An investigation of the dynamics of ribosomal protein L9 using heteronuclear NMR relaxation measurements.

The dynamic properties of ribosomal protein L9 from Bacillus stearothermophilus were investigated in solution using an analysis of nitrogen-15 longitudinal and transverse relaxation rates and amide nitrogen-proton nuclear Overhauser effects. The relaxation rates of the amide nitrogen nuclei were found to be correlated with the angle between the amide nitrogen-proton bond vectors and the long axis of the protein. This directional dependence of the nuclear relaxation rates is consistent with the protein having a highly elongated shape in solution, consistent with that observed in previous X-ray crystallographic studies of the crystalline form. Analysis of the nuclear relaxation data shows that the solvent-exposed nine-turn alpha helix connecting the two domains has a relatively high degree of order, in contrast to the connecting helix in the similarly shaped, but functionally different, calmodulin protein. The rotational correlation times associated with the amide nitrogen atoms of the N-terminal domain are on average slightly shorter than those of the C-terminal domain and connecting helix, providing evidence that the N-terminal domain exhibits some degree of independence in tumbling, in addition to other fast internal motions. The putative RNA-binding surfaces in each of the protein domains are characterized by relatively low order parameters, indicating that these are the most flexible regions of the molecule. Overall, the picture of the internal dynamics provided by nuclear relaxation measurements is similar to that obtained from a detailed study of amide proton exchange rates, but differs markedly from the picture provided by crystallographic temperature factors. The present study describes a molecule with unusual and complex dynamic properties, and supports a model where the protein functions as a "molecular strut" within the ribosome.