The C-terminal of the RNA binding domain from ribosomal protein L11, L11- C76, recognizes a 58 nucleotide region of the large ribosomal RNA subunit that has been highly conserved during evolution. L11 and its interactions with rRNA are conserved in prokaryotes and eukaryotes and L11 is required for efficient protein synthesis. Following our determination of the three dimensional structure of the free L11 domain, we have now determined the structure of the domain bound to its rRNA target. We find that while most of the structure of the free protein is retained in the bound state, that the large flexible loop in the free protein becomes ordered in the protein-RNA complex. In addition NOESY data show that the loop makes direct contact with the rRNA. Other regions of the protein that interact with the RNA are a loop that bridges helices two and three, and helix three itself. These results provide the first experimental data about protein residues that are involved in rRNA interactions. In order to further characterize these interactions, we aim to solve the structure of the rRNA in the complex. To this end we have worked out methodology for obtaining 15N/13C labeled rRNA, and have prepared labeled samples of both a 12 residue model tetraloop RNA and the 58nt L11-C76 rRNA target. The tetraloop has been used to test multidimensional triple resonance pulse sequences which will be used to assign the signals of the RNA in the L11- C76/rRNA complex. Because of severe signal overlap in the RNA and the large size of the complex, 27kDa, determining the bound RNA structure will be a formidable task, and much effort has been devoted to determining solution conditions where the complex behaves as a stable, monomeric (non- aggregating) molecule. At this point or preliminary data encourage us to believe that it will be possible to determine the structure of the complex. Binding of the protein S4 to 16S rRNA is critical for the subsequent binding of other proteins and mutations in S4 affect the accuracy of translation. S4 regulates its own translation and that of three other ribosomal proteins by binding to its own messenger RNA. Since deleting the first 41 residues of S4 (yielding S4 delta41) does not affect binding to RNA we have chosen to determine the structure of the truncated protein. We have obtained complete signal assignments and have delineated the secondary structure of the protein. So far, over 1000 interresidue distance restraints have been derived from NOESY data. These restraints together with X-PLOR show that S4 delta41 folds into a compact shape, containing a several long alpha helices and a four-stranded antiparallel beta-sheet. We expect that we will be able to solve its high resolution structure, using spectra separated into four dimensions and 3D spectra acquired at 750 MHz to improve resolution. Based on 15N T2 measurements, S4 delta41 appears to be relatively rigid on the picosecond-to-nanosecond time scale. This may reflect S4's role in ribosome assembly. A relatively rigid S4 may bind to a flexible 16S RNA and force it to adopt a conformation suitable for the subsequent binding of other ribosomal proteins. After the completion of a high resolution structure for the protein, we will probe its interactions with RNA. So far, a small RNA target, suitable for detailed structural studies, has not been identified. However, we may be able to identify residues affected by binding to large RNAs using chemical shift perturbations.
NIH ExPorter
NIH ExPorter