Low-Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit

Low-resolution molecular models can provide appropriate and efficient ways for studying large biomolecular systems such as the ribosome. We have developed computer codes that use the Yammp Under Python modeling package to assemble low-resolution force fields for RNA-protein complexes, and that connect these to the Amber molecular simulation package. This pipeline combines many of the complementary strengths of these two packages. Our target here is the 30S ribosomal subunit from Thermus thermophilus. One hundred nanosecond Langevin dynamics simulations were performed for the bound and the unbound 16S RNA, and conformational changes of the 16S RNA and its interaction with the 30S proteins were examined to establish the fidelity of our model. The S7 protein assembly pathway was also examined, and the effects of protein binding order on the 16S RNA were analyzed. The simulations suggest that ribosomal proteins play important roles in maintaining the native 16S RNA structure. “Primary” proteins (in terms of assembly) help more in stabilizing the conformation of the RNA than do secondary and tertiary proteins. Ribosomal proteins appear to bind to the RNA in an organized fashion wherein primary and secondary proteins help to prepare the binding sites for tertiary proteins. The methodology and tools described here should provide useful ways to explore other aspects of ribosomal conformational changes by means of molecular dynamics simulations.