The stability and dynamics of ribosomal protein L9: investigations of a molecular strut by amide proton exchange and circular dichroism

Abstract

Nuclear magnetic resonance and circular dichroism experiments were used to investigate the stability and dynamic aspects of ribosomal protein L9 from Bacillus stearothermophilus in solution. This unusually shaped protein, with its two widely spaced RNA-binding domains linked by a connecting helix, has been hypothesized to serve as a “molecular strut”, most likely playing a role in ribosome assembly and/or maintaining the catalytically active conformation of ribosomal RNA. Protection factors for amide proton exchange were quantitatively measured in an extensive series of NMR experiments, providing probes of the stability and dynamics of localized regions of the protein. Results show that each of the two RNA-binding domains contains a highly stable core. The exposed central helix that connects the two domains is helical in solution, albeit not rigid, a result that is supported by amide proton protection factors, circular dichroism measurements, and carbon-13 and proton chemical shift index values. A conserved glycine and lysine-rich loop in the N-terminal domain is ordered and quite stable, a surprising result, since this loop had been presumed to be disordered in the original crystallographic analysis. Interestingly, the most dynamic parts of the protein are the regions that contain the likely RNA-binding residues in each of the two domains. The present results add further support to the notion that the L9 protein plays an architectural role within the ribosome, with the central helix serving as a molecular strut, or perhaps a spring, linking the two widely spaced RNA-binding domains.