and Harvey have used an energy minimization technique to produce a set of possible conformations for 16S rRNA; their study, however, depends on electron microscopic studies on the molecule to provide initial information on surface topology (Malhotra, 1994).