L11 is highly conserved ribosomal protein and its interaction with the ribosomal RNA segment from 23S subunit is considered to undergo an „induced fit“-conformational adjustment of both the protein and the RNA with respect to their conformations in the unbound state (Leulliot and Varani, 2001; Draper et al., 1996). Furthermore, the conformational dynamics of L11 are thought to play an important role in the binding process.
Binding of the C-terminal domain of L11 stabilizes the tertiary structure of a compactly folded RNA domain whereas the N-terminus is implicated in the binding to the antibiotic thiostrepton (Xing and Draper, 1996). The conformation of the RNA-L11-complex is structurally well characterized (Wimberly et al., 1999, Conn et al., 1999). In addition, the conformation of the C-terminal domain of L11 from Bacillus stearothermophilus has been characterized in its RNA bound and free form by NMR (Hinck et al., 1997, Markus et al., 1997). Yet, to obtain a more detailed picture of the dynamic processes accompanying RNA-protein interactions we characterize in detail the conformation and the dynamics of the full-length protein free in solution. In particular, the relative orientation of the N- and C-terminal domain of the protein in its free form is being investigated by NMR-spectroscopy. By analysis of long-range structural information derived from heteronuclear relaxation rates and residual dipolar couplings, it can be shown that the two domains are connected by a relatively rigid poly-Proline helix, their relative flexibility is low and the prominent conformation in solution preorganizes the correct conformation in complex with RNA.
![](/sites/default/files/images/L11.gif)
Overlay of the backbones of the 20 best structures out of 50. a) Backbone atoms of residues 5-70 that define N-terminus were fit by a least-square method. The r.m.s.d. for this superimposition is 0.28 Å for backbone atoms and 0.77 Å for all heavy atoms. b) Backbone atoms of resides 75-140 that define C-terminus. The r.m.s.d. for the superimposition of the well defined regions 97-111 and 121-140 is 0.295 Å for the backbone atoms and 0.82 Å for all heavy atoms. The beta-sheets and alpha-helices are color-coded and their first and last residues are indicated.