Dynamics in the assembly of the 30S ribosomal subunit investigated by coarse-grained simulations

Abstract

The ribosome is a large biomolecular complex responsible for protein synthesis. In <i>Escherichia coli</i> (<i>E. coli</i>), a complete ribosome is composed of a 30S small subunit and a 50S large subunit. For approximately half a century, the 30S subunit has been a key model system for studying the in vitro assembly of the ribosome, and an assembly map has been proposed. However, structural details in the assembly of this protein‒RNA complex remain elusive. In this paper, we conducted a series of coarse-grained simulations following the order of the assembly map to investigate conformational dynamics during the assembly process of the 30S subunit. It has been found that the tertiary structure of naked 16S rRNA is very unstable, which is the case after binding of early-assembly proteins. The mid-assembly proteins can significantly restrict the mobility of the 16S rRNA and make the latter close to the native structure. The final binding of the late-assembly proteins would fully obtain the collective motion of the 16S rRNA. In particular, proteins S9 and S3 may have more important contributions to the assembly of the 30S subunit than other S proteins. Our strategy of coarse-grained simulations can be generally used to study assembly dynamics of large biomolecular complexes as long as the assembly map is available.